Protein flexibility in the light of structural alphabets
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performe...
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
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Format: | Article |
Language: | English |
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Frontiers Media S.A.
2015-05-01
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Series: | Frontiers in Molecular Biosciences |
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Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmolb.2015.00020/full |
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language |
English |
format |
Article |
sources |
DOAJ |
author |
Pierrick eCraveur Pierrick eCraveur Pierrick eCraveur Pierrick eCraveur Agnel Praveen eJoseph Jeremy eEsque Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Floriane eNoel Floriane eNoel Floriane eNoel Floriane eNoel Nicolas eShinada Nicolas eShinada Nicolas eShinada Nicolas eShinada Matthieu eGoguet Matthieu eGoguet Matthieu eGoguet Matthieu eGoguet Léonard eSylvain Léonard eSylvain Léonard eSylvain Léonard eSylvain Pierre ePoulain Pierre ePoulain Pierre ePoulain Pierre ePoulain Pierre ePoulain Olivier eBertrand Olivier eBertrand Olivier eBertrand Olivier eBertrand Guilhem eFaure Joseph eRebehmed Amine eGhozlane Lakshmipuram S Swapna Lakshmipuram S Swapna Ramachandra M Bhaskara Ramachandra M Bhaskara Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Vincent eJallu Jiri eCerny Bohdan eSchneider Catherine eEtchebest Catherine eEtchebest Catherine eEtchebest Catherine eEtchebest Narayanaswamy eSrinivasan Jean-Christophe eGelly Jean-Christophe eGelly Jean-Christophe eGelly Jean-Christophe eGelly Alexandre G. de Brevern Alexandre G. de Brevern Alexandre G. de Brevern Alexandre G. de Brevern |
spellingShingle |
Pierrick eCraveur Pierrick eCraveur Pierrick eCraveur Pierrick eCraveur Agnel Praveen eJoseph Jeremy eEsque Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Floriane eNoel Floriane eNoel Floriane eNoel Floriane eNoel Nicolas eShinada Nicolas eShinada Nicolas eShinada Nicolas eShinada Matthieu eGoguet Matthieu eGoguet Matthieu eGoguet Matthieu eGoguet Léonard eSylvain Léonard eSylvain Léonard eSylvain Léonard eSylvain Pierre ePoulain Pierre ePoulain Pierre ePoulain Pierre ePoulain Pierre ePoulain Olivier eBertrand Olivier eBertrand Olivier eBertrand Olivier eBertrand Guilhem eFaure Joseph eRebehmed Amine eGhozlane Lakshmipuram S Swapna Lakshmipuram S Swapna Ramachandra M Bhaskara Ramachandra M Bhaskara Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Vincent eJallu Jiri eCerny Bohdan eSchneider Catherine eEtchebest Catherine eEtchebest Catherine eEtchebest Catherine eEtchebest Narayanaswamy eSrinivasan Jean-Christophe eGelly Jean-Christophe eGelly Jean-Christophe eGelly Jean-Christophe eGelly Alexandre G. de Brevern Alexandre G. de Brevern Alexandre G. de Brevern Alexandre G. de Brevern Protein flexibility in the light of structural alphabets Frontiers in Molecular Biosciences Amino Acids Protein Folding disorder Flexibility allostery Protein complexes |
author_facet |
Pierrick eCraveur Pierrick eCraveur Pierrick eCraveur Pierrick eCraveur Agnel Praveen eJoseph Jeremy eEsque Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Tarun JaiRaj eNarwani Floriane eNoel Floriane eNoel Floriane eNoel Floriane eNoel Nicolas eShinada Nicolas eShinada Nicolas eShinada Nicolas eShinada Matthieu eGoguet Matthieu eGoguet Matthieu eGoguet Matthieu eGoguet Léonard eSylvain Léonard eSylvain Léonard eSylvain Léonard eSylvain Pierre ePoulain Pierre ePoulain Pierre ePoulain Pierre ePoulain Pierre ePoulain Olivier eBertrand Olivier eBertrand Olivier eBertrand Olivier eBertrand Guilhem eFaure Joseph eRebehmed Amine eGhozlane Lakshmipuram S Swapna Lakshmipuram S Swapna Ramachandra M Bhaskara Ramachandra M Bhaskara Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Jonathan eBarnoud Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Stéphane eTéletchéa Vincent eJallu Jiri eCerny Bohdan eSchneider Catherine eEtchebest Catherine eEtchebest Catherine eEtchebest Catherine eEtchebest Narayanaswamy eSrinivasan Jean-Christophe eGelly Jean-Christophe eGelly Jean-Christophe eGelly Jean-Christophe eGelly Alexandre G. de Brevern Alexandre G. de Brevern Alexandre G. de Brevern Alexandre G. de Brevern |
