Links to Exploration step
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information</title><author><name sortKey="Cheng, Ryan R" sort="Cheng, Ryan R" uniqKey="Cheng R" first="Ryan R." last="Cheng">Ryan R. Cheng</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation></author><author><name sortKey="Morcos, Faruck" sort="Morcos, Faruck" uniqKey="Morcos F" first="Faruck" last="Morcos">Faruck Morcos</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation></author><author><name sortKey="Levine, Herbert" sort="Levine, Herbert" uniqKey="Levine H" first="Herbert" last="Levine">Herbert Levine</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Onuchic, Jose N" sort="Onuchic, Jose N" uniqKey="Onuchic J" first="José N." last="Onuchic">José N. Onuchic</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Physics and Astronomy,<institution>Rice University</institution>, Houston,<addr-line>TX</addr-line> 77005</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24449878</idno><idno type="pmc">3918776</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918776</idno><idno type="RBID">PMC:3918776</idno><idno type="doi">10.1073/pnas.1323734111</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000407</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information</title><author><name sortKey="Cheng, Ryan R" sort="Cheng, Ryan R" uniqKey="Cheng R" first="Ryan R." last="Cheng">Ryan R. Cheng</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation></author><author><name sortKey="Morcos, Faruck" sort="Morcos, Faruck" uniqKey="Morcos F" first="Faruck" last="Morcos">Faruck Morcos</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation></author><author><name sortKey="Levine, Herbert" sort="Levine, Herbert" uniqKey="Levine H" first="Herbert" last="Levine">Herbert Levine</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Onuchic, Jose N" sort="Onuchic, Jose N" uniqKey="Onuchic J" first="José N." last="Onuchic">José N. Onuchic</name><affiliation><nlm:aff wicri:cut=", and" id="aff1">Center for Theoretical Biological Physics</nlm:aff></affiliation><affiliation><nlm:aff id="aff3">Physics and Astronomy,<institution>Rice University</institution>, Houston,<addr-line>TX</addr-line> 77005</nlm:aff></affiliation></author></analytic><series><title level="j">Proceedings of the National Academy of Sciences of the United States of America</title><idno type="ISSN">0027-8424</idno><idno type="eISSN">1091-6490</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Significance</title><p>Our study uses amino acid coevolutionary information to better understand how bacterial two-component signaling (TCS) proteins preferentially interact with their correct partners while avoiding interactions with nonpartners. We extract coevolutionary couplings from sequences of TCS partners and study how coevolution is necessary to maintain their ability to transfer signals with high specificity. We use these coevolving couplings to devise a metric, which can predict the effects of mutations in the quality of signal transmission observed in vitro and provide support to the hypothesis that hybrid TCS proteins have reduced specificity. Our metric can potentially be used to redesign a TCS protein to preferentially interact with a nonpartner. Furthermore, our study can potentially be extended to networks of interacting proteins.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Proc Natl Acad Sci U S A</journal-id><journal-id journal-id-type="iso-abbrev">Proc. Natl. Acad. Sci. U.S.A</journal-id><journal-id journal-id-type="hwp">pnas</journal-id><journal-id journal-id-type="pmc">pnas</journal-id><journal-id journal-id-type="publisher-id">PNAS</journal-id><journal-title-group><journal-title>Proceedings of the National Academy of Sciences of the United States of America</journal-title></journal-title-group><issn pub-type="ppub">0027-8424</issn><issn pub-type="epub">1091-6490</issn><publisher><publisher-name>National Academy of Sciences</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24449878</article-id><article-id pub-id-type="pmc">3918776</article-id><article-id pub-id-type="publisher-id">201323734</article-id><article-id pub-id-type="doi">10.1073/pnas.1323734111</article-id><article-categories><subj-group subj-group-type="heading"><subject>PNAS Plus</subject></subj-group><subj-group subj-group-type="heading"><subject>Biological Sciences</subject><subj-group><subject>Biophysics and Computational Biology</subject></subj-group></subj-group><series-title>PNAS Plus</series-title></article-categories><title-group><article-title>Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information</article-title><alt-title alt-title-type="short">Exploring the sequence coevolution of TCS proteins</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Cheng</surname><given-names>Ryan R.