https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Emily+Forschler 2026-09-21T18:27:45Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1057973 2010-03-18T20:55:59Z

<p>Emily Forschler: /* Thanks */</p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked &quot;What is wrong with this picture?&quot; to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.&lt;br/&gt;<br /> my best&lt;br/&gt;<br /> Tom&lt;br/&gt;<br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy &lt;nowiki&gt;&lt;scene&gt;...&lt;scene/&gt;&lt;/nowiki&gt; (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the &lt;img src=&quot;www.filename.jpg&quot;&gt; code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making &quot;metalloprotease&quot; as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says &quot;calcium atoms (yellow)&quot; but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a &quot;GNU Free Documentation License&quot;<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.<br /> <br /> ==molscript2Jmol==<br /> <br /> Hi,<br /> <br /> Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?<br /> <br /> ==Request for categories adding==<br /> <br /> Could I add in &quot;Categories&quot; chapter my own specific markups? For example, I would like to classify restriction endonucleases complexes with DNA in respect of what native methyltranferases are: 6-methyl adenine, 5- or 4- methyl cytosine?<br /> <br /> Dima<br /> <br /> ==Thanks==<br /> Eran- <br /> <br /> Wow, I randomly checked in on Proteopedia today after being away for a while and saw your message. That's great that you were able to make a un-do button. It will be a good tool, especially for those who are new to Proteopedia and experimenting with how things work. <br /> <br /> PS. I just tried it out and I'm excited there's also a re-do button. It's even better than I expected.<br /> <br /> [[User:Emily Forschler|Emily Forschler]] 22:48, 18 March 2010 (IST)</div>

Emily Forschler https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1057972 2010-03-18T20:55:26Z

<p>Emily Forschler: </p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked &quot;What is wrong with this picture?&quot; to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.&lt;br/&gt;<br /> my best&lt;br/&gt;<br /> Tom&lt;br/&gt;<br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy &lt;nowiki&gt;&lt;scene&gt;...&lt;scene/&gt;&lt;/nowiki&gt; (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the &lt;img src=&quot;www.filename.jpg&quot;&gt; code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making &quot;metalloprotease&quot; as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says &quot;calcium atoms (yellow)&quot; but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a &quot;GNU Free Documentation License&quot;<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.<br /> <br /> ==molscript2Jmol==<br /> <br /> Hi,<br /> <br /> Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?<br /> <br /> ==Request for categories adding==<br /> <br /> Could I add in &quot;Categories&quot; chapter my own specific markups? For example, I would like to classify restriction endonucleases complexes with DNA in respect of what native methyltranferases are: 6-methyl adenine, 5- or 4- methyl cytosine?<br /> <br /> Dima<br /> <br /> ==Thanks==<br /> Eran- <br /> <br /> Wow, I randomly checked in on Proteopedia today after being away for a while and saw your message. That's great that you were able to make a un-do button. It will be a good tool, especially for those who are new to Proteopedia and experimenting with how things work. <br /> -Emily<br /> <br /> PS. I just tried it out and I'm excited there's also a re-do button. It's even better than I expected.<br /> <br /> [[User:Emily Forschler|Emily Forschler]] 22:48, 18 March 2010 (IST)</div>

Emily Forschler https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=1057970 2010-03-18T20:48:59Z

<p>Emily Forschler: </p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> Hi Eran. How are you? I'm Maria Ambrazi..do you remember from Erice? Can you send me your e-mail...I would like to ask you something on proteopedia!<br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked &quot;What is wrong with this picture?&quot; to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.&lt;br/&gt;<br /> my best&lt;br/&gt;<br /> Tom&lt;br/&gt;<br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy &lt;nowiki&gt;&lt;scene&gt;...&lt;scene/&gt;&lt;/nowiki&gt; (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the &lt;img src=&quot;www.filename.jpg&quot;&gt; code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making &quot;metalloprotease&quot; as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says &quot;calcium atoms (yellow)&quot; but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ditto leah. thanks! becca<br /> <br /> ==Scrambled Eggs ==<br /> Any chance you are referring to egg cells and fertilization ? :)<br /> == Applet Behavior ==<br /> <br /> Eran, the applets in Z-DNA page seem to be behaving erratically. At times there <br /> is no display and at times they are not in the frame. There is also a problem<br /> with the sugar puckering option in DNA page. The applet freezes when this is selected.<br /> Could you please verify if you are facing the same problems?<br /> <br /> [[User:Adithya Sagar|Adithya Sagar]] 21:06, 22 October 2009 (IST)<br /> <br /> ==Image license==<br /> <br /> Originally from {Molecular cell biology. Lodish, Harvey 5 ed: - New York : W. H. Freeman and Co., 2003, 973 s. b ill. ISBN: 0-7167-4366-3. Libris: 8926100.}<br /> <br /> Original uploader was Roadnottaken at en.wikipedia 2007-03-22<br /> <br /> The image was found from Wikipedia and was a modified image that is a &quot;GNU Free Documentation License&quot;<br /> I changed the properties of my image file and it should give the proper acknowledgments.<br /> <br /> -Matt<br /> <br /> ==Restriction endonucleases complexes with DNA - PspGI (3bm3) case==<br /> <br /> Hi, Eran!<br /> <br /> It is nice to see such quick assistance with tech bug.<br /> It is pity I found proteopedia after we published article on two protein-DNA structures.<br /> I will try in my Ph.D. thesis to visualise review of REase-DNA complexes with proteopedia.<br /> <br /> greatings from Vilne,<br /> Dima<br /> <br /> Now I see it was not bug but database case.<br /> <br /> ==molscript2Jmol==<br /> <br /> Hi,<br /> <br /> Is it possible simple coversion or implementation of molscript input and/or .mols files to Jmol script?<br /> <br /> ==Request for categories adding==<br /> <br /> Could I add in &quot;Categories&quot; chapter my own specific markups? For example, I would like to classify restriction endonucleases complexes with DNA in respect of what native methyltranferases are: 6-methyl adenine, 5- or 4- methyl cytosine?<br /> <br /> Dima<br /> <br /> ==Thanks==<br /> Eran- <br /> Wow, I randomly checked in on Proteopedia today after being away for a while and saw your message. That's great that you were able to create a un-do button. I think it will be a good tool, especially for those who are new to Proteopedia and experimenting with how things work. <br /> [[User:Emily Forschler|Emily Forschler]] 22:48, 18 March 2010 (IST)</div>

Emily Forschler https://proteopedia.org/index.php?title=User_talk:Emily_Forschler&diff=994833 2009-09-15T15:28:23Z

