https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=David+S.+GoodsellProteopedia - User contributions [en]2026-09-22T10:39:51ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza&diff=953399Avian Influenza Neuraminidase, Tamiflu and Relenza2009-04-30T21:44:55Z<p>David S. Goodsell: </p>
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<div><big><br />
This article was updated April 29, 2009.<br />
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==Influenza==<br />
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Influenza <ref name="flu">[http://en.wikipedia.org/wiki/Influenza Influenza] (in Wikipedia).</ref> is a contagious disease caused by a virus. Influenza A<ref name="flu_a">See [http://en.wikipedia.org/wiki/Influenza#Types_of_influenza_virus Influenza A Types of Influenza Virus] (in Wikipedia).</ref> (one of several genera and species of influenza) is the most virulent form infecting humans. Largely by facilitating secondary bacterial pneumonias, influenza kills 500,000 people worldwide annually (including about 36,000 in the USA), mostly during seasonal [http://en.wikipedia.org/wiki/Epidemic epidemics] each year. Most people killed in the annual influenza epidemics are people whose immune defenses are weak, including the very young and the old. Influenza also kills large numbers of animals and birds, both domestic and wild<ref name="animals">[http://www.fao.org/avianflu/en/clinical.html Epidemiology of Avian Influenza] at the [http://fao.org Food and Agriculture Organization of the United Nations].</ref>.<br />
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==Influenza Virus Neuraminidase==<br />
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[[Image:3D_Influenza_virus.png|frame|Structure of an influenza virus <ref>[http://en.wikipedia.org/wiki/Image:3D_Influenza_virus.png Image of influenza virus structure] was obtained from Wikipedia.</ref>.]]<br />
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The surfaces of influenza viruses include, among other molecules, two glycoproteins named '''hemagglutinin''' and '''neuraminidase''', coded for by the viral segmented RNA genome. Each of these molecules is required for successful infection and spread in a host animal. The hemagglutinin attaches influenza to sialic acid on the surfaces of cells, enabling them to enter and infect cells. After the virus has replicated, neuraminidase (also called sialidase) removes sialic acid from the cell, enabling the newly assembled virions to be released in order to spread and infect other cells. For more about the structure and biology, including references for the points made here, please see [http://en.wikipedia.org/wiki/Influenza Influenza at Wikipedia].<br />
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<applet load='2hu4_1.pdb' size='500' frame='true' align='right' caption='Influenza Neuraminidase N1 (2hu4).' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/1' /><br />
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===Neuraminidase Structure and Conserved Amino Acids===<br />
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*Influenza neuraminidase is a homotetramer<ref>The tetramer is one of two [[Biological Unit|biological units]] in the [[Asymmetric Unit|asymmetric unit]] of [[2hu4]].</ref> (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/1'>restore initial scene</scene>). <br />
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*Each of the four protein chains in the tetramer has a catalytic site, indicated in <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/3'>this scene</scene> by the positions of the bound <font color='red'>'''Tamiflu'''</font> inhibitors.<br />
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*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/5'>substrate binding site</scene> involves only a single protein chain, being distant from neighboring chains.<br />
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*The <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/6'>secondary structure</scene> is mostly beta, consisting of several beta sheets with three short alpha helices ({{Template:ColorKey_Strand}}, {{Template:ColorKey_Helix}}).<br />
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*The residues contacting the <font color='red'>'''Tamiflu inhibitory substrate analog'''</font> are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/7'>highly conserved</scene><ref>See [[Evolutionary Conservation]]. Coloring by ConSurf on chain A of 2hu4 based on 100 unique homologs using default conditions, done on September 23, 2008.</ref>.<br />
<center>{{Template:ColorKey_ConSurf}}</center><br />
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*These highly conserved residues include some known to be crucial to binding sialic acid substrate: Arg 118, Arg 292 and Arg 371 bind the carboxylate; Arg 152 interacts with the acetamido substituent; and Glu 276 forms hydrogen bonds with the 8- and 9-hydroxyl groups of the substrate. These residues are <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/2hu4_tetramer/8'>highlighted here</scene> in contact with the sialic acid substrate analog Tamiflu. In this scene, atoms and bonds in Tamiflu and the highlighted residues are colored by element: {{Template:ColorKey_Element_C}}, {{Template:ColorKey_Element_O}}, {{Template:ColorKey_Element_N}}.<br />
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==Pandemic Influenza==<br />
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[http://en.wikipedia.org/wiki/Pandemic Pandemics] occur when localized [http://en.wikipedia.org/wiki/Epidemic epidemics] spread through large regions of the world.<br />
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===Past Influenza Pandemics===<br />
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The hemagglutinin ('''H''') and neuraminidase ('''N''') of influenza A are classified into various numbered serotypes or subtypes, such as H1N1, H2N2, H3N2, H5N1, and so forth<ref name="fluwikipedia">[http://en.wikipedia.org/wiki/Influenza Influenza] at Wikipedia.</ref>.<br />
