Espace des ressources électronique en libre accès Bibliothèque de la Faculté SNVST de L'UAMOB
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Titre : Conformational selection or induced fit? New insights from old principles Type de document : document électronique Auteurs : Denis Michel, Auteur Editeur : Elsevier Année de publication : 2016 Importance : Volumes 128–129, Pages 48-54 Langues : Anglais (eng) Catégories : 572 Biochimie Tags : 'Conformational selection Induced fit Net flux Kinetic cooperativity Glucokinase Steady state Quantitative Methods (q-bio.QM)'. Index. décimale : 572 Résumé : A long standing debate in biochemistry is to determine whether the conformational changes observed during biomolecular interactions proceed through conformational selection (of preexisting isoforms) or induced fit (ligand-induced 3D reshaping). The latter mechanism had been invoked in certain circumstances, for example to explain the non-Michaelian activity of monomeric enzymes like glucokinase. But the relative importance of induced fit has been recently depreciated in favor of conformational selection, assumed to be always sufficient, predominant in general and in particular for glucokinase. The relative contributions of conformational selection and induced fit are reconsidered here in and out of equilibrium, in the light of earlier concepts such as the cyclic equilibrium rule and the turning wheel of Wyman, using single molecule state probability, one-way fluxes and net fluxes. The conditions for a switch from conformational selection to induced fit at a given ligand concentration are explicitly determined. Out of equilibrium, the inspection of the enzyme states circuit shows that conformational selection alone would give a Michaelian reaction rate but not the established nonlinear behaviour of glucokinase. Moreover, when induced fit and conformational selection coexist and allow kinetic cooperativity, the net flux emerging in the linkage cycle necessarily corresponds to the induced fit path. En ligne : https://arxiv.org/abs/0902.3147 Format de la ressource électronique : Conformational selection or induced fit? New insights from old principles [document électronique] / Denis Michel, Auteur . - Elsevier, 2016 . - Volumes 128–129, Pages 48-54.
Langues : Anglais (eng)
Catégories : 572 Biochimie Tags : 'Conformational selection Induced fit Net flux Kinetic cooperativity Glucokinase Steady state Quantitative Methods (q-bio.QM)'. Index. décimale : 572 Résumé : A long standing debate in biochemistry is to determine whether the conformational changes observed during biomolecular interactions proceed through conformational selection (of preexisting isoforms) or induced fit (ligand-induced 3D reshaping). The latter mechanism had been invoked in certain circumstances, for example to explain the non-Michaelian activity of monomeric enzymes like glucokinase. But the relative importance of induced fit has been recently depreciated in favor of conformational selection, assumed to be always sufficient, predominant in general and in particular for glucokinase. The relative contributions of conformational selection and induced fit are reconsidered here in and out of equilibrium, in the light of earlier concepts such as the cyclic equilibrium rule and the turning wheel of Wyman, using single molecule state probability, one-way fluxes and net fluxes. The conditions for a switch from conformational selection to induced fit at a given ligand concentration are explicitly determined. Out of equilibrium, the inspection of the enzyme states circuit shows that conformational selection alone would give a Michaelian reaction rate but not the established nonlinear behaviour of glucokinase. Moreover, when induced fit and conformational selection coexist and allow kinetic cooperativity, the net flux emerging in the linkage cycle necessarily corresponds to the induced fit path. En ligne : https://arxiv.org/abs/0902.3147 Format de la ressource électronique : Exemplaires (3)
Code-barres Cote Support Localisation Section Disponibilité 15 572 MIC Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 16 572 MIC Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 17 572 MIC Cartes et plans Biblio Libre Albums Enfants Exclu du prêt
Titre : Global analysis of VHHs framework regions with a structural alphabet Type de document : document électronique Auteurs : Floriane Noël, Auteur ; Alain Malpertuy, Auteur ; Alexandre De Brevern, Auteur Editeur : Elsevier Année de publication : 2016 Importance : Volume 131, Pages 11-19 Langues : Anglais (eng) Catégories : 572 Biochimie Tags : 'Secondary structure Sequence structure relationship Structural alphabet Antibodies Frameworks Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM)'. Index. décimale : 572 Résumé : The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models. En ligne : https://arxiv.org/abs/1610.01391 Format de la ressource électronique : Global analysis of VHHs framework regions with a structural alphabet [document électronique] / Floriane Noël, Auteur ; Alain Malpertuy, Auteur ; Alexandre De Brevern, Auteur . - Elsevier, 2016 . - Volume 131, Pages 11-19.
