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THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES

Identifieur interne : 000E02 ( Main/Exploration ); précédent : 000E01; suivant : 000E03

THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES

Auteurs : Fabio Sterpone [France] ; Simone Melchionna [Italie] ; Pierre Tuffery [France] ; Samuela Pasquali [France] ; Normand Mousseau [Canada] ; Tristan Cragnolini [France] ; Yassmine Chebaro [France] ; Jean-Francois Saint-Pierre [Canada] ; Maria Kalimeri [France] ; Alessandro Barducci [Suisse] ; Yohan Laurin [France] ; Alex Tek [France] ; Marc Baaden [France] ; Phuong Hoang Nguyen [France] ; Philippe Derreumaux [France]

Source :

RBID : PMC:4426487

Abstract

The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the on-going developments.


Url:
DOI: 10.1039/c4cs00048j
PubMed: 24759934
PubMed Central: 4426487


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<title xml:lang="en" level="a" type="main">THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES</title>
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<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name>
<affiliation wicri:level="3">
<nlm:aff id="A1">Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Nguyen, Phuong Hoang" sort="Nguyen, Phuong Hoang" uniqKey="Nguyen P" first="Phuong Hoang" last="Nguyen">Phuong Hoang Nguyen</name>
<affiliation wicri:level="3">
<nlm:aff id="A1">Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author>
<name sortKey="Derreumaux, Philippe" sort="Derreumaux, Philippe" uniqKey="Derreumaux P" first="Philippe" last="Derreumaux">Philippe Derreumaux</name>
<affiliation wicri:level="3">
<nlm:aff id="A1">Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
<affiliation wicri:level="3">
<nlm:aff id="A6">Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005, Paris, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005, Paris</wicri:regionArea>
<placeName>
<region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series>
<title level="j">Chemical Society reviews</title>
<idno type="ISSN">0306-0012</idno>
<idno type="eISSN">1460-4744</idno>
<imprint>
<date when="2014">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass></textClass>
</profileDesc>
</teiHeader>
<front>
<div type="abstract" xml:lang="en">
<p id="P4">The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows studying single protein properties, DNA/RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the on-going developments.</p>
</div>
</front>
</TEI>
<affiliations>
<list>
<country>
<li>Canada</li>
<li>France</li>
<li>Italie</li>
<li>Suisse</li>
</country>
<region>
<li>Latium</li>
<li>Île-de-France</li>
</region>
<settlement>
<li>Paris</li>
<li>Rome</li>
</settlement>
</list>
<tree>
<country name="France">
<region name="Île-de-France">
<name sortKey="Sterpone, Fabio" sort="Sterpone, Fabio" uniqKey="Sterpone F" first="Fabio" last="Sterpone">Fabio Sterpone</name>
</region>
<name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name>
<name sortKey="Chebaro, Yassmine" sort="Chebaro, Yassmine" uniqKey="Chebaro Y" first="Yassmine" last="Chebaro">Yassmine Chebaro</name>
<name sortKey="Cragnolini, Tristan" sort="Cragnolini, Tristan" uniqKey="Cragnolini T" first="Tristan" last="Cragnolini">Tristan Cragnolini</name>
<name sortKey="Derreumaux, Philippe" sort="Derreumaux, Philippe" uniqKey="Derreumaux P" first="Philippe" last="Derreumaux">Philippe Derreumaux</name>
<name sortKey="Derreumaux, Philippe" sort="Derreumaux, Philippe" uniqKey="Derreumaux P" first="Philippe" last="Derreumaux">Philippe Derreumaux</name>
<name sortKey="Kalimeri, Maria" sort="Kalimeri, Maria" uniqKey="Kalimeri M" first="Maria" last="Kalimeri">Maria Kalimeri</name>
<name sortKey="Laurin, Yohan" sort="Laurin, Yohan" uniqKey="Laurin Y" first="Yohan" last="Laurin">Yohan Laurin</name>
<name sortKey="Nguyen, Phuong Hoang" sort="Nguyen, Phuong Hoang" uniqKey="Nguyen P" first="Phuong Hoang" last="Nguyen">Phuong Hoang Nguyen</name>
<name sortKey="Pasquali, Samuela" sort="Pasquali, Samuela" uniqKey="Pasquali S" first="Samuela" last="Pasquali">Samuela Pasquali</name>
<name sortKey="Tek, Alex" sort="Tek, Alex" uniqKey="Tek A" first="Alex" last="Tek">Alex Tek</name>
<name sortKey="Tuffery, Pierre" sort="Tuffery, Pierre" uniqKey="Tuffery P" first="Pierre" last="Tuffery">Pierre Tuffery</name>
</country>
<country name="Italie">
<region name="Latium">
<name sortKey="Melchionna, Simone" sort="Melchionna, Simone" uniqKey="Melchionna S" first="Simone" last="Melchionna">Simone Melchionna</name>
</region>
</country>
<country name="Canada">
<noRegion>
<name sortKey="Mousseau, Normand" sort="Mousseau, Normand" uniqKey="Mousseau N" first="Normand" last="Mousseau">Normand Mousseau</name>
</noRegion>
<name sortKey="Saint Pierre, Jean Francois" sort="Saint Pierre, Jean Francois" uniqKey="Saint Pierre J" first="Jean-Francois" last="Saint-Pierre">Jean-Francois Saint-Pierre</name>
</country>
<country name="Suisse">
<noRegion>
<name sortKey="Barducci, Alessandro" sort="Barducci, Alessandro" uniqKey="Barducci A" first="Alessandro" last="Barducci">Alessandro Barducci</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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   |texte=   THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES
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