<p>Emily Forschler: /* Messiah College Newsletter */</p> <hr /> <div>Hi Emily,<br /> You have definitely suceeded in figuring out how to use the &quot;user talk&quot; feature. We were just delighted to find that you were able to use the authoring tools to create a wonderful page without so much as one email exchange between us! Of course I would encourage you to email/usertalk us with any questions, like your labelling question, but it was sort of a proof of useability to us that you experienced such a success. Could you identify any parts of the experience that were especially difficult to figure out?<br /> <br /> As to the labelling, Jmol puts the same label on every atom that is selected instead of somehow just labelling that mass of atoms with one label. So, let's say you wanted to label a particular residue, what you would do is select just one atom of that residue and then apply the label. Usually the best way to do that is to use the &quot;mouse click selects&quot; feature present either in the &quot;selections&quot; tab or in the &quot;labels&quot; tab in the Scene Authoring Tools. By default your mouse clicks in Jmol do not affect the selection. If you choose one of the alternate modes in the &quot;mouse click selects&quot; box, for instance &quot;atom&quot;, then you can start with nothing selected, and then just choose a single atom to add to your selection by clicking on it. Once your selection consists of only one atom, you can label it. Currently you cannot change the placement of the label, so if the label does not look good on one atom, try a different atom. Please do try to add a few labels to the Photosystem II page, my feeling is it will improve it greatly.<br /> <br /> I like your idea for a reset feature in the Scene Authoring Tools, would you mind adding the suggestion to the [[Proteopedia:Wishlist]] page? We try to put all of the suggestions and desires for Proteopedia features/improvements there, along with the users that suggested them, and it's just an easier way to keep track of them.<br /> <br /> We're very glad you're a part of Proteopedia, and look forward to any future pages you may create or improve!<br /> <br /> Cheers,<br /> Eran<br /> <br /> <br /> Hi Emily,<br /> The Photosystem II page that you've been working on has really progressed nicely! I think it's just great, and I'm sure that it will only continue to improve as you, and others, continue to refine the page. I noticed that several of the green links are far down the page, away from the 3D applet. This means that the 3D applet will not be in view when the user clicks on the final few green links. What do you think about adding another applet to the page to handle the 2nd half of the green links? In case you didn't know, green links will act on the applet directly above them in the wikitext (and if you want to pull some real fancy stuff, you can even go so far as to tell any green links to target any applet by adding some simple code).<br /> <br /> Best,<br /> --[[User:Eran Hodis|Eran Hodis]] 21:39, 6 May 2008 (IDT)<br /> <br /> == Messiah College Newsletter ==<br /> <br /> Hi Emily,<br /> <br /> Just saw you mentioned in this [http://www.messiah.edu/schools/health_nat_sci/good_news_notes/2009/Good%20News%20notes-spring%202009.pdf Messiah College Newsletter]. Nice! I take it you just graduated? What are your plans for the future?<br /> <br /> --Eran<br /> --[[User:Eran Hodis|Eran Hodis]] 00:30, 7 September 2009 (IDT)<br /> <br /> <br /> <br /> <br /> Hello Eran-<br /> <br /> Good thing I signed it to check in on Proteopedia. Dr. Sussman recently contacted me after having seen the same newsletter, so I figured I'd check for any messages. Thanks for sending me the PDF of the newsletter since I hadn't actually seen it (and the typo on my graduation year - I actually graduated in May 2008.) Since then, I have been attending a Master's program to be a physician assistant at Albany Medical College, in Albany, NY. I don't know that they have physician assistants in Israel, but they are popular here in the USA as mid-level health care providers. This link explains better than I could about what they do, especially the third paragraph. [http://www.aapa.org/about-pas/our-history PA History] I'm not sure what area of medicine I want to get into, but I'm thinking maybe Emergency Medicine right now. We have a year of rotations in a variety of areas, so I'm hoping something grabs my interest then. <br /> <br /> Have you still been working much on Proteopedia or are you on to other projects? I hope everything is going well for you. <br /> <br /> -Emily<br /> <br /> Not sure if I used the &quot;user talk&quot; feature correctly. Let me know if I done it correctly or if there is a better way to do it.</div>

Emily Forschler https://proteopedia.org/index.php?title=User_talk:Emily_Forschler&diff=994832 2009-09-15T15:26:18Z

<p>Emily Forschler: /* Messiah College Newsletter */</p> <hr /> <div>Hi Emily,<br /> You have definitely suceeded in figuring out how to use the &quot;user talk&quot; feature. We were just delighted to find that you were able to use the authoring tools to create a wonderful page without so much as one email exchange between us! Of course I would encourage you to email/usertalk us with any questions, like your labelling question, but it was sort of a proof of useability to us that you experienced such a success. Could you identify any parts of the experience that were especially difficult to figure out?<br /> <br /> As to the labelling, Jmol puts the same label on every atom that is selected instead of somehow just labelling that mass of atoms with one label. So, let's say you wanted to label a particular residue, what you would do is select just one atom of that residue and then apply the label. Usually the best way to do that is to use the &quot;mouse click selects&quot; feature present either in the &quot;selections&quot; tab or in the &quot;labels&quot; tab in the Scene Authoring Tools. By default your mouse clicks in Jmol do not affect the selection. If you choose one of the alternate modes in the &quot;mouse click selects&quot; box, for instance &quot;atom&quot;, then you can start with nothing selected, and then just choose a single atom to add to your selection by clicking on it. Once your selection consists of only one atom, you can label it. Currently you cannot change the placement of the label, so if the label does not look good on one atom, try a different atom. Please do try to add a few labels to the Photosystem II page, my feeling is it will improve it greatly.<br /> <br /> I like your idea for a reset feature in the Scene Authoring Tools, would you mind adding the suggestion to the [[Proteopedia:Wishlist]] page? We try to put all of the suggestions and desires for Proteopedia features/improvements there, along with the users that suggested them, and it's just an easier way to keep track of them.<br /> <br /> We're very glad you're a part of Proteopedia, and look forward to any future pages you may create or improve!<br /> <br /> Cheers,<br /> Eran<br /> <br /> <br /> Hi Emily,<br /> The Photosystem II page that you've been working on has really progressed nicely! I think it's just great, and I'm sure that it will only continue to improve as you, and others, continue to refine the page. I noticed that several of the green links are far down the page, away from the 3D applet. This means that the 3D applet will not be in view when the user clicks on the final few green links. What do you think about adding another applet to the page to handle the 2nd half of the green links? In case you didn't know, green links will act on the applet directly above them in the wikitext (and if you want to pull some real fancy stuff, you can even go so far as to tell any green links to target any applet by adding some simple code).<br /> <br /> Best,<br /> --[[User:Eran Hodis|Eran Hodis]] 21:39, 6 May 2008 (IDT)<br /> <br /> == Messiah College Newsletter ==<br /> <br /> Hi Emily,<br /> <br /> Just saw you mentioned in this [http://www.messiah.edu/schools/health_nat_sci/good_news_notes/2009/Good%20News%20notes-spring%202009.pdf Messiah College Newsletter]. Nice! I take it you just graduated? What are your plans for the future?<br /> <br /> --Eran<br /> --[[User:Eran Hodis|Eran Hodis]] 00:30, 7 September 2009 (IDT)<br /> <br /> <br /> <br /> <br /> Hello Eran-<br /> <br /> Good thing I signed it to check in on Proteopedia. Dr. Sussman recently contacted me after having seen the same newsletter, so I figured I'd check for any messages. Thanks for sending me the PDF of the newsletter since I hadn't actually seen it (and the typo on my graduation year - I actually graduated in May 2008.) Since then, I have been attending a Master's program to be a physician assistant at Albany Medical College, in Albany, NY. I don't know that they have physician assistants in Israel, but they are popular here in the USA as mid-level health care providers. This link explains better than I could about what they do, especially the third paragraph. [http://www.aapa.org/about-pas/our-history] I'm not sure what area of medicine I want to get into, but I'm thinking maybe Emergency Medicine right now. We have a year of rotations in a variety of areas, so I'm hoping something grabs my interest then. <br /> <br /> Have you still been working much on Proteopedia or are you on to other projects? I hope everything is going well for you. <br /> <br /> -Emily<br /> <br /> Not sure if I used the &quot;user talk&quot; feature correctly. Let me know if I done it correctly or if there is a better way to do it.</div>