author_sort |
Pierrick eCraveur |
title |
Protein flexibility in the light of structural alphabets |
title_short |
Protein flexibility in the light of structural alphabets |
title_full |
Protein flexibility in the light of structural alphabets |
title_fullStr |
Protein flexibility in the light of structural alphabets |
title_full_unstemmed |
Protein flexibility in the light of structural alphabets |
title_sort |
protein flexibility in the light of structural alphabets |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Molecular Biosciences |
issn |
2296-889X |
publishDate |
2015-05-01 |
description |
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e. the classical secondary structures. . More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures.Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g. B-factor) and computational methodology (e.g. Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g. to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. |
topic |
Amino Acids Protein Folding disorder Flexibility allostery Protein complexes |
url |
http://journal.frontiersin.org/Journal/10.3389/fmolb.2015.00020/full |
work_keys_str_mv |
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doaj-332e3c89c5ef442a917153f5c97b87202020-11-24T23:55:36ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2015-05-01210.3389/fmolb.2015.00020140502Protein flexibility in the light of structural alphabetsPierrick eCraveur0Pierrick eCraveur1Pierrick eCraveur2Pierrick eCraveur3Agnel Praveen eJoseph4Jeremy eEsque5Tarun JaiRaj eNarwani6Tarun JaiRaj eNarwani7Tarun JaiRaj eNarwani8Tarun JaiRaj eNarwani9Floriane eNoel10Floriane eNoel11Floriane eNoel12Floriane eNoel13Nicolas eShinada14Nicolas eShinada15Nicolas eShinada16Nicolas eShinada17Matthieu eGoguet18Matthieu eGoguet19Matthieu eGoguet20Matthieu eGoguet21Léonard eSylvain22Léonard eSylvain23Léonard eSylvain24Léonard eSylvain25Pierre ePoulain26Pierre ePoulain27Pierre ePoulain28Pierre ePoulain29Pierre ePoulain30Olivier eBertrand31Olivier eBertrand32Olivier eBertrand33Olivier eBertrand34Guilhem eFaure35Joseph eRebehmed36Amine eGhozlane37Lakshmipuram S Swapna38Lakshmipuram S Swapna39Ramachandra M Bhaskara40Ramachandra M Bhaskara41Jonathan eBarnoud42Jonathan eBarnoud43Jonathan eBarnoud44Jonathan eBarnoud45Jonathan eBarnoud46Stéphane eTéletchéa47Stéphane eTéletchéa48Stéphane eTéletchéa49Stéphane eTéletchéa50Stéphane eTéletchéa51Vincent eJallu52Jiri eCerny53Bohdan eSchneider54Catherine eEtchebest55Catherine eEtchebest56Catherine eEtchebest57Catherine eEtchebest58Narayanaswamy eSrinivasan59Jean-Christophe eGelly60Jean-Christophe eGelly61Jean-Christophe eGelly62Jean-Christophe eGelly63Alexandre G. de Brevern64Alexandre G. de Brevern65Alexandre G. de Brevern66Alexandre G. de Brevern67INSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExRutherford Appleton LaboratoryIGBMC,INSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExEts PoulainINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExNCBI, NLM, NIHSorbonne Universités, Université Pierre et Marie Curie-Paris6 – MNHN – IRD – IUC, Paris, FranceMetagenopolisIndian Institute of ScienceUniversity of TorontoIndian Institute of ScienceMax Planck Institute of BiophysicsINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExUniversite de Lyon, Ecole Normale, Laboratoire de Physique²INSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExFaculté des Sciences et Techniques, Univ NantesINTSInstitute of Biotechnology AS CRInstitute of Biotechnology AS CRINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExIndian Institute of ScienceINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExINSERMUniv Paris Diderot, Sorbonne Paris CiteINTSLaboratory of Excellence, GR-ExProtein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e. the classical secondary structures. . More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures.Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g. B-factor) and computational methodology (e.g. Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g. to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.http://journal.frontiersin.org/Journal/10.3389/fmolb.2015.00020/fullAmino AcidsProtein FoldingdisorderFlexibilityallosteryProtein complexes |