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* '''H1N1 1918-20''': The [http://en.wikipedia.org/wiki/Spanish_flu Spanish Flu] pandemic killed tens of millions of people worldwide (about twice as many as were killed in World War I). One in five suffered with this disease, and about one in 30 died. This pandemic may have killed more people than did the [http://en.wikipedia.org/wiki/Black_Death Black Plague]. Spanish Flu was caused by a particularly virulent form of [http://en.wikipedia.org/wiki/H1N1 H1N1] believed to be derived from influenza A viruses in the natural reservoir of wild birds.<br />
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* '''H2N2 1957-58''': The ''Asian Flu'' pandemic originated when a virus mutation in the wild duck reservoir of influenza virus combined with a human strain. This virus, of subtype [http://en.wikipedia.org/wiki/H2N2 H2N2], killed nearly 70,000 people in the USA and infected millions worldwide. It was contained in part by a vaccine developed during the pandemic. H2N2 is also suspected of causing the ''Russian Flu'' pandemic that killed about one million people in 1889-90.<br />
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* '''H3N2 1968-69''': The ''Hong Kong Flu'' pandemic was caused by an H3N2 subtype derived by genetic recombination ([http://en.wikipedia.org/wiki/Antigenic_shift antigenic shift]) between virus subtypes, believed to have occurred during co-infection of pigs by multiple virus subtypes including H2N2. Although it infected hundreds of millions of people worldwide, its modest virulence prevented the death rate from greatly exceeding that of normal flu seasons.<br />
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===H1N1 "Swine Flu" Pandemic Threat in 2009===<br />
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Although scientists and public health officials have been worried about an H5N1 "bird flu" pandemic for many years (see next section below), the first new influenza virus to emerge in the twenty-first century<ref>Severe acute respiratory syndrome, SARS, was a near-pandemic in 2002-2003: see [http://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome Severe Acute Respiratory Syndrome] (in Wikipedia).</ref> that shows pandemic potential is an H1N1 "swine flu"<ref name="swinefluoutbreak">[http://en.wikipedia.org/wiki/2009_swine_flu_outbreak 2009 Swine Flu Outbreak] (in Wikipedia).</ref> that was recognized by the US Centers for Disease Control and Prevention (CDC) in mid-April, 2009<ref name="swineflu1">[http://www.cdc.gov/swineflu/updates/investigation_042309.htm Human Swine Influenza Investigation], April 23, 2009.</ref>. &quot;The viruses contain a unique combination of gene segments that have not been reported previously among swine or human influenza viruses in the U.S. or elsewhere.&quot;<ref>From the CDC: [http://cdc.gov/swineflu/pdf/HAN_042509.pdf Investigation and Interim Recommendations: Swine Influenza (H1N1)].</ref> <br />
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Although, not surprisingly, this emergent flu is resistant to amantadine and rimantadine (see [[#Amantadine and Rimantadine|below]]), as of late April, 2009, it is susceptible to both Tamiflu and Relenza<ref name="anti-swine-drugs">CDC document on [http://cdc.gov/swineflu/antiviral_swine.htm Antiviral Drugs and Swine Influenza].</ref>.<br />
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The majority of the approximately 500,000 fatalities worldwide during the annual seasonal influenza epidemics occur in old or very young people, or others with weak immune defenses<ref name="mortality_age">PMID:19230159</ref>. In contrast, the deaths from H1N1 "swine flu" in Mexico appear to be occurring in young, otherwise healthy people, although firm data are not yet available.<br />
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On April 29, 2009, the World Health Organization (WHO) raised its pandemic alert to level five on a six point scale, indicating that a pandemic is imminent.<br />
The CDC is maintaining frequent updates at [http://cdc.gov/swineflu cdc.gov/swineflu].<br />
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===H5N1 "Bird Flu" Pandemic Threat===<br />
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A new influenza pandemic is one of our greatest threats because it might well kill a large fraction of the human population<ref name="flu_pandemic">[http://en.wikipedia.org/wiki/Flu_pandemic Influenza Pandemic] at Wikipedia.</ref>. The subtype [http://en.wikipedia.org/wiki/H5n1 H5N1] is most feared because of the large reservoir in wild birds, and the recent emergence of strains called ''highly pathogenic avian influenza (HPAI)'' that have high virulence and mortality in birds. Hundreds of millions of domestic poultry have been culled at great economic cost in an effort to stem the spread of H5N1. Although transmission from birds to humans has apparently been very inefficient, over half of the people known to have been infected died from the disease. The emergence of a high-virulence form of H5N1 that is highly transmissable among humans seems nearly inevitable, and would cause a devastating pandemic.<br />
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==Prophylaxis and Treatment of Influenza==<br />
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'''Vaccines''' are effective at preventing influenza, but only if they target the relevant viral subtypes. New vaccines against the annual epidemics of influenza A and B are prepared each year, separately in the northern and southern hemispheres. These are designed to target the subtypes predicted to be prevalent in any given flu season, but sometimes those predictions are wrong, leading to that year's vaccine being ineffective. A vaccine for a pandemic strain of H5N1 could not be prepared until after the pandemic began, because only then would the relevant subtype be known<ref>[http://en.wikipedia.org/wiki/Influenza#Vaccination_and_infection_control Vaccination for Influenza] at Wikipedia</ref>.<br />
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'''Drugs''' against influenza, stockpiled in advance of a panedmic, appear to be the best preparation, given the limitations of vaccines. Tens of billions of dollars have been spent on pandemic preparedness in the USA alone, and a large portion of these expenditures is for [http://en.wikipedia.org/wiki/Oseltamivir stockpiling of anti-influenza drugs]. Similar expenditures have been made in many developed countries. The World Health Organization is poised to distribute anti-influenza drugs at the first signs of an epidemic of H5N1.<br />