Emily Forschler https://proteopedia.org/index.php?title=User:Emily_Forschler&diff=953679 2009-05-06T04:05:01Z

<p>Emily Forschler: </p> <hr /> <div>2008 graduate of Messiah College, Grantham, Pennsylvania, USA; BS Biochemistry.<br /> <br /> ''&lt;email&gt;emily.g.forschler@gmail.com&lt;/email&gt;''<br /> <br /> [[Photosystem II]]</div>

Emily Forschler https://proteopedia.org/index.php?title=User:Emily_Forschler&diff=953678 2009-05-06T04:04:38Z

<p>Emily Forschler: </p> <hr /> <div>2008 graduate of Messiah College, Grantham, Pennsylvania; BS Biochemistry.<br /> <br /> ''&lt;email&gt;emily.g.forschler@gmail.com&lt;/email&gt;''<br /> <br /> [[Photosystem II]]</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=755578 2008-08-21T00:43:39Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the cyanobacteria, ''Thermosynechococcus elongatus'', at 3.0Å &lt;ref&gt;Loll, B., Kern, J., Saenger, W., Zouni, A., Biesiadka, J., &quot;Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II.&quot; Nature, Dec 15, 2005, 438(7070), 1040-4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16355230 16355230]&lt;/ref&gt; and at 3.50 Å &lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt;. PDB codes are [[2axt]] and [[1s5l]], respectively. Cyanobacteria and plants both contain Photosystem II while photosynthetic bacteria contain the bacterial reaction center. This photosynthetic protein complex is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein complex that in plants is associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Located between each pair of quinones, an iron helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Emily Forschler https://proteopedia.org/index.php?title=User:Emily_Forschler&diff=564633 2008-06-23T02:35:52Z

<p>Emily Forschler: </p> <hr /> <div>2008 graduate of Messiah College, Grantham, Pennsylvania; Biochemistry major<br /> <br /> ''&lt;email&gt;emily.g.forschler@gmail.com&lt;/email&gt;''<br /> <br /> [[Photosystem II]]</div>

Emily Forschler https://proteopedia.org/index.php?title=User:Emily_Forschler&diff=564632 2008-06-23T02:33:21Z

<p>Emily Forschler: </p> <hr /> <div>2008 graduate of Messiah College, Grantham, Pennsylvania; Biochemistry major<br /> <br /> <br /> <br /> [[Photosystem II]]</div>

Emily Forschler https://proteopedia.org/index.php?title=Proteopedia:Wishlist&diff=546584 2008-06-06T00:14:17Z

