https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Khaja+Muneeruddin 2026-09-23T13:03:39Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Molecular_Playground/Transferrin&diff=1634727 2012-12-12T23:33:02Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Human Se-Met transferrin complex with citrate and glycerol [[2hau]]' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. At low pH iron is released from N-lobe by protonation of &lt;scene name='Molecular_Playground/Transferrin/N_lobe_fe_release/2'&gt;Lysines&lt;/scene&gt; 206 and 296 &lt;ref&gt;PMID: 9609685&lt;/ref&gt; and Lys534 and Arg632 in C-lobe.&lt;ref&gt;PMID: 19917294&lt;/ref&gt;<br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Intracellular delivery of iron by transferrin is carried out by clathrin-dependent receptor-mediated endocytosis. At pH 7.4 diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized and in the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. Apo hTf-hTfR complex is recycled back to the cell surface and at pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> <br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> <br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> ==3D structures of transferrin==<br /> <br /> [[Transferrin]]<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=Molecular_Playground/Transferrin&diff=1634726 2012-12-12T23:30:08Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Human Se-Met transferrin complex with citrate and glycerol [[2hau]]' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. At low pH iron is released from N-lobe by protonation of &lt;scene name='Molecular_Playground/Transferrin/N_lobe_fe_release/2'&gt;Lysines&lt;/scene&gt; 206 and 296 &lt;ref&gt;PMID: 9609685&lt;/ref&gt; and from C-lobe Lys534 and Arg 632&lt;ref&gt;PMID: 19917294&lt;/ref&gt;<br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> <br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> <br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> ==3D structures of transferrin==<br /> <br /> [[Transferrin]]<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=Molecular_Playground/Transferrin&diff=1630895 2012-12-11T20:27:38Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Human Se-Met transferrin complex with citrate and glycerol [[2hau]]' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> At low pH iron is released from N-lobe by protonation of &lt;scene name='Molecular_Playground/Transferrin/N_lobe_fe_release/2'&gt;Lysines&lt;/scene&gt; 206 and 296 &lt;ref&gt;PMID: 9609685&lt;/ref&gt; and from C-lobe<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> <br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> ==3D structures of transferrin==<br /> <br /> [[Transferrin]]<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1630893 2012-12-11T20:24:04Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as &quot;in progress&quot; until you are finished. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not -- I may be able to request additions to the author list).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> Peyton Lab<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! The new goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''<br /> <br /> Fall 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.<br /> <br /> You are encouraged to collaborate on this year's CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 4. Your final pages should be called &quot;Molecular Playground/your molecule&quot; and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them &quot;in progress&quot; until you are finished.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1333025 2011-12-17T02:08:02Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> : New Fall 2011''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> Peyton Lab<br /> : NEW FALL 2011! '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : NEW FALL 2011! '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Tew Lab<br /> <br /> : NEW FALL 2011!! '''[http://www.proteopedia.com/wiki/index.php/Molecular_Playground/HIV_Tat Molecular Playground/HIV Tat]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : New Fall 2011 '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1333024 2011-12-17T02:07:09Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita <br /> <br /> <br /> : New Fall 2011'''[[Molecular Playground/Transferrin]]''', Khaja Muneeruddin<br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> Peyton Lab<br /> : NEW FALL 2011! '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : NEW FALL 2011! '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> <br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Tew Lab<br /> <br /> : NEW FALL 2011!! '''[http://www.proteopedia.com/wiki/index.php/Molecular_Playground/HIV_Tat Molecular Playground/HIV Tat]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : New Fall 2011 '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1332980 2011-12-16T21:44:50Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita <br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> Peyton Lab<br /> : NEW FALL 2011! '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : New Fall 2011 '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1332979 2011-12-16T21:44:06Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita <br /> <br /> : New Fall 2011'''[[Molecular Playground/Transferrin]]''', Khaja Muneeruddin <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> Peyton Lab<br /> : NEW FALL 2011! '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : New Fall 2011 '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1332925 2011-12-16T16:35:31Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita <br /> <br /> <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> [http://robertsgroup.ecs.umass.edu/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1332924 2011-12-16T16:33:57Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita <br /> <br /> : '''[[Molecular Playground/Transferrin]]''', Khaja Muneeruddin New Fall 2011 <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> [http://robertsgroup.ecs.umass.edu/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=CBI_Molecules&diff=1332923 2011-12-16T16:32:39Z