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===Amantadine and Rimantadine===<br />
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[http://en.wikipedia.org/wiki/Amantadine Amantadine] and [http://en.wikipedia.org/wiki/Rimantadine Rimantadine] are an anti-viral drugs believed to work by blocking an ion-channel (M2) required for viruses to infect cells. Ion-channel function appears to be required for uncoating during endocytosis. Amantadine was approved for anti-viral uses beginning in 1966 by the US FDA. Subsequent widespread use has selected amantadine-resistant influenza in humans and birds. By 2005-2006, the US CDC found 92% of H3N2 isolates were resistant, and 2 of 8 H1N1 isolates. In Asia, resistance is close to 100%. The most common mutation responsible for resistance is S31N in M2, which confers resistance to both amantadine and rimantadine<ref>[http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5502a7.htm Report on amantadine resistance], CDC Morbidity and Mortality Weekly Reports, January 2006.</ref>. References for this paragraph will be found in the [http://en.wikipedia.org/wiki/Amantadine ''Amantadine'' article in Wikipedia].<br />
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===Tamiflu&reg; (oseltamivir) and Relenza&reg; (zanamivir)===<br />
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[http://en.wikipedia.org/wiki/Oseltamivir Tamiflu (oseltamivir)] is an inhibitor of influenza neuraminidase that binds to the enzyme active site. (''Tamiflu'' is [http://en.wikipedia.org/wiki/Hoffmann-La_Roche Roche]'s trade name; oseltamivir is the [http://en.wikipedia.org/wiki/International_Nonproprietary_Name generic] name.) Tamiflu is a [[Transition state analog|transition state analog]], and was the first orally active neuraminidase inhibitor commercially developed. Because neuraminidase is required for the viral life cycle, its enzymatic active site is highly conserved, and Tamflu is effective on a range of neuraminidase subtypes. It is indicated both for prophylaxis and for treatment within two days of the onset of symptoms.<br />
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[http://en.wikipedia.org/wiki/Zanamivir Relenza (zanamivir)] is also an inhibitor of influenze neuraminidase that binds to the enzyme active site. (''Relenza'' is [http://en.wikipedia.org/wiki/GlaxoSmithKline GlaxoSmithKline]'s trade name; zanamivir is the [http://en.wikipedia.org/wiki/International_Nonproprietary_Name generic] name.) Unlike Tamiflu, which is given orally, Relenza is usually administered by '''inhalation, or can be injected'''.<br />
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'''Structure-based drug design''' was employed in the development of both Tamiflu and Relenza<ref name='Russell2006'>The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design, Russell ''et al., Nature'' '''443''':45, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16915235 PubMed 16915235].</ref> . A structure of N2 at 2.9 &Aring; [[resolution]] was published in 1983<ref>Varghese, Laver & Colman, ''Nature'' '''303''':35, 1983. [http://www.ncbi.nlm.nih.gov/pubmed/6843658 PubMed 6843658]</ref>, and a 2.2 &Aring; structure, [[1nn2]], was deposited by the same authors in the [[PDB]] in 1991. The structure of N9 was determined by the same group, e.g. [[7nn9]].<br />
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====Resistance to Tamiflu and Relenza====<br />
<applet size='300' frame='true' align='right' scene='User:Eric_Martz/Sandbox_6/3ckz_relenza_tyr274/2' caption='Relenza binding to N1 mutant H274Y (3ckz).' /><br />
Because Tamiflu and Relenza closely resemble the natural sialic acid substrate of neuraminidase, it was hoped that mutations conferring resistance to these drugs would greatly lower the virulence of influenza carrying such mutations. This hope has proven false in the case of Tamiflu<ref name="collins2008">Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants, Collins ''et al., Nature'' '''453''':1248, 2008. [http://www.ncbi.nlm.nih.gov/pubmed/18480754 PubMed 18480754].</ref>. Furthermore, by early 2009, 98% of influenza A/H1N1 strains circulating in North America had become resistant to Tamiflu<ref>Layne, S. P., A. S Monto, and J. K. Taubenberger, Letter: Pandemic Influenza: An Inconvenient Mutation. ''Science'' 323:1560-1, March 2009.</ref><br />
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Two common mutations that confer resistance to Tamiflu did not confer resistance to Relenza<ref name="collins2008" />. At right is Relenza binding to the H274Y mutant of N1. This suggests that it would be prudent to stockpile Relenza in addition to Tamiflu, and that combination therapy might be the most effective weapon against a new pandemic, prior to development and deployment of a vaccine.<br />
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====Tamiflu Binds to N1 by Induced Fit====<br />
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<applet load='2hty2hu4_j.pdb' size='500' frame='true' align='right' caption='Morph of N1 alone (2hty) to N1 complexed with Tamiflu (2hu4). The position where Tamiflu will bind is shown translucent except when bound in the empirically-determined model.' scene='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/2' /><br />
Tamiflu was designed to fit N2/N9, so it is serendipitous that it works on N1. In fact, when the structure of N1 was determined<ref name='Russell2006' />, the <font color='#e07000'><b>loop comprising residues 147-152</b></font> was not in a suitable position to participate in binding Tamiflu. However, the complex of N1 with Tamiflu revealed that this loop is pulled into proper contact with the drug in an [[Induced fit|induced fit]] manner<ref name='Russell2006' />. A [[Morphs|morph]] from N1 alone ([[2hty]]) to N1 complexed with Tamiflu ([[2hu4]])<ref>Chain A from [[2hty]] was morphed to chain A of [[2hu4]] by linear interpolation, inserting 6 intermediate interpolated frames, using the freely available [http://www.umass.edu/microbio/rasmol/pdbtools.htm#martz morph2 program].</ref> shows the change in position of this loop (<scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/8'>replay initial morph</scene>).<br />