<p>Emily Forschler: </p> <hr /> <div>This is the page to list features you wish Proteopedia had. As Proteopedia grows and develops, we will try to include the best and most appropriate ideas.<br /> <br /> If you want to report a problem in an existing feature, please do so at [[Proteopedia:Problems]].<br /> <br /> When adding a suggestion, please identify yourself by adding &lt;nowiki&gt;~~~~&lt;/nowiki&gt; at the end. This is wikitext that is converted into your name and the date.<br /> <br /> This list has the most important items at the top.<br /> ----<br /> <br /> *&lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' There is now a link to FirstGlance underneath the molecule for every automatically seeded page.'' In every article titled with a single PDB id code, a link to (for a random case) &quot;Explore 2ace&quot; that goes to '''FirstGlance in Jmol'''. The link syntax is [http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace].<br /> * '''Searching''' for a '''plural''' should find the '''singular''' match, and vice versa. For example: I searched for &quot;histocompatibility antigens&quot; and did not find the page &quot;Category: Histocompatibility antigen&quot;. Searching for &quot;histocompatibility antigen&quot; did find this page. [[User:Emartz|Emartz]] 19:00, 8 March 2008 (IST)<br /> * '''Color keys''' displayed beneath Jmol, changing as needed with each green link. For example &quot;alpha helix&quot; and &quot;beta strand&quot; colored in the standard Jmol secondary colors. The standard keys should be pre-built and callable by name, perhaps by a parameter in the &amp;lt;scene ...&amp;gt; tag. [[User:Emartz|Emartz]] 01:59, 19 March 2008 (IST) This is a really good idea! I've had to go to other sites to figure out what things stand for and was actually wondering if there was a way to make a key, but I guess not right now. [[User:Emily Forschler|Emily Forschler]] 03:14, 6 June 2008 (IDT)<br /> * '''Biological units''' (from RCSB) should be the default initial scenes, with a view of the asymmetric unit optional, as agreed in discussion. Eric Martz plans to provide a mock-up of an advanced page that would have views from EBI PQS, EBI PISA, and RCSB biological units, with brief explanations of each. <br /> * '''ConSurf coloring''' can be provided as discussed with Nir Ben-Tal and Elana Erez. This could be one of the standard scenes on the proposed menu of standard scenes.<br /> * '''Several standard scenes''', such as those in FirstGlance in Jmol, could be provided in a pull-down menu on the auto-seeded pages. It could be one more row in the table below Jmol. Eric Martz plans to provide the scripts and HTML color keys for these. [[User:Eric Martz|Eric Martz]] 19:54, 13 April 2008 (IDT)<br /> * '''All models in NMR ensembles''' (and the 118 multiple-model X-ray entries) should be the initial view in auto-seeded pages. Eric Martz plans to provide the script for this.<br /> * '''Molprobity''' could be added under ''About this structure'' in the auto-seeded pages. Eric Martz plans to write a short explanation to accompany a link. [[User:Eric Martz|Eric Martz]] 20:00, 13 April 2008 (IDT)<br /> * '''Sequence and structure-related''' entries could be linked to every entry. Currently, at [[2ic8]], I can click the link to PDBSum, and there click a mysterious plus button, which gives me a list of sequence-related entries. However, I must then enter each one by hand into Proteopedia. It would be great if this list, already linked, were at the bottom of every PDB-code-titled page. OCA already does sequence-based searching. All we need is a structure-based search as well for &quot;structure neighbors&quot;. [[User:Eric Martz|Eric Martz]] 04:30, 26 April 2008 (IDT)<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' Green links are now bold by default.'' A user-settable preference to make all '''green links bold''' or underlined (when not touched with the mouse) (I prefer underlined, with bold onMouseover) because in Windows browsers, the font is very thin, and the green color is hard to see. It is hard to scan a paragraph and find the green links. Also 9% of males are colorblind. [[User:Emartz|Emartz]] 19:51, 9 March 2008 (IST)<br /> * To encourage authors to follow [[Proteopedia:Policy]] regarding links to Wikipedia, automatically detect ''wikipedia'' during every preview/save and refer the author to [[Proteopedia:Policy]]. [[User:Emartz|Emartz]] 02:10, 16 March 2008 (IST)<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' When saving a scene (in the &quot;save scene&quot; dialog), a radio button to choose between &quot;force '''spinning''' on&quot;, &quot;force spinning off&quot;, &quot;inherit spinning set by the user with 'toggle spinning'&quot;. (inherit spinning not implemented on purpose --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT))<br /> * '''Tabulate characteristics''' of PDB codes on Category pages (in this order): PDB code, resolution, year, title, authors (ideally first and last author names like &quot;Harel/Sussman&quot; for 2ace), number of chains in the asymmetric unit, and ligand abbreviations. 2ace would look like this:<br /> &lt;table border=1 cellpadding=1&gt;&lt;tr&gt;&lt;td&gt;<br /> 2ace&lt;/td&gt;&lt;td&gt;2.50A&lt;/td&gt;&lt;td&gt;1996&lt;/td&gt;&lt;td&gt;NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA&lt;/td&gt;&lt;td&gt; Harel/Sussman&lt;/td&gt;&lt;td&gt;Chains=1&lt;/td&gt;&lt;td&gt;ACH<br /> &lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;<br /> Topic pages should be listed first, before PDB code pages, and without any additional characteristics.<br /> * Mechanism to spawn (open) a '''child window containing only Jmol''' with the current scene. Advantages: the child window can be resized, thereby resizing Jmol; the child window can be kept in view while the text in the parent Proteopedia window is scrolled. It should be possible to have green links work on both the Jmol on the Proteopedia page, and the child Jmol. [[User:Emartz|Emartz]] 00:06, 17 March 2008 (IST)<br /> * Automatically '''front, center, and size''' ligands and sites when their green links are clicked. That is, the molecule should rotate to put the selected entity in front of its center of mass, the selected entity should become the center of rotation/zoom, and the molecule should be zoomed (up or down) to make the selected entity fill e.g. 75% of the Jmol diameter.<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt; (March 2, 2008): Quality (antialiasing) chosen by the user with &quot;toggle quality&quot; should remain in effect for all green links within that page. Imagine that you're projecting scenes to a class. Currently, with every new scene, you have to click &quot;toggle quality&quot; again to get high quality.<br /> * Support '''two Jmols side by side''', for comparisons. (''this is already possible, but not possible to sync them yet: see [[2b8n]]'' --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT))<br /> ** '''Synchronize''' mouse-directed rotations and zooms (this now works amazingly well, see Chapter 4 in the Demo Tutorial at http://bioinformatics.org/jmol-tutorials -- where by the way you can also see &quot;toggle quality&quot; working very clearly -- my links are labeled &quot;smoother rotation&quot; and &quot;smoother graphics&quot; to the lower left of Jmol).<br /> ** Provide a mechanism for '''one green link that sends separate scripts to each Jmol''' simultaneously. Maybe not necessary? Just use two green links? What is cool is to start with scenes that align the two molecules. Then they stay aligned as you rotate/zoom with the mouse (provided spin is left off at the beginning -- when it is on, one molecule tends to lag behind the other).<br /> *Have selenomethionine (MSE) treated as any other amino acid in the (Jmol) default settings - [[User:Morten Grøftehauge]]- June 1, 2008<br /> *Create a '''&quot;reset&quot; button for scene authoring tools''', in particular the representations tab. Or an &quot;undo&quot; button. Something to allow the image to be returned to normal after experimenting with different representations without reloading. [[User:Emily Forschler|Emily Forschler]] 00:07, 6 June 2008 (IDT)</div>

Emily Forschler https://proteopedia.org/index.php?title=Proteopedia:Wishlist&diff=546576 2008-06-05T21:07:39Z

