Detail
Článek
Článek online
FT
Medvik - BMČ
  • Je něco špatně v tomto záznamu ?

Protein flexibility in the light of structural alphabets

P. Craveur, AP. Joseph, J. Esque, TJ. Narwani, F. Noël, N. Shinada, M. Goguet, S. Leonard, P. Poulain, O. Bertrand, G. Faure, J. Rebehmed, A. Ghozlane, LS. Swapna, RM. Bhaskara, J. Barnoud, S. Téletchéa, V. Jallu, J. Cerny, B. Schneider, C....

. 2015 ; 2 (-) : 20.

Jazyk angličtina Země Švýcarsko

Typ dokumentu časopisecké články, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/bmc15023680

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.

Centre National de la Recherche Scientifique UMR7590 Sorbonne Universités Université Pierre et Marie Curie MNHN IRD IUC Paris France

Department of Theoretical Biophysics Max Planck Institute of Biophysics Frankfurt Germany

Ets Poulain Pointe Noire Congo

Faculté des Sciences et Techniques Université de Nantes Unité Fonctionnalité et Ingénierie des Protéines Centre National de la Recherche Scientifique UMR 6286 Université Nantes Nantes France

Hospital for Sick Children and Departments of Biochemistry and Molecular Genetics University of Toronto Toronto ON Canada

Institut National de la Santé et de la Recherche Médicale U 1134 Paris France

Institut National de la Santé et de la Recherche Médicale U964 7 UMR Centre National de la Recherche Scientifique 7104 IGBMC Université de Strasbourg Illkirch France

Institut National de la Transfusion Sanguine DSIMB Paris France

Institute of Biotechnology The Czech Academy of Sciences Prague Czech Republic

Laboratoire de Physique École Normale Supérieure de Lyon Université de Lyon Centre National de la Recherche Scientifique UMR 5672 Lyon France

Metagenopolis INRA Jouy en Josas France

Molecular Biophysics Unit Indian Institute of Science Bangalore Bangalore India

National Library of Medicine National Center for Biotechnology Information National Institutes of Health Bethesda MD USA

Platelet Unit Institut National de la Transfusion Sanguine Paris France

Rutherford Appleton Laboratory Science and Technology Facilities Council Didcot UK

UMR_S 1134 DSIMB Laboratory of Excellence GR Ex Paris France

UMR_S 1134 DSIMB Université Paris Diderot Sorbonne Paris Cite Paris France

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc15023680
003      
CZ-PrNML
005      
20160309105724.0
007      
ta
008      
150709s2015 sz f 000 0|eng||
009      
AR
024    7_
$a 10.3389/fmolb.2015.00020 $2 doi
035    __
$a (PubMed)26075209
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a sz
100    1_
$a Craveur, Pierrick $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
245    10
$a Protein flexibility in the light of structural alphabets / $c P. Craveur, AP. Joseph, J. Esque, TJ. Narwani, F. Noël, N. Shinada, M. Goguet, S. Leonard, P. Poulain, O. Bertrand, G. Faure, J. Rebehmed, A. Ghozlane, LS. Swapna, RM. Bhaskara, J. Barnoud, S. Téletchéa, V. Jallu, J. Cerny, B. Schneider, C. Etchebest, N. Srinivasan, JC. Gelly, AG. de Brevern,
520    9_
$a 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.
655    _2
$a časopisecké články $7 D016428
655    _2
$a přehledy $7 D016454
700    1_
$a Joseph, Agnel P $u Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK.
700    1_
$a Esque, Jeremy $u Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France.
700    1_
$a Narwani, Tarun J $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Noël, Floriane $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Shinada, Nicolas $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Goguet, Matthieu $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Leonard, Sylvain $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Poulain, Pierre $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo.
700    1_
$a Bertrand, Olivier $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Faure, Guilhem $u National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA.
700    1_
$a Rebehmed, Joseph $u Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France.
700    1_
$a Ghozlane, Amine $u Metagenopolis, INRA Jouy-en-Josas, France.
700    1_
$a Swapna, Lakshmipuram S $u Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada.
700    1_
$a Bhaskara, Ramachandra M $u Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany.
700    1_
$a Barnoud, Jonathan $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France.
700    1_
$a Téletchéa, Stéphane $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France.
700    1_
$a Jallu, Vincent $u Platelet Unit, Institut National de la Transfusion Sanguine Paris, France.
700    1_
$a Cerny, Jiri $u Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic.
700    1_
$a Schneider, Bohdan $u Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic.
700    1_
$a Etchebest, Catherine $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a Srinivasan, Narayanaswamy $u Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India.
700    1_
$a Gelly, Jean-Christophe $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
700    1_
$a de Brevern, Alexandre G $u Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France.
773    0_
$w MED00188065 $t Frontiers in molecular biosciences $x 2296-889X $g Roč. 2, č. - (2015), s. 20
856    41
$u https://pubmed.ncbi.nlm.nih.gov/26075209 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20150709 $b ABA008
991    __
$a 20160309105739 $b ABA008
999    __
$a ind $b bmc $g 1084012 $s 906673
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2015 $b 2 $c - $d 20 $i 2296-889X $m Frontiers in molecular biosciences $n Front Mol Biosci $x MED00188065
LZP    __
$a Pubmed-20150709

Najít záznam

Citační ukazatele

Možnosti archivace