<p>Khaja Muneeruddin: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> It's great to build on a previous entry, but you must leave the earlier one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> Fall 2011: New entries are due 12/16/11. Please append the designation (new Fall 2011) to your new entries. <br /> <br /> <br /> ==Molecules==<br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> Forbes Lab<br /> <br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : NEW Fall 2011! '''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano<br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita <br /> <br /> : '''[[Molecular Playground/Human Transferrin]]''', Khaja Muneeruddin New Fall 2011 <br /> <br /> <br /> Knapp lab<br /> <br /> :'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> : '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : '''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : NEW Fall 2011! '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> [http://robertsgroup.ecs.umass.edu/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> Schnarr Lab <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> Thayumanavan Lab<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecule page and/or scene will be awarded in summer 2012!'''<br /> <br /> Fall 2011: Complete steps 1-4 by 12/1/11, in preparation for the CBI Molecule Workshop.<br /> <br /> Choose a molecule that is part of your research project. If someone in your group has already made a page for your research molecule, you can improve on that previous entry. You must leave the previously created page intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.<br /> <br /> 2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]). <br /> <br /> 3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.<br /> <br /> 4. Add a link to your sandbox page at [[Sandbox_CBI]] (CBI Molecules in Progress).<br /> <br /> 5. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.<br /> <br /> 6. Choose a &quot;green scene&quot; on your Proteopedia page to suggest for display at the Molecular Playground and specify a &quot;banner&quot; which will be projected with the molecule. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: &quot;Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to &quot;smell&quot; their environment.&quot;<br /> <br /> 7. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter &quot;Molecular Playground/your molecule&quot; (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.<br /> <br /> 8. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the examples above, and be sure to mark it as NEW FALL 2011. If you are improving a previously created page, leave the old one intact and make a copy that you improve and mark as new. Later we will retain the new one with a merged author list. When multiple authors contribute to a Molecular Playground page, please indicate your scene with your initials. Please link the lab names to web pages too.<br /> <br /> ==Links to HELP pages==<br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=Molecular_Playground/Transferrin&diff=1332920 2011-12-16T16:24:56Z

<p>Khaja Muneeruddin: New page: &lt;Structure load=&#039;2HAU&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Insert caption here&#039; scene=&#039;Insert optional scene name here&#039; /&gt;One of the CBI Molecules being studied in the Universit...</p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> <br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332915 2011-12-16T16:11:36Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> <br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332914 2011-12-16T16:11:03Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> <br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332913 2011-12-16T16:10:37Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332911 2011-12-16T16:10:07Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however crystal structure information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332910 2011-12-16T16:07:48Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332908 2011-12-16T16:07:29Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. <br /> After binding iron N-lobe and C-lobe undergo a conformational change. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332906 2011-12-16T16:05:10Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron in blood and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. N-lobe and C-lobe undergo a conformational change after binding ferric ion. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferric hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt;<br /> Molecular Playground banner: A bilobal protein that binds iron and transport it inside the cell.<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332903 2011-12-16T15:50:35Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo hTf (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron inside human system and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII, and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping of iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding iron. N-lobe and C-lobe undergo a conformational change after binding ferric ion. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332796 2011-12-16T04:23:29Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind one ferric ion each to regulate the concentration of free iron inside human system and also transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. Structurally both N-lobe and C-lobe contain two sub domains namely NI and NII and CI and CII which come together to form a cleft for binding iron. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;binding site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also plays an important role in binding ferric ion. In ApohTf, N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind iron.