<p>Emily Forschler: </p> <hr /> <div>This is the page to list features you wish Proteopedia had. As Proteopedia grows and develops, we will try to include the best and most appropriate ideas.<br /> <br /> If you want to report a problem in an existing feature, please do so at [[Proteopedia:Problems]].<br /> <br /> When adding a suggestion, please identify yourself by adding &lt;nowiki&gt;~~~~&lt;/nowiki&gt; at the end. This is wikitext that is converted into your name and the date.<br /> <br /> This list has the most important items at the top.<br /> ----<br /> <br /> *&lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' There is now a link to FirstGlance underneath the molecule for every automatically seeded page.'' In every article titled with a single PDB id code, a link to (for a random case) &quot;Explore 2ace&quot; that goes to '''FirstGlance in Jmol'''. The link syntax is [http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace].<br /> * '''Searching''' for a '''plural''' should find the '''singular''' match, and vice versa. For example: I searched for &quot;histocompatibility antigens&quot; and did not find the page &quot;Category: Histocompatibility antigen&quot;. Searching for &quot;histocompatibility antigen&quot; did find this page. [[User:Emartz|Emartz]] 19:00, 8 March 2008 (IST)<br /> * '''Color keys''' displayed beneath Jmol, changing as needed with each green link. For example &quot;alpha helix&quot; and &quot;beta strand&quot; colored in the standard Jmol secondary colors. The standard keys should be pre-built and callable by name, perhaps by a parameter in the &amp;lt;scene ...&amp;gt; tag. [[User:Emartz|Emartz]] 01:59, 19 March 2008 (IST)<br /> * '''Biological units''' (from RCSB) should be the default initial scenes, with a view of the asymmetric unit optional, as agreed in discussion. Eric Martz plans to provide a mock-up of an advanced page that would have views from EBI PQS, EBI PISA, and RCSB biological units, with brief explanations of each. <br /> * '''ConSurf coloring''' can be provided as discussed with Nir Ben-Tal and Elana Erez. This could be one of the standard scenes on the proposed menu of standard scenes.<br /> * '''Several standard scenes''', such as those in FirstGlance in Jmol, could be provided in a pull-down menu on the auto-seeded pages. It could be one more row in the table below Jmol. Eric Martz plans to provide the scripts and HTML color keys for these. [[User:Eric Martz|Eric Martz]] 19:54, 13 April 2008 (IDT)<br /> * '''All models in NMR ensembles''' (and the 118 multiple-model X-ray entries) should be the initial view in auto-seeded pages. Eric Martz plans to provide the script for this.<br /> * '''Molprobity''' could be added under ''About this structure'' in the auto-seeded pages. Eric Martz plans to write a short explanation to accompany a link. [[User:Eric Martz|Eric Martz]] 20:00, 13 April 2008 (IDT)<br /> * '''Sequence and structure-related''' entries could be linked to every entry. Currently, at [[2ic8]], I can click the link to PDBSum, and there click a mysterious plus button, which gives me a list of sequence-related entries. However, I must then enter each one by hand into Proteopedia. It would be great if this list, already linked, were at the bottom of every PDB-code-titled page. OCA already does sequence-based searching. All we need is a structure-based search as well for &quot;structure neighbors&quot;. [[User:Eric Martz|Eric Martz]] 04:30, 26 April 2008 (IDT)<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' Green links are now bold by default.'' A user-settable preference to make all '''green links bold''' or underlined (when not touched with the mouse) (I prefer underlined, with bold onMouseover) because in Windows browsers, the font is very thin, and the green color is hard to see. It is hard to scan a paragraph and find the green links. Also 9% of males are colorblind. [[User:Emartz|Emartz]] 19:51, 9 March 2008 (IST)<br /> * To encourage authors to follow [[Proteopedia:Policy]] regarding links to Wikipedia, automatically detect ''wikipedia'' during every preview/save and refer the author to [[Proteopedia:Policy]]. [[User:Emartz|Emartz]] 02:10, 16 March 2008 (IST)<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' When saving a scene (in the &quot;save scene&quot; dialog), a radio button to choose between &quot;force '''spinning''' on&quot;, &quot;force spinning off&quot;, &quot;inherit spinning set by the user with 'toggle spinning'&quot;. (inherit spinning not implemented on purpose --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT))<br /> * '''Tabulate characteristics''' of PDB codes on Category pages (in this order): PDB code, resolution, year, title, authors (ideally first and last author names like &quot;Harel/Sussman&quot; for 2ace), number of chains in the asymmetric unit, and ligand abbreviations. 2ace would look like this:<br /> &lt;table border=1 cellpadding=1&gt;&lt;tr&gt;&lt;td&gt;<br /> 2ace&lt;/td&gt;&lt;td&gt;2.50A&lt;/td&gt;&lt;td&gt;1996&lt;/td&gt;&lt;td&gt;NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA&lt;/td&gt;&lt;td&gt; Harel/Sussman&lt;/td&gt;&lt;td&gt;Chains=1&lt;/td&gt;&lt;td&gt;ACH<br /> &lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;<br /> Topic pages should be listed first, before PDB code pages, and without any additional characteristics.<br /> * Mechanism to spawn (open) a '''child window containing only Jmol''' with the current scene. Advantages: the child window can be resized, thereby resizing Jmol; the child window can be kept in view while the text in the parent Proteopedia window is scrolled. It should be possible to have green links work on both the Jmol on the Proteopedia page, and the child Jmol. [[User:Emartz|Emartz]] 00:06, 17 March 2008 (IST)<br /> * Automatically '''front, center, and size''' ligands and sites when their green links are clicked. That is, the molecule should rotate to put the selected entity in front of its center of mass, the selected entity should become the center of rotation/zoom, and the molecule should be zoomed (up or down) to make the selected entity fill e.g. 75% of the Jmol diameter.<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt; (March 2, 2008): Quality (antialiasing) chosen by the user with &quot;toggle quality&quot; should remain in effect for all green links within that page. Imagine that you're projecting scenes to a class. Currently, with every new scene, you have to click &quot;toggle quality&quot; again to get high quality.<br /> * Support '''two Jmols side by side''', for comparisons. (''this is already possible, but not possible to sync them yet: see [[2b8n]]'' --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT))<br /> ** '''Synchronize''' mouse-directed rotations and zooms (this now works amazingly well, see Chapter 4 in the Demo Tutorial at http://bioinformatics.org/jmol-tutorials -- where by the way you can also see &quot;toggle quality&quot; working very clearly -- my links are labeled &quot;smoother rotation&quot; and &quot;smoother graphics&quot; to the lower left of Jmol).<br /> ** Provide a mechanism for '''one green link that sends separate scripts to each Jmol''' simultaneously. Maybe not necessary? Just use two green links? What is cool is to start with scenes that align the two molecules. Then they stay aligned as you rotate/zoom with the mouse (provided spin is left off at the beginning -- when it is on, one molecule tends to lag behind the other).<br /> *Have selenomethionine (MSE) treated as any other amino acid in the (Jmol) default settings - [[User:Morten Grøftehauge]]- June 1, 2008<br /> *Create a '''&quot;reset&quot; button for scene authoring tools''', in particular the representations tab. Or an &quot;undo&quot; button. Something to allow the image to be returned to normal after experimenting with different representations without reloading. [[User:Emily Forschler|Emily Forschler]] 00:07, 6 June 2008 (IDT)</div>