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The binding of Tamiflu to N1 pulls the sidechains of two conserved residues, <scene name='Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza/Morph_2hty_to_2hu4/7'>Asp151, Glu119</scene>, closer to the inhibitor.<br />
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===Cavity in N1: An Opportunity for Drug Design===<br />
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N1 has a larger surface-accessible cavity in the substrate binding region than is present in N2/N9. The larger end of this cavity is not occupied by Tamiflu. Thus, this cavity presents an opportunity to design a drug with greater specificity and potency for N1<ref name='Russell2006' />.<br />
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For technical reasons, the cavity cannot be shown yet in Jmol in Proteopedia. (We are working to resolve this problem.) However, it may be seen in View 2 of<br />
[http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_view2/chapter.htm this Chapter]<br />
of the [http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo Jmol Tutorial-Authoring Template (JTAT) Demonstration Tutorial].<br />
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==Links==<br />
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*[http://www.cdc.gov/flu cdc.gov/flu], the official influenza resource of the US Center for Disease Control.<br />
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*[http://www.PandemicToolKit.com/ Pandemic Planning Toolkit] (by Roche).<br />
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*[http://relenza.com Relenza] offical website by GlaxoSmithKline.<br />
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*[http://tamiflu.com Tamiflu] official website by Roche.<br />
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*[http://www.foreignaffairs.org/20050701faessay84401/laurie-garrett/the-next-pandemic.html The Next Pandemic?] An authoritative overview of economic and political factors written in 2005 by Laurie Garrett.<br />
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==Notes and Literature References==<br />
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<references/></div>David S. Goodsellhttps://proteopedia.org/index.php?title=File:Tmv_ring_carbox2.pdb&diff=804958File:Tmv ring carbox2.pdb2008-12-03T19:37:19Z<p>David S. Goodsell: uploaded a new version of "Image:Tmv ring carbox2.pdb": tmv ring CA with caspar carboxylate</p>
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<div>PDB file 2tmv lockwasher ring CA with all atom Caspar carboxylates--non CA atoms at the end, so that Jmol does the correct backbone</div>David S. Goodsellhttps://proteopedia.org/index.php?title=File:Tmv_ring_carbox2.pdb&diff=804955File:Tmv ring carbox2.pdb2008-12-03T19:02:41Z<p>David S. Goodsell: PDB file 2tmv lockwasher ring CA with all atom Caspar carboxylates--non CA atoms at the end, so that Jmol does the correct backbone</p>
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<div>PDB file 2tmv lockwasher ring CA with all atom Caspar carboxylates--non CA atoms at the end, so that Jmol does the correct backbone</div>David S. Goodsellhttps://proteopedia.org/index.php?title=File:Tmv_ring_carbox.pdb&diff=804954File:Tmv ring carbox.pdb2008-12-03T18:42:25Z<p>David S. Goodsell: PDB file 2tmv lockwasher ring CA with all atom Caspar carboxylates</p>
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<div>PDB file 2tmv lockwasher ring CA with all atom Caspar carboxylates</div>David S. Goodsellhttps://proteopedia.org/index.php?title=2oar&diff=7623942oar2008-09-23T17:36:28Z<p>David S. Goodsell: </p>
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===Mechanosensitive Channel of Large Conductance (MscL)===<br />
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==About this Structure==<br />
2OAR <ref>Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel., Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC, Science. 1998 Dec 18;282(5397):2220-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9856938 9856938]</ref> is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1msl 1msl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OAR OCA].<br />
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==Model of Channel Opening==<br />
Models the <scene name='Goodsell_Sandbox/1kyk/1'>closed, </scene><scene name='Goodsell_Sandbox/1kyl/1'>intermediate,</scene> and <scene name='Goodsell_Sandbox/1kym/1'>open</scene> forms of the channel have been generated based on data from electron paramagnetic resonance spectroscopy, using mutant forms of the protein with spin labels attached to engineered cysteine amino acids in the transmembrane segments<ref>Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Perozo, E, Cortes DM, Sompornpisut, P, Kloda, A, Martinac, B. Nature 2002, 418, 942-948. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198539 12198539]</ref>. <br />
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==Reference==<br />
<references/><br />
[[Category: Mycobacterium tuberculosis]]<br />
[[Category: Single protein]]<br />
[[Category: Chang, G.]]<br />
[[Category: Lee, A T.]]<br />
[[Category: Rees, D C.]]<br />
[[Category: Spencer, R H.]]<br />
[[Category: Steinbacher, S.]]<br />
[[Category: Strop, P.]]<br />
[[Category: Stretch activated ion channel mechanosensitive]]<br />
<br />
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:12:19 2008''</div>David S. Goodsellhttps://proteopedia.org/index.php?title=2oar&diff=7623932oar2008-09-23T17:35:46Z<p>David S. Goodsell: </p>
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[[Image:2oar.png|left|200px]]<br />
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===Mechanosensitive Channel of Large Conductance (MscL)===<br />
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{{ABSTRACT_PUBMED_9856938}}<br />
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==About this Structure==<br />