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Morcos</surname><given-names>Faruck</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Levine</surname><given-names>Herbert</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Onuchic</surname><given-names>José N.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><sup>a</sup>Center for Theoretical Biological Physics, and</aff><aff id="aff2">Departments of<sup>b</sup>Bioengineering and</aff><aff id="aff3"><sup>c</sup>Physics and Astronomy,<institution>Rice University</institution>, Houston,<addr-line>TX</addr-line> 77005</aff></contrib-group><author-notes><corresp id="cor1"><sup>1</sup>To whom correspondence should be addressed. E-mail: <email>jonuchic@rice.edu</email>.</corresp><fn fn-type="edited-by"><p>Contributed by José N. Onuchic, December 20, 2013 (sent for review November 6, 2013)</p></fn><fn fn-type="con"><p>Author contributions: R.R.C., F.M., H.L., and J.N.O. designed research; R.R.C. and F.M. performed research; R.R.C. and F.M. contributed new reagents/analytic tools; R.R.C., F.M., H.L., and J.N.O. analyzed data; and R.R.C., F.M., H.L., and J.N.O. wrote the paper.</p></fn></author-notes><pub-date pub-type="ppub"><day>4</day><month>2</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>21</day><month>1</month><year>2014</year></pub-date><volume>111</volume><issue>5</issue><fpage>E563</fpage><lpage>E571</lpage><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="pnas.201323734.pdf"></self-uri><abstract abstract-type="executive-summary"><title>Significance</title><p>Our study uses amino acid coevolutionary information to better understand how bacterial two-component signaling (TCS) proteins preferentially interact with their correct partners while avoiding interactions with nonpartners. We extract coevolutionary couplings from sequences of TCS partners and study how coevolution is necessary to maintain their ability to transfer signals with high specificity. We use these coevolving couplings to devise a metric, which can predict the effects of mutations in the quality of signal transmission observed in vitro and provide support to the hypothesis that hybrid TCS proteins have reduced specificity. Our metric can potentially be used to redesign a TCS protein to preferentially interact with a nonpartner. Furthermore, our study can potentially be extended to networks of interacting proteins.</p></abstract><abstract><p>A challenge in molecular biology is to distinguish the key subset of residues that allow two-component signaling (TCS) proteins to recognize their correct signaling partner such that they can transiently bind and transfer signal, i.e., phosphoryl group. Detailed knowledge of this information would allow one to search sequence space for mutations that can be used to systematically tune the signal transmission between TCS partners as well as potentially encode a TCS protein to preferentially transfer signals to a nonpartner. Motivated by the notion that this detailed information is found in sequence data, we explore the sequence coevolution between signaling partners to better understand how mutations can positively or negatively alter their ability to transfer signal. Using direct coupling analysis for determining evolutionarily conserved protein–protein interactions, we apply a metric called the direct information score to quantify mutational changes in the interaction between TCS proteins and demonstrate that it accurately correlates with experimental mutagenesis studies probing the mutational change in measured in vitro phosphotransfer. Furthermore, by subtracting from our metric an appropriate null model corresponding to generic, conserved features in TCS signaling pairs, we can isolate the determinants that give rise to interaction specificity and recognition, which are variable among different TCS partners. Our methodology forms a potential framework for the rational design of TCS systems by allowing one to quickly search sequence space for mutations or even entirely new sequences that can increase or decrease our metric, as a proxy for increasing or decreasing phosphotransfer ability between TCS proteins.</p></abstract><kwd-group><kwd>statistical inference</kwd><kwd>signal transduction</kwd><kwd>information theory</kwd><kwd>covariation</kwd><kwd>protein recognition</kwd></kwd-group><counts><page-count count="9"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000407 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000407 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Pmc
|étape= Corpus
|type= RBID
|clé=
|texte=
}}
| This area was generated with Dilib version V0.6.25. |  |