Emily Forschler https://proteopedia.org/index.php?title=Proteopedia:Wishlist&diff=546575 2008-06-05T21:07:00Z

<p>Emily Forschler: </p> <hr /> <div>This is the page to list features you wish Proteopedia had. As Proteopedia grows and develops, we will try to include the best and most appropriate ideas.<br /> <br /> If you want to report a problem in an existing feature, please do so at [[Proteopedia:Problems]].<br /> <br /> When adding a suggestion, please identify yourself by adding &lt;nowiki&gt;~~~~&lt;/nowiki&gt; at the end. This is wikitext that is converted into your name and the date.<br /> <br /> This list has the most important items at the top.<br /> ----<br /> <br /> *&lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' There is now a link to FirstGlance underneath the molecule for every automatically seeded page.'' In every article titled with a single PDB id code, a link to (for a random case) &quot;Explore 2ace&quot; that goes to '''FirstGlance in Jmol'''. The link syntax is [http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace http://bioportal.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ace].<br /> * '''Searching''' for a '''plural''' should find the '''singular''' match, and vice versa. For example: I searched for &quot;histocompatibility antigens&quot; and did not find the page &quot;Category: Histocompatibility antigen&quot;. Searching for &quot;histocompatibility antigen&quot; did find this page. [[User:Emartz|Emartz]] 19:00, 8 March 2008 (IST)<br /> * '''Color keys''' displayed beneath Jmol, changing as needed with each green link. For example &quot;alpha helix&quot; and &quot;beta strand&quot; colored in the standard Jmol secondary colors. The standard keys should be pre-built and callable by name, perhaps by a parameter in the &amp;lt;scene ...&amp;gt; tag. [[User:Emartz|Emartz]] 01:59, 19 March 2008 (IST)<br /> * '''Biological units''' (from RCSB) should be the default initial scenes, with a view of the asymmetric unit optional, as agreed in discussion. Eric Martz plans to provide a mock-up of an advanced page that would have views from EBI PQS, EBI PISA, and RCSB biological units, with brief explanations of each. <br /> * '''ConSurf coloring''' can be provided as discussed with Nir Ben-Tal and Elana Erez. This could be one of the standard scenes on the proposed menu of standard scenes.<br /> * '''Several standard scenes''', such as those in FirstGlance in Jmol, could be provided in a pull-down menu on the auto-seeded pages. It could be one more row in the table below Jmol. Eric Martz plans to provide the scripts and HTML color keys for these. [[User:Eric Martz|Eric Martz]] 19:54, 13 April 2008 (IDT)<br /> * '''All models in NMR ensembles''' (and the 118 multiple-model X-ray entries) should be the initial view in auto-seeded pages. Eric Martz plans to provide the script for this.<br /> * '''Molprobity''' could be added under ''About this structure'' in the auto-seeded pages. Eric Martz plans to write a short explanation to accompany a link. [[User:Eric Martz|Eric Martz]] 20:00, 13 April 2008 (IDT)<br /> * '''Sequence and structure-related''' entries could be linked to every entry. Currently, at [[2ic8]], I can click the link to PDBSum, and there click a mysterious plus button, which gives me a list of sequence-related entries. However, I must then enter each one by hand into Proteopedia. It would be great if this list, already linked, were at the bottom of every PDB-code-titled page. OCA already does sequence-based searching. All we need is a structure-based search as well for &quot;structure neighbors&quot;. [[User:Eric Martz|Eric Martz]] 04:30, 26 April 2008 (IDT)<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' Green links are now bold by default.'' A user-settable preference to make all '''green links bold''' or underlined (when not touched with the mouse) (I prefer underlined, with bold onMouseover) because in Windows browsers, the font is very thin, and the green color is hard to see. It is hard to scan a paragraph and find the green links. Also 9% of males are colorblind. [[User:Emartz|Emartz]] 19:51, 9 March 2008 (IST)<br /> * To encourage authors to follow [[Proteopedia:Policy]] regarding links to Wikipedia, automatically detect ''wikipedia'' during every preview/save and refer the author to [[Proteopedia:Policy]]. [[User:Emartz|Emartz]] 02:10, 16 March 2008 (IST)<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt;'' When saving a scene (in the &quot;save scene&quot; dialog), a radio button to choose between &quot;force '''spinning''' on&quot;, &quot;force spinning off&quot;, &quot;inherit spinning set by the user with 'toggle spinning'&quot;. (inherit spinning not implemented on purpose --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT))<br /> * '''Tabulate characteristics''' of PDB codes on Category pages (in this order): PDB code, resolution, year, title, authors (ideally first and last author names like &quot;Harel/Sussman&quot; for 2ace), number of chains in the asymmetric unit, and ligand abbreviations. 2ace would look like this:<br /> &lt;table border=1 cellpadding=1&gt;&lt;tr&gt;&lt;td&gt;<br /> 2ace&lt;/td&gt;&lt;td&gt;2.50A&lt;/td&gt;&lt;td&gt;1996&lt;/td&gt;&lt;td&gt;NATIVE ACETYLCHOLINESTERASE (E.C. 3.1.1.7) FROM TORPEDO CALIFORNICA&lt;/td&gt;&lt;td&gt; Harel/Sussman&lt;/td&gt;&lt;td&gt;Chains=1&lt;/td&gt;&lt;td&gt;ACH<br /> &lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;<br /> Topic pages should be listed first, before PDB code pages, and without any additional characteristics.<br /> * Mechanism to spawn (open) a '''child window containing only Jmol''' with the current scene. Advantages: the child window can be resized, thereby resizing Jmol; the child window can be kept in view while the text in the parent Proteopedia window is scrolled. It should be possible to have green links work on both the Jmol on the Proteopedia page, and the child Jmol. [[User:Emartz|Emartz]] 00:06, 17 March 2008 (IST)<br /> * Automatically '''front, center, and size''' ligands and sites when their green links are clicked. That is, the molecule should rotate to put the selected entity in front of its center of mass, the selected entity should become the center of rotation/zoom, and the molecule should be zoomed (up or down) to make the selected entity fill e.g. 75% of the Jmol diameter.<br /> * &lt;span style=&quot;background-color:yellow;color:green&quot;&gt;'''SOLVED:'''&lt;/span&gt; (March 2, 2008): Quality (antialiasing) chosen by the user with &quot;toggle quality&quot; should remain in effect for all green links within that page. Imagine that you're projecting scenes to a class. Currently, with every new scene, you have to click &quot;toggle quality&quot; again to get high quality.<br /> * Support '''two Jmols side by side''', for comparisons. (''this is already possible, but not possible to sync them yet: see [[2b8n]]'' --[[User:Eran Hodis|Eran Hodis]] 22:23, 5 April 2008 (IDT))<br /> ** '''Synchronize''' mouse-directed rotations and zooms (this now works amazingly well, see Chapter 4 in the Demo Tutorial at http://bioinformatics.org/jmol-tutorials -- where by the way you can also see &quot;toggle quality&quot; working very clearly -- my links are labeled &quot;smoother rotation&quot; and &quot;smoother graphics&quot; to the lower left of Jmol).<br /> ** Provide a mechanism for '''one green link that sends separate scripts to each Jmol''' simultaneously. Maybe not necessary? Just use two green links? What is cool is to start with scenes that align the two molecules. Then they stay aligned as you rotate/zoom with the mouse (provided spin is left off at the beginning -- when it is on, one molecule tends to lag behind the other).<br /> *Have selenomethionine (MSE) treated as any other amino acid in the (Jmol) default settings - [[User:Morten Grøftehauge]]- June 1, 2008<br /> *Create a &quot;reset&quot; button for scene authoring tools, in particular the representations tab. Or an &quot;undo&quot; button. Something to allow the image to be returned to normal after experimenting with different representations without reloading. [[User:Emily Forschler|Emily Forschler]] 00:07, 6 June 2008 (IDT)</div>