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332791 2011-12-16T04:02:24Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/3'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/3'&gt;bind site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332787 2011-12-16T03:30:11Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the &lt;scene &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/2'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/C-lobe_binding_sites/1'&gt;bind site of C-lobe&lt;/scene&gt; include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332784 2011-12-16T02:30:13Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the &lt;scene &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/2'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332783 2011-12-16T02:28:13Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Nlobe_binding_sites/1'&gt;binding site of N-lobe&lt;/scene&gt; Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332782 2011-12-16T02:08:30Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332781 2011-12-16T02:05:50Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332780 2011-12-16T02:03:08Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf_check/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/1'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_nlobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332779 2011-12-16T01:59:49Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf_check/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/1'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Opennlobe/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_nlobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332778 2011-12-16T01:47:56Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf_check/1'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/1'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_nlobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332777 2011-12-16T01:43:26Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apotf/1'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_nlobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332776 2011-12-16T00:47:26Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/6'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_nlobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332775 2011-12-16T00:38:41Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/6'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_n_lobe1/1'&gt;TextToBeDisplayed&lt;/scene&gt; &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_n_lobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332774 2011-12-16T00:36:28Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/6'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Open_n_lobe/1'&gt;open conformation&lt;/scene&gt; and upon binding ferric ion it shows a &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/1'&gt;closed conformation&lt;/scene&gt; characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.&lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Closed/2'&gt;TextToBeDisplayed&lt;/scene&gt;<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332771 2011-12-16T00:10:42Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/6'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it shows a closed conformation characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332761 2011-12-15T23:13:31Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it shows a closed conformation characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;&lt;ref&gt;PMID: 6300904&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332759 2011-12-15T23:11:16Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it shows a closed conformation characterized by rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR to bind to iron again.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332757 2011-12-15T23:07:07Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg-124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it has closed conformation characterized by a rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric human transferrin binds to human transferrin receptor (hTfR). Upon binding, diferic hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from diferric hTf-hTfR complex into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf dissociates from the TfR.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332753 2011-12-15T23:02:29Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg-124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it has closed conformation characterized by a rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface iron bound human transferrin (Fe== 2 ==-hTf binds to human transferrin receptor (hTfR). Upon binding, Fe== 2 ==hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from Fe== 2 ==hTf-hTfR into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf unbound from the TfR.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332751 2011-12-15T23:02:09Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg-124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it has closed conformation characterized by a rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of hTf is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface iron bound human transferrin (Fe== 2 ==hTf binds to human transferrin receptor (hTfR). Upon binding, Fe== 2 ==hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from Fe== 2 ==hTf-hTfR into the cells. The ApohTf-hTfR complex is recycled back to the cell surface and at the basic pH of cell surface Tf unbound from the TfR.&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332747 2011-12-15T22:51:38Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein found in blood. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. N-lobe and C-lobe can be further divided into two sub domains namely N-I and N-II, and C I and C-II respectively. These two subdomains at each lobe forms a cleft which traps ferric ion. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg-124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. In addition to these amino acids, at both the lobes a carbonate ion also play an important role in binding ferric ion. In ApoTf the N lobe has an open conformation and upon binding ferric ion it has closed conformation characterized by a rotation of N-II sub domain by 63°&lt;ref&gt;PMID: 9760232&lt;/ref&gt;. C-lobe also undergo a similar conformational change upon binding to ferric ion, however structural information of the C lobe of human transferrin is limited due to difficulty in production&lt;ref&gt;PMID: 15924420&lt;/ref&gt;&lt;ref&gt;PMID: 9337853&lt;/ref&gt;.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332713 2011-12-15T18:18:57Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells.<br /> <br /> N-lobe and C-lobe are homologous and contain identical iron binding amino acid residues. At the '''binding site of N-lobe''' Asp63, Tyr188, Tyr95, His249 and Arg-124 are involved in trapping iron&lt;ref&gt;PMID: 9609685&lt;/ref&gt;. The amino acids involved in trapping of iron at the '''bind site of C-lobe''' include Asp392, Tyr426, Tyr517, His585, Arg456. Apart from these amino acid, at both the lobes a carbonate ion also play an important role in binding ferric ion&lt;ref&gt;PMID: 15924420&lt;/ref&gt;. N lobe and C lobe undergoes a large conformational change upon binding to ferric ion. Open N-lobe characteristics and upon binding to iron closed N lobe looks like this.