2OAR <ref>Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel., Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC, Science. 1998 Dec 18;282(5397):2220-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9856938 9856938]</ref> is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1msl 1msl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OAR OCA].<br />
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==Model of Channel Opening==<br />
Models the <scene name='Goodsell_Sandbox/1kyk/1'>closed, </scene><scene name='Goodsell_Sandbox/1kyl/1'>intermediate,</scene> and <scene name='Goodsell_Sandbox/1kym/1'>open</scene> forms of the channel have been generated based on data from electron paramagnetic resonance spectroscopy, using mutant forms of the protein with spin labels attached to engineered cysteine amino acids in the transmembrane segments<ref>Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Perozo, E, Cortes DM, Sompornpisut, P, Kloda, A, Martinac, B. Nature 2002, 418, 942-948. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198539 12198539]</ref>. <br />
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==Reference==<br />
Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel., Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC, Science. 1998 Dec 18;282(5397):2220-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9856938 9856938]<br />
<references/><br />
[[Category: Mycobacterium tuberculosis]]<br />
[[Category: Single protein]]<br />
[[Category: Chang, G.]]<br />
[[Category: Lee, A T.]]<br />
[[Category: Rees, D C.]]<br />
[[Category: Spencer, R H.]]<br />
[[Category: Steinbacher, S.]]<br />
[[Category: Strop, P.]]<br />
[[Category: Stretch activated ion channel mechanosensitive]]<br />
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:12:19 2008''</div>David S. Goodsellhttps://proteopedia.org/index.php?title=2oar&diff=7623922oar2008-09-23T17:33:17Z<p>David S. Goodsell: </p>
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<br />
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{{STRUCTURE_2oar| PDB=2oar | SCENE= }} <br />
<br />
===Mechanosensitive Channel of Large Conductance (MscL)===<br />
<br />
<br />
<!-- <br />
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--><br />
{{ABSTRACT_PUBMED_9856938}}<br />
<br />
==About this Structure==<br />
2OAR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1msl 1msl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OAR OCA].<br />
<br />
==Model of Channel Opening==<br />
Models the <scene name='Goodsell_Sandbox/1kyk/1'>closed, </scene><scene name='Goodsell_Sandbox/1kyl/1'>intermediate,</scene> and <scene name='Goodsell_Sandbox/1kym/1'>open</scene> forms of the channel have been generated based on data from electron paramagnetic resonance spectroscopy, using mutant forms of the protein with spin labels attached to engineered cysteine amino acids in the transmembrane segments<ref>Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Perozo, E, Cortes DM, Sompornpisut, P, Kloda, A, Martinac, B. Nature 2002, 418, 942-948. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198539 12198539]</ref>. <br />
<br />
==Reference==<br />
Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel., Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC, Science. 1998 Dec 18;282(5397):2220-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9856938 9856938]<br />
<br />
[[Category: Mycobacterium tuberculosis]]<br />
[[Category: Single protein]]<br />
[[Category: Chang, G.]]<br />
[[Category: Lee, A T.]]<br />
[[Category: Rees, D C.]]<br />
[[Category: Spencer, R H.]]<br />
[[Category: Steinbacher, S.]]<br />
[[Category: Strop, P.]]<br />
[[Category: Stretch activated ion channel mechanosensitive]]<br />
<br />
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:12:19 2008''</div>David S. Goodsellhttps://proteopedia.org/index.php?title=2oar&diff=7623912oar2008-09-23T17:32:08Z<p>David S. Goodsell: </p>
<hr />
<div>{{Seed}}<br />
[[Image:2oar.png|left|200px]]<br />
<br />
<!--<br />
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{{STRUCTURE_2oar| PDB=2oar | SCENE= }} <br />
<br />
===Mechanosensitive Channel of Large Conductance (MscL)===<br />
<br />
<br />
<!-- <br />
The line below this paragraph, {{ABSTRACT_PUBMED_9856938}}, adds the Publication Abstract to the page <br />
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--><br />
{{ABSTRACT_PUBMED_9856938}}<br />
<br />
==About this Structure==<br />
2OAR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1msl 1msl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OAR OCA].<br />
<br />
==Model of Channel Opening==<br />
Models the <scene name='Goodsell_Sandbox/1kyk/1'>closed, </scene><scene name='Goodsell_Sandbox/1kyl/1'>intermediate,</scene> and <scene name='Goodsell_Sandbox/1kym/1'>open</scene> forms of the channel have been generated based on data from electron paramagnetic resonance spectroscopy, using mutant forms of the protein with spin labels attached to engineered cysteine amino acids in the transmembrane segments<ref>Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Perozo, E, Cortes DM, Sompornpisut, P, Kloda, A, Martinac, B. Nature 2002, 418, 942-948. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198539 12198539]</ref>. <br />
<br />
==Reference==<br />
Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel., Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC, Science. 1998 Dec 18;282(5397):2220-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9856938 9856938]<br />
Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Perozo, E, Cortes DM, Sompornpisut, P, Kloda, A, Martinac, B. Nature 2002, 418, 942-948. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198539 12198539]<br />
[[Category: Mycobacterium tuberculosis]]<br />
[[Category: Single protein]]<br />
[[Category: Chang, G.]]<br />
[[Category: Lee, A T.]]<br />
[[Category: Rees, D C.]]<br />
[[Category: Spencer, R H.]]<br />
[[Category: Steinbacher, S.]]<br />
[[Category: Strop, P.]]<br />
[[Category: Stretch activated ion channel mechanosensitive]]<br />
<br />
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:12:19 2008''</div>David S. Goodsellhttps://proteopedia.org/index.php?title=2oar&diff=7623902oar2008-09-23T17:29:41Z<p>David S. Goodsell: </p>
<hr />
<div>{{Seed}}<br />
[[Image:2oar.png|left|200px]]<br />
<br />