Emily Forschler https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=545229 2008-06-03T21:50:20Z

<p>Emily Forschler: </p> <hr /> <div>Eran-<br /> Let's see how my attempts to figure out &quot;user talk&quot; go. I have been meaning to get back to you for a long time, but as you can see, it hasn't happened until now. It was a good experience to work on Proteopedia and interesting how the page I made would change without me knowing it as things were worked out on your end. Karl shared with me how you have been sharing the Photosystem II page in Italy. It was surprising to me to find that others were interested in seeing it too, but that's the point of it all! The interface Proteopedia has for J-mol is definitely better than many others. My classmates were all jealous that I got to use Proteopedia and they had to use other, more clunky interfaces. <br /> One thing that I attempted and couldn't figure out was labeling. Photosystem II has a lot of ligands and my attempts to label them as well as other individual atoms resulted in the labeling of every atom! Maybe I was just missing something, but that could be something to work on. Another feature which might be helpful would be a representations &quot;reset&quot; button. Sometimes, I would try things and then not like them, but since the original settings aren't given, it took a more round about approach to return to the original view. Reset would just make things easier. <br /> Thanks for letting me be a part of Proteopedia. <br /> -Emily Forschler<br /> [[User:Emily Forschler|Emily Forschler]] 17:48, 3 June 2008 (EDT)<br /> <br /> <br /> <br /> Dear Eran, please see Sandbox 30. We uploaded a file from PQS. The filename is 1nsb_mmol.pdb. We tried to display it in Jmol on Sandbox 30 but failed. Please help us, thanks, -Eric in Osaka<br /> <br /> Hi Eran, I was wanting to delete the extra &quot;Tom Garrett&quot; page but could not see ho to delete a page Is this possible... Tom</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537174 2008-05-15T15:35:37Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537173 2008-05-15T15:35:23Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;450&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537172 2008-05-15T15:35:09Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;425&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537171 2008-05-15T15:32:16Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537170 2008-05-15T15:30:28Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;left&quot; /&gt;<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537169 2008-05-15T15:28:38Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;left&quot; /&gt;<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537168 2008-05-15T15:27:45Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;left&quot; /&gt;<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537167 2008-05-15T15:27:21Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537166 2008-05-15T15:26:56Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;400&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=537165 2008-05-15T15:26:00Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535562 2008-05-06T21:17:31Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535561 2008-05-06T21:17:10Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> &lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;left&quot; /&gt;<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535531 2008-05-06T18:11:49Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535530 2008-05-06T17:16:13Z

<p>Emily Forschler: /* References */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|200px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535529 2008-05-06T17:16:00Z

<p>Emily Forschler: /* References */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|200px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535528 2008-05-06T17:15:42Z

<p>Emily Forschler: /* References */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|200px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> 2. Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535527 2008-05-06T17:13:10Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|200px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;ref&gt;Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14764885 14764885]&lt;/ref&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> &lt;references/&gt; <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535523 2008-05-06T02:21:51Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of Photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535522 2008-05-06T02:21:41Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/11'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535521 2008-05-06T02:14:01Z

<p>Emily Forschler: /* Electron Transfer */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. The &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535520 2008-05-06T02:12:38Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structures with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535519 2008-05-06T02:12:27Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structure with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535518 2008-05-06T02:12:10Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are a &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structure with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535517 2008-05-06T02:11:33Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These centers are shown to be a &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;cubane-like&lt;/scene&gt; structure with 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#C11B17&quot;&gt;oxygen&lt;/FONT&gt;''' and a '''&lt;FONT COLOR=&quot;#59E817&quot;&gt;calcium&lt;/FONT&gt;''' linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535516 2008-05-06T02:08:52Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be a cubane-like structure with a 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#4CC417&quot;&gt;C11B17&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#00FF00&quot;&gt;calcium&lt;/FONT&gt;''' structure linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluste<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535515 2008-05-06T02:07:17Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be a cubane-like structure with a 3 '''&lt;FONT COLOR=&quot;#8D38C9&quot;&gt;manganese&lt;/FONT&gt;''', 4 '''&lt;FONT COLOR=&quot;#4CC417&quot;&gt;oxygen&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;calcium&lt;/FONT&gt;''' structure linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluste<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535514 2008-05-06T02:05:34Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be a cubane-like structure with a 3 manganese, 4 oxygen and calcium strucure linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluste<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535513 2008-05-06T02:05:03Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be a cubane-like structure with a 3 manganese, 4 oxygen and calcium strucure linked to a fourth manganese.&lt;sup&gt;[1]&lt;/sup&gt; Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluste<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535512 2008-05-06T02:03:27Z

<p>Emily Forschler: /* Oxygen Evolution */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge.&lt;sup&gt;[1]&lt;/sup&gt; Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535511 2008-05-06T02:02:27Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. &lt;ref&gt;{{cite journal |author=Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. |title=Architecture of the photosynthetic oxygen-evolving center.|journal=Science|volume=303 |issue=5665 |pages=1831-8 |year=2004 |pmid=1096767}}&lt;/ref&gt; Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535510 2008-05-06T01:46:03Z