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332695 2011-12-15T16:48:48Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells<br /> <br /> Both at the N-lobe and C-lobe specific amino acid residues are involved in binding to ferric ion. At the '''binding site of C-lobe''' so and so residues are involved in trapping iron. The amino acids involved in trapping of iron at the '''bind site of N-lobe''' includes. N lobe and C lobe undergoes a large conformational change upon binding to ferric ion. Open N-lobe characteristics and upon binding to iron closed N lobe looks like this.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==<br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1332693 2011-12-15T16:47:07Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells<br /> <br /> Both at the N-lobe and C-lobe specific amino acid residues are involved in binding to ferric ion. At the '''binding site of C-lobe''' so and so residues are involved in trapping iron. The amino acids involved in trapping of iron at the '''bind site of N-lobe''' includes. N lobe and C lobe undergoes a large conformational change upon binding to ferric ion. Open N-lobe characteristics and upon binding to iron closed N lobe looks like this.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR&lt;ref&gt;PMID: 16271884&lt;/ref&gt;. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> <br /> <br /> ==References==</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1329989 2011-12-14T03:53:31Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells<br /> <br /> Both at the N-lobe and C-lobe specific amino acid residues are involved in binding to ferric ion. At the '''binding site of C-lobe''' so and so residues are involved in trapping iron. The amino acids involved in trapping of iron at the '''bind site of N-lobe''' includes. N lobe and C lobe undergoes a large conformational change upon binding to ferric ion. Open N-lobe characteristics and upon binding to iron closed N lobe looks like this.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.<br /> <br /> &lt;references/&gt;</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1329988 2011-12-14T03:46:56Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells<br /> <br /> Both at the N-lobe and C-lobe specific amino acid residues are involved in binding to ferric ion. At the '''binding site of C-lobe''' so and so residues are involved in trapping iron. The amino acids involved in trapping of iron at the '''bind site of N-lobe''' includes. N lobe and C lobe undergoes a large conformational change upon binding to ferric ion. Open N-lobe characteristics and upon binding to iron closed N lobe looks like this.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=Sandbox_CBI&diff=1329987 2011-12-14T03:44:07Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;!-- <br /> Please use the &quot;3D&quot; button above this box to insert a Jmol applet (molecule) on this page.<br /> Or use the four-green-boxes-button to insert scrollable text adjacent<br /> to a Jmol applet. Check out the other buttons as well! <br /> --&gt;<br /> <br /> This page is for links to CBI Molecules in Progress (user sandbox pages).<br /> <br /> http://proteopedia.org/wiki/index.php/Ketan_Mathavan/Sandbox_1<br /> <br /> http://proteopedia.org/wiki/index.php/Brittany_deRonde/Sandbox_1<br /> <br /> <br /> http://proteopedia.org/wiki/index.php/Heidi_Hu/Sandbox_1<br /> <br /> http://proteopedia.org/wiki/index.php/User:Xuni_Li/Sandbox_1<br /> <br /> http://proteopedia.org/wiki/index.php/Gustavo_Elberto_Epalza_Sanchez/Sandbox_1<br /> <br /> http://proteopedia.org/wiki/index.php/Scott_Eron/Sandbox_1<br /> <br /> http://www.proteopedia.org/wiki/index.php/User:Jing_Liu/Sandbox_1</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1329986 2011-12-14T03:43:20Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells<br /> <br /> Both at the N-lobe and C-lobe specific amino acid residues are involved in binding to ferric ion. At the '''binding site of C-lobe''' so and so residues are involved in trapping iron. The amino acids involved in trapping of iron at the '''bind site of N-lobe''' includes. N lobe and C lobe undergoes a large conformational change upon binding to ferric ion.<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR. Both N-lobe and C-lobe undergoes<br /> <br /> show each binding site and label residues.</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1329956 2011-12-12T23:17:28Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal, iron binding glycoprotein. In Apo transferrin (iron free form), N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells<br /> <br /> Transferrin delivers iron to iron requiring cells by receptor-mediated endocytosis. At basic pH of cell surface diferric HTf binds to human transferrin receptor (hTfR). Upon binding, iron bound hTf-hTfR is internalized in the cell by endocytosis. In the acidic condition of endosome iron is release from hTf into the cells. The ApohTf-HTfR complex is recycled back to the cell surface and at the basic pH of cell surface transferrin unbounds from the TfR. Both N-lobe and C-lobe undergoes</div>

Khaja Muneeruddin https://proteopedia.org/index.php?title=User:Khaja_Muneeruddin/Sandbox_1&diff=1329955 2011-12-12T22:22:51Z

<p>Khaja Muneeruddin: </p> <hr /> <div>&lt;Structure load='2HAU' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /&gt;One of the CBI Molecules being studied in the University of Massachusetts Amherst Chemistry-Biology Interface Program at UMass Amherst and on display at the Molecular Playground.<br /> <br /> &lt;scene name='User:Khaja_Muneeruddin/Sandbox_1/Apo_transferrin/5'&gt;Human Transferrin (hTf)&lt;/scene&gt; is a 80 KDa bilobal glycoprotein. In Apo transferrin, N-lobe (brown) and C-lobe (green) bind to one ferric ion each to keep ferric ion in solution or transport to iron requiring cells. <br /> <br /> Diferric HTf binds to human transferrin receptor (hTfR) expressed on the surface of iron requiring cells. Upon binding, Fe2hTf-hTfR is internalized in the cell by endocytosis. The acidic condition of endosome causes the release of ferric ions in cells and the ApohTf-HTfR is recycled back to cell surface to release ApohTf in plasma where it can bind to ferric ions again.</div>

Khaja Muneeruddin