<!--<br />
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{{STRUCTURE_2oar| PDB=2oar | SCENE= }} <br />
<br />
===Mechanosensitive Channel of Large Conductance (MscL)===<br />
<br />
<br />
<!-- <br />
The line below this paragraph, {{ABSTRACT_PUBMED_9856938}}, adds the Publication Abstract to the page <br />
(as it appears on PubMed at http://www.pubmed.gov), where 9856938 is the PubMed ID number.<br />
--><br />
{{ABSTRACT_PUBMED_9856938}}<br />
<br />
==About this Structure==<br />
2OAR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1msl 1msl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OAR OCA].<br />
<br />
==Model of Channel Opening==<br />
Models the <scene name='Goodsell_Sandbox/1kyk/1'>closed, </scene><scene name='Goodsell_Sandbox/1kyl/1'>intermediate,</scene> and <scene name='Goodsell_Sandbox/1kym/1'>open</scene>forms of the channel have been generated based on data from electron paramagnetic resonance spectroscopy, using mutant forms of the protein with spin labels attached to engineered cysteine amino acids in the transmembrane segments. <br />
<br />
==Reference==<br />
Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel., Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC, Science. 1998 Dec 18;282(5397):2220-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9856938 9856938]<br />
Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Perozo, E, Cortes DM, Sompornpisut, P, Kloda, A, Martinac, B. Nature 2002, 418, 942-948. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12198539 12198539]<br />
[[Category: Mycobacterium tuberculosis]]<br />
[[Category: Single protein]]<br />
[[Category: Chang, G.]]<br />
[[Category: Lee, A T.]]<br />
[[Category: Rees, D C.]]<br />
[[Category: Spencer, R H.]]<br />
[[Category: Steinbacher, S.]]<br />
[[Category: Strop, P.]]<br />
[[Category: Stretch activated ion channel mechanosensitive]]<br />
<br />
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 12:12:19 2008''</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Poly(A)_Polymerase&diff=760109Poly(A) Polymerase2008-09-12T16:37:22Z<p>David S. Goodsell: </p>
<hr />
<div>{{Seed}}<br />
[[Image:2q66.png|left|200px]]<br />
<br />
<!--<br />
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{{STRUCTURE_2q66| PDB=2q66 | SCENE= }} <br />
<br />
===Structure of Yeast Poly(A) Polymerase with ATP and oligo(A)===<br />
<br />
<br />
<!-- <br />
The line below this paragraph, {{ABSTRACT_PUBMED_17850751}}, adds the Publication Abstract to the page <br />
(as it appears on PubMed at http://www.pubmed.gov), where 17850751 is the PubMed ID number.<br />
--><br />
{{ABSTRACT_PUBMED_17850751}}<br />
<br />
==About this Structure==<br />
2Q66 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q66 OCA].<br />
<br />
==Determinants of ATP Recognition==<br />
Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The enzyme is an inactive mutant with the catalytic aspartate 154 changed to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for ATP. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead of forming specific hydrogen bonds with the enzyme, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>buried water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_c2/3'>adenine C2 (in white) and the sidechains of THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position that would be too bulky to fit against these amino acids.<br />
<br />
==Reference==<br />
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis., Balbo PB, Bohm A, Structure. 2007 Sep;15(9):1117-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17850751 17850751]<br />
[[Category: Polynucleotide adenylyltransferase]]<br />
[[Category: Saccharomyces cerevisiae]]<br />
[[Category: Single protein]]<br />
[[Category: Balbo, P.]]<br />
[[Category: Bohm, A.]]<br />
[[Category: Protein rna complex atp polymerase complex]]<br />
[[Category: Transferase/rna complex]]<br />
<br />
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:16:40 2008''</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=760108Goodsell Sandbox2008-09-12T16:33:14Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_2q66 | PDB=2q66 | SCENE=Goodsell_Sandbox/2q66_summary/1 }}<br />
<br />
ATP Recognition<br />
<br />
Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains an oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The enzyme is an inactive mutant with the catalytic aspartate 154 changed to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for ATP. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead of forming specific hydrogen bonds with the enzyme, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>buried water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_c2/3'>adenine C2 (in white) and the sidechains of THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position that would be too bulky to fit against these amino acids.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=760107Goodsell Sandbox2008-09-11T22:31:42Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_2q66 | PDB=2q66 | SCENE=Goodsell_Sandbox/2q66_summary/1 }}<br />
<br />
ATP Recognition<br />
<br />
Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_c2/2'>adenine C2 and THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position, and would be too bulky to fit against these amino acids.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=760106Goodsell Sandbox2008-09-11T22:30:00Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_2q66 | PDB=2q66 | SCENE=Goodsell_Sandbox/PAP_summary/1 }}<br />
<br />
ATP Recognition<br />
<br />