<p>Emily Forschler: </p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/5'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/9'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. [1] Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535509 2008-05-06T01:43:27Z

<p>Emily Forschler: /* Electron Transfer */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/4'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/3'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/5'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/4'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/3'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/8'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. [1] Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535508 2008-05-06T01:38:06Z

<p>Emily Forschler: /* Electron Transfer */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/1'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/2'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/4'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/4'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/2'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/8'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. [1] Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535507 2008-05-06T01:37:57Z

<p>Emily Forschler: /* Electron Transfer */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/2'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/2'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/4'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/4'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/2'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/8'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. [1] Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535506 2008-05-06T01:35:50Z

<p>Emily Forschler: /* Electron Transfer */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/3'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/2'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/4'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/4'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/2'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/8'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. [1] Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler https://proteopedia.org/index.php?title=Photosystem_II&diff=535505 2008-05-06T01:34:31Z

<p>Emily Forschler: /* Electron Transfer */</p> <hr /> <div>&lt;applet load=&quot;1s5l&quot; size=&quot;500&quot; frame=&quot;true&quot; align=&quot;right&quot; /&gt;<br /> [[Image:1s5l.gif|250px|left]]<br /> ==Background==<br /> This structure of Photosystem II was crystallized from the bacteria, ''Thermosynechococcus elongatus'', at 3.50 Å. Cyanobacteria and plants both contain Photosystem II with a similar structure. This photosynthetic protein is associated with a variety of functional ligands. It is a &lt;scene name='Photosystem_II/Psii_dimer/1'&gt;dimer&lt;/scene&gt; composed mainly of alpha-helices. Nineteen &lt;scene name='Photosystem_II/Protein_only/1'&gt;subunits&lt;/scene&gt; are in each monomer, with multiple extrinsic subunits associated with the oxygen evolving complex missing from this crystallization. Photosystem II is a membrane bound protein associated with the thylakoid membrane of chloroplasts. &lt;scene name='Photosystem_II/Hydrophobic_polar/1'&gt;Polar and hydrophobic&lt;/scene&gt; regions correlate with membrane associated nature of the protein. '''&lt;FONT COLOR=&quot;#616D7E&quot;&gt;Hydrophobic&lt;/FONT&gt;''' helices make up the transmembranal portion, while '''&lt;FONT COLOR=&quot;#C031C7&quot;&gt;polar&lt;/FONT&gt;''' residues are concentrated externally on either side of the membrane.<br /> <br /> ==Photosynthesis==<br /> Photosystem II is an integral part of photosynthesis, the conversion of light energy into chemical energy by living organisms. Photosystem II is linked to a variety of other proteins, including Photosytem I. These proteins ultimately produce NADPH and ATP that power the Calvin cycle. Using this energy, glucose is synthesized from carbon dioxide and water.<br /> <br /> ==Electron Transfer==<br /> [[Image:Chlorophyll_a.svg.png|thumb|170px|left|structure of chlorophyll ''a'']]<br /> &lt;scene name='Photosystem_II/Chlorophyll_green/3'&gt;Chlorophyll&lt;/scene&gt; surround Photosystem II and capture energy from sunlight, exciting electrons. Chlorophyll are highly conjugated and absorb visible light, along with accessory light harvesting pigments such as &lt;scene name='Photosystem_II/Betacarotene/1'&gt;beta carotene&lt;/scene&gt;. Beta carotene absorbs visible light of other wavelengths and also protects Photosystem II by destroying reactive oxygen species that result from this photoexcitation. [[Image:b-car.svg.png|b-car.svg.png|thumb|right|400px|structure of beta carotene]] Electrons are passed from chlorophyll to &lt;scene name='Photosystem_II/Pheophytin_purple/4'&gt;pheophytin&lt;/scene&gt;. Pheophytin are very similar to chlorophyll except they contain 2 H&lt;sup&gt;+&lt;/sup&gt; instead of a Mg&lt;sup&gt;2+&lt;/sup&gt; ion. From the pheophytin, electrons transferred to &lt;scene name='Photosystem_II/Quinone_pink/4'&gt;plastoquinones&lt;/scene&gt;, which are reduced. Between each pair of quinones, an iron, in red, helps to transfer the electron. These plastoquinones eventually move to a plastoquinone pool which travels to another large protein subunit, cytochrome b &lt;sub&gt;6&lt;/sub&gt;/ f. Eventually these electrons reduce NADP&lt;sup&gt;+&lt;/sup&gt; to NADPH. Here the &lt;scene name='Photosystem_II/Electron_pathway/2'&gt;electron pathway&lt;/scene&gt; through Photosystem II is shown, with '''&lt;FONT COLOR=&quot;#F87217&quot;&gt;beta-carotenes&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#571B7e&quot;&gt;pheophytins&lt;/FONT&gt;''', '''&lt;FONT COLOR=&quot;#E42217&quot;&gt;iron&lt;/FONT&gt;''' and '''&lt;FONT COLOR=&quot;#F535AA&quot;&gt;plasotoquinones&lt;/FONT&gt;'''.<br /> [[Image:plastoquinone.jpg|thumb|300px|right|reduced plastoquinone]]<br /> <br /> ==Oxygen Evolution==<br /> Another important facet of photosystem II is its ability to oxidize water to oxygen with its &lt;scene name='Photosystem_II/Oxygen_evolving_centers/8'&gt;oxygen evolving centers&lt;/scene&gt;. These &lt;scene name='Photosystem_II/Oxygen_evolving_centers/3'&gt;centers&lt;/scene&gt; were shown to be cubane-like Mn&lt;sub&gt;3&lt;/sub&gt;CaO&lt;sub&gt;4&lt;/sub&gt;cluster linked to a fourth Mn by a mono-μ-oxo bridge. [1] Purple represents manganese, red represents oxygen and green is for calcium. Oxidation of water to leaves 2 H &lt;sup&gt;+&lt;/sup&gt; on the lumenal side of the membrane, helping to establish the proton gradient essential for ATP synthesis in the CF&lt;sub&gt;1&lt;/sub&gt;CF&lt;sub&gt;0&lt;/sub&gt;-ATP sythase protein.<br /> <br /> ==References==<br /> [1] Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S. &quot;Architecture of the photosynthetic oxygen-evolving center.&quot; Science, March 19, 2004, 303 (5665), 1831-8. <br /> <br /> [2] Garrett, R.H., Grisham, C.M. ''Biochemistry, 3rd Edition.'' Belmont, CA: Thomson Brooks/ Cole, 2005.</div>

Emily Forschler