R LaverySummaryCountry: France Publications
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Publications
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNARichard Lavery
Institut de Biologie et Chimie des Proteines, CNRS UMR 5086 Universite de Lyon, Lyon, France
Nucleic Acids Res 38:299-313. 2010..Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA...- Conformational analysis of nucleic acids revisited: Curves+R Lavery
Institut de Biologie et Chimie des Proteines, CNRS UMR 5086 Universite de Lyon, 7 passage du Vercors, 69367 Lyon, France
Nucleic Acids Res 37:5917-29. 2009..With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics... - Protein mechanics: a route from structure to functionRichard Lavery
Institut de Biologie et Chimie des Proteines, CNRS UMR 5086 Universite de Lyon, 7 passage du Vercors, Lyon 69367, France
J Biosci 32:891-8. 2007..This finding offers a novel means for detecting functional sites and also potentially provides a route for understanding the links between structure and function in more general terms... - Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assembliesKrystyna Zakrzewska
Institut de Biologie et Chimie des Proteines, CNRS UMR 5086 Universite de Lyon, 7 passage du Vercors, 69367 Lyon, France
Phys Chem Chem Phys 11:10712-21. 2009..Although they all involve significant DNA deformation, it is found that this does not necessarily imply that the recognition will be dominated by the sequence-dependent mechanical properties of DNA... - A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulationsBenjamin Bouvier
Institut de Biologie et Chimie des Proteines, UMR 5086 CNRS 7, Passage du Vercors, F 69007 Lyon, France
J Am Chem Soc 131:9864-5. 2009..The resulting free energy profile provides a detailed view of protein-DNA binding and identifies a metastable intermediate state... - Cadherin mechanics and complexation: the importance of calcium bindingFabien Cailliez
, CNRS, UPR 9080, Institut de Biologie Physico-Chimique, Paris 75005, France
Biophys J 89:3895-903. 2005..Here again, it is shown that the presence of calcium is an important factor in both rigidifying and stabilizing the complex... - Macromolecular recognitionCyril Deremble
, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
Curr Opin Struct Biol 15:171-5. 2005..Although backbone flexibility and solvent effects continue to pose problems, encouraging results have been obtained for both protein-protein and protein-DNA complexes... - Docking macromolecules with flexible segmentsKarine Bastard
, CNRS-UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
J Comput Chem 24:1910-20. 2003..et al., Cell 1995, 80, 639. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA... - Looking into DNA recognition: zinc finger binding specificityGuillaume Paillard
, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
Nucleic Acids Res 32:6673-82. 2004.... - Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulationsEmmanuel Giudice
, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
Nucleic Acids Res 31:1434-43. 2003..Partial opening also leads to well defined water bridging sites, which may play a role in stabilizing the perturbed base pairs... - Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculationsEmmanuel Giudice
, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
J Am Chem Soc 125:4998-9. 2003.... - Interactions between neuronal fusion proteins explored by molecular dynamicsMarie Pierre Durrieu
Institut de Biologie Physico Chimique, Laboratoire de Biochimie Theorique, Centre National de la Recherche Scientifique, UPR 9080, Paris, France
Biophys J 94:3436-46. 2008..The interaction patterns we observe provide a new tool for interpreting the impact of mutations on the complex... - Analyzing protein-DNA recognition mechanismsGuillaume Paillard
, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
Structure 12:113-22. 2004.... - Locating the active sites of enzymes using mechanical propertiesSophie Sacquin Mora
Laboratoire de Biochimie Theorique, CNRS UPR 9080, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
Proteins 67:350-9. 2007..It is however noted that active sites near the protein surface are more difficult to detect and that non-catalytic, but structurally key residues may also exhibit high force constants... - Dynamics and stability of E