Poly(A) polymerase binds specifically to ATP and adds it the end of a messenger RNA chain. This structure contains a oligo(A) polynucleotide with five nucleotides, an ATP molecule, and a magnesium ion. The protein is a mutant that changes the catalytic aspartate 154 to alanine. In the <scene name='Goodsell_Sandbox/2q66_summary/1'>summary picture</scene>, the enzyme is in blue backbone representation, the RNA chain is in yellow, the ATP is in red, the magnesium is in green, and ALA154 is in magenta. Several mechanisms are used to achieve the specificity for adenosine nucleotides. The magnesium is coordinated by <scene name='Goodsell_Sandbox/2q66_asp/3'>ASP100 and ASP102</scene>, and the magnesium coordinates with the phosphates of ATP, positioning the nucleotide in the active site. The adenine base is sandwiched between the <scene name='Goodsell_Sandbox/2q66_stacking/2'>terminal base of the RNA (in yellow) and VAL234 (in cyan)</scene>. Surprisingly, there are very few contacts with the hydrogen-bonding groups in the adenine base. <scene name='Goodsell_Sandbox/2q66_asn/1'>ASN 236</scene> may form a hydrogen bond to adenine in the active enzyme, but the distance it a bit too long in this mutant structure. Instead, most of the hydrogen-bonding groups in the base, sugar and phosphate interact with a shell of <scene name='Goodsell_Sandbox/2q66_water/2'>water molecules</scene>. Discrimination between ATP and GTP is achieved through a close steric contact between the <scene name='Goodsell_Sandbox/2q66_C2/2'>adenine C2 and THR 304 and MET310 (shown in cyan)</scene>. Guanine bases have an extra amino group at this position, and would be too bulky to fit against these amino acids.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=User:David_S._Goodsell&diff=760105User:David S. Goodsell2008-09-11T16:45:06Z<p>David S. Goodsell: </p>
<hr />
<div>[[Image:goodsell.jpg|left]]<br />
David S. Goodsell<br />
<br />
Author of [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month.]<br />
<br />
Homepage: [http://mgl.scripps.edu/people/goodsell/ David S. Goodsell's Homepage]<br />
<br />
{{Clear}}</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=754891Goodsell Sandbox2008-08-19T17:26:52Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1rta | PDB=1rta | SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1 }}<br />
<br />
Ribonuclease A Active Site<br />
<br />
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon on the DNA is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves RNA strands best next to cytidine and uridine nucleotides--the reason for this may be seen in a <scene name='Goodsell_Sandbox/Ribonuclease_recognition/1'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=754890Goodsell Sandbox2008-08-19T17:25:38Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1rta | PDB=1rta | SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1 }}<br />
<br />
Ribonuclease A Active Site<br />
<br />
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon on the DNA is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves cytidine and uridine best--the reason for this may be seen in a <scene name='Goodsell_Sandbox/Ribonuclease_recognition/1'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=754889Goodsell Sandbox2008-08-19T17:24:15Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1rta | PDB=1rta | SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1 }}<br />
<br />
Ribonuclease A Active Site<br />
<br />
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves cytidine and uridine best--the reason for this may be seen in a <scene name='Goodsell_Sandbox/Ribonuclease_recognition/1'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=754888Goodsell Sandbox2008-08-19T17:22:30Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1rta | PDB=1rta | SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1 }}<br />
<br />
Ribonuclease A Active Site<br />
<br />
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A bound to short DNA strand composed of four thymidines. Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves cytidine and uridine best--the reason for this may be seen in a <scene name='Goodsell_Sandbox/Ribonuclease_recognition/1'>spacefilling representation</scene>. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.</div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=754887Goodsell Sandbox2008-08-19T17:18:23Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1rta | PDB=1rta | SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1 }}<br />
<br />
Ribonuclease A Active Site<br />
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A bound to short DNA strand composed of four thymidines. Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. <scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>Three amino acids</scene> are shown that are important for catalysis. The 3' carbon is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves cytidine and uridine best--the reason for this may be seen in a spacefilling representation. Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.<br />
<br />
<br />
<scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=754880Goodsell Sandbox2008-08-19T17:00:53Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1rta | PDB=1rta | SCENE=Goodsell_Sandbox/Ribonuclease_catalytic_site/1 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/3'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>arginine 606.</scene><br />
<scene name='Goodsell_Sandbox/Ribonuclease_catalytic_site/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=SelB&diff=641334SelB2008-07-22T15:32:34Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }}<br />
<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Sandbox_14/1wsu-recognition1/4'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Sandbox_14/1wsu-recognition2/2'>three amino acids</scene> in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Sandbox_14/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Sandbox_14/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Sandbox_14/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=SelB&diff=641333SelB2008-07-22T15:29:46Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }}<br />
<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Sandbox_14/1wsu-recognition1/4'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Sandbox_14/1wsu-recognition2/2'>three amino acids</scene> in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Sandbox_14/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Sandbox_14/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Sandbox_14/1wsu-recognition5/1'>arginine 606.</scene><br />
<br />
<I>(technical note: if you don't see the hydrogen bonds in the first and fifth links, refresh the page. A problem with jmol causes the hydrogen bonds to be displayed only the first time you click on the link)</I></div>David S. Goodsellhttps://proteopedia.org/index.php?title=SelB&diff=641332SelB2008-07-22T15:25:44Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }}<br />