Langues : Anglais (eng)
Catégories : 572 Biochimie Tags : 'Secondary structure Sequence structure relationship Structural alphabet Antibodies Frameworks Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM)'. Index. décimale : 572 Résumé : The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models. En ligne : https://arxiv.org/abs/1610.01391 Format de la ressource électronique :
Titre : In silico prediction of protein flexibility with local structure approach Type de document : document électronique Auteurs : Tarun Narwani, Auteur ; Catherine Etchebest, Auteur ; Pierrick Craveur, Auteur Editeur : Elsevier Autre Editeur : arXiv Importance : Volume 165, Pages 150-155 Format : Langues : Anglais (eng) Catégories : 572 Biochimie Tags : 'Amino acid Structural alphabet Long structural prototypes Protein folds Disorder Bioinformatics Structural bioinformatics Software Support vector machines Evolutionary information Protein data bank Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM)' Index. décimale : 572 Résumé : Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible.PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community. It support parallelization features and can be run on a local cluster using multiple cores.The entire project is available under an open-source license at this http URL. En ligne : https://arxiv.org/abs/1908.05120 Format de la ressource électronique : In silico prediction of protein flexibility with local structure approach [document électronique] / Tarun Narwani, Auteur ; Catherine Etchebest, Auteur ; Pierrick Craveur, Auteur . - Elsevier : arXiv, [s.d.] . - Volume 165, Pages 150-155 ; PDF.
Langues : Anglais (eng)
Catégories : 572 Biochimie Tags : 'Amino acid Structural alphabet Long structural prototypes Protein folds Disorder Bioinformatics Structural bioinformatics Software Support vector machines Evolutionary information Protein data bank Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM)' Index. décimale : 572 Résumé : Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as the only indicator of protein's inner flexibility and predicts them as rigid or flexible.PredyFlexy stands differently from other approaches as it relies on the definition of protein flexibility (i) not only taken from crystallographic data, but also (ii) from Root Mean Square Fluctuation (RMSFs) observed in Molecular Dynamics simulations. It also uses a specific representation of protein structures, named Long Structural Prototypes (LSPs). From Position-Specific Scoring Matrix, the 120 LSPs are predicted with a good accuracy and directly used to predict (i) the protein flexibility in three categories (flexible, intermediate and rigid), (ii) the normalized B-factors, (iii) the normalized RMSFs, and (iv) a confidence index. Prediction accuracy among these three classes is equivalent to the best two class prediction methods, while the normalized B-factors and normalized RMSFs have a good correlation with experimental and in silico values. Thus, PredyFlexy is a unique approach, which is of major utility for the scientific community. It support parallelization features and can be run on a local cluster using multiple cores.The entire project is available under an open-source license at this http URL. En ligne : https://arxiv.org/abs/1908.05120 Format de la ressource électronique : A minimum set of stable blocks for rational design of polypeptide chains Running head: A set of stable blocks for protein rational design / Alexei Nekrasov
Titre : A minimum set of stable blocks for rational design of polypeptide chains Running head: A set of stable blocks for protein rational design Type de document : document électronique Auteurs : Alexei Nekrasov, Auteur ; Ludmila Alekseeva, Auteur ; Rudolf A. Pogosyan, Auteur ; Dmitry Dolgikh ; Anastasia Anashkina, Auteur Editeur : Elsevier Année de publication : 2019 Autre Editeur : arXiv Note générale : Volume 160, pp.88-92 Langues : Anglais (eng) Catégories : 572 Biochimie Tags : 'Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM) Protein structures Peptides Protein dynamics Molecular dynamics Stable conformations Local protein conformations' Index. décimale : 572 Résumé : The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we generated peptide sequences with no more than three functional groups, based on the alanine pentapeptide AAAAA. We analyzed 44,860 structures of peptides by the molecular dynamics method and found that 1,225 pentapeptides over 80% of the simulation time were in a stable conformation. Clustering of these conformations revealed 54 topological types of conformationally stable pentapeptides. These conformations relate to different combined elements of the protein secondary structure. So, we obtained a minimal set of amino acid structures of conformationally stable pentapeptides, creating a complete set of different topologies that ensure the formation of pre-folded conformation of protein structures. En ligne : https://arxiv.org/abs/1908.05126 Format de la ressource électronique : A minimum set of stable blocks for rational design of polypeptide chains Running head: A set of stable blocks for protein rational design [document électronique] / Alexei Nekrasov, Auteur ; Ludmila Alekseeva, Auteur ; Rudolf A. Pogosyan, Auteur ; Dmitry Dolgikh ; Anastasia Anashkina, Auteur . - Elsevier : arXiv, 2019.
Volume 160, pp.88-92
Langues : Anglais (eng)
Catégories : 572 Biochimie Tags : 'Quantitative Methods (q-bio.QM) Biomolecules (q-bio.BM) Protein structures Peptides Protein dynamics Molecular dynamics Stable conformations Local protein conformations' Index. décimale : 572 Résumé : The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we generated peptide sequences with no more than three functional groups, based on the alanine pentapeptide AAAAA. We analyzed 44,860 structures of peptides by the molecular dynamics method and found that 1,225 pentapeptides over 80% of the simulation time were in a stable conformation. Clustering of these conformations revealed 54 topological types of conformationally stable pentapeptides. These conformations relate to different combined elements of the protein secondary structure. So, we obtained a minimal set of amino acid structures of conformationally stable pentapeptides, creating a complete set of different topologies that ensure the formation of pre-folded conformation of protein structures. En ligne : https://arxiv.org/abs/1908.05126 Format de la ressource électronique : Exemplaires (2)
Code-barres Cote Support Localisation Section Disponibilité 98 572 NEK Cartes et plans Biblio Libre Albums Enfants Exclu du prêt 99 572 NEK Cartes et plans Biblio Libre Albums Enfants Exclu du prêt