<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Sandbox_14/1wsu-recognition1/4'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Sandbox_14/1wsu-recognition2/2'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Sandbox_14/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Sandbox_14/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Sandbox_14/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=SelB&diff=641331SelB2008-07-22T15:25:14Z<p>David S. Goodsell: New page: {{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }} Molecular Recognition in SelB Elongation factor SelB uses several methods to recognize the selenocysteine i...</p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Sandbox_14/1wsu-recognition1/4'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Sandbox_14/1wsu-recognition2/2'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Sandbox_14/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Sandbox_14/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Sandbox_14/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Sandbox_14&diff=641275Sandbox 142008-07-16T15:48:06Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition0/1 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Sandbox_14/1wsu-recognition1/4'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Sandbox_14/1wsu-recognition2/2'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Sandbox_14/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Sandbox_14/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Sandbox_14/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640437Goodsell Sandbox2008-07-15T18:18:31Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition1/3 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/3'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640436Goodsell Sandbox2008-07-15T18:13:17Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition1/2 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/2'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640435Goodsell Sandbox2008-07-15T18:13:03Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition1/1 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/2'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640434Goodsell Sandbox2008-07-15T18:06:37Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition1/1 }}<br />
<br />
Molecular Recognition in SelB<br />
Elongation factor SelB uses several methods to recognize the selenocysteine insertion sequence found in messenger RNA. The insertion sequence forms a hairpin loop with an unstacked guanine base in the loop. This guanine forms <br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/1'>specific hydrogen bonds with the protein and with two bridging water molecules (shown in cyan in the jmol).</scene><br />
The planar base is also sandwiched between<br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>three amino acids</scene>in the protein, which form a tight hydrophobic pocket. This is best seen using a<br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>spacefilling diagram.</scene><br />
The overall shape of the hairpin is recognized by contacts with several<br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>arginine and lysine amino acids.</scene><br />
In particular, notice the intimate contact formed by both the charged nitrogen and hydrophobic carbon chain of<br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>arginine 606.</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640433Goodsell Sandbox2008-07-15T17:58:38Z<p>David S. Goodsell: </p>
<hr />
<div>{{STRUCTURE_1wsu | PDB=1wsu | SCENE=Goodsell_Sandbox/1wsu-recognition1/1 }}<br />
<br />
<br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640432Goodsell Sandbox2008-07-15T17:54:40Z<p>David S. Goodsell: </p>
<hr />
<div><br />
{{STRUCTURE_1wsu | PDB=1wsu | SCENE=1wsu-recognition1/1 }}<br />
<br />
<br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition3/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition4/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640431Goodsell Sandbox2008-07-15T17:52:03Z<p>David S. Goodsell: </p>
<hr />
<div>==This is a placeholder==<br />
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<br />
<scene name='Goodsell_Sandbox/1wsu-recognition1/1'>TextToBeDisplayed</scene><br />
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<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640430Goodsell Sandbox2008-07-15T17:51:49Z<p>David S. Goodsell: </p>
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<div>==This is a placeholder==<br />
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<scene name='Goodsell_Sandbox/1wsu-recognition2/1'>TextToBeDisplayed</scene<br />
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<scene name='Goodsell_Sandbox/1wsu-recognition5/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640386Goodsell Sandbox2008-07-14T18:41:32Z<p>David S. Goodsell: </p>
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<div>==This is a placeholder==<br />
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<scene name='Goodsell_Sandbox/1wsu-test/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu_test2/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640385Goodsell Sandbox2008-07-14T18:39:57Z<p>David S. Goodsell: </p>
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<div>==This is a placeholder==<br />
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{{STRUCTURE_3cin | PDB=3cin | SCENE= }}<br />
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<scene name='Goodsell_Sandbox/1wsu-test/1'>TextToBeDisplayed</scene><br />
<scene name='Goodsell_Sandbox/1wsu_test2/1'>TextToBeDisplayed</scene></div>David S. Goodsellhttps://proteopedia.org/index.php?title=Goodsell_Sandbox&diff=640384Goodsell Sandbox2008-07-14T18:36:39Z<p>David S. Goodsell: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...</p>
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{{STRUCTURE_3cin | PDB=3cin | SCENE= }}<br />
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<scene name='Goodsell_Sandbox/1wsu-test/1'>TextToBeDisplayed</scene></div>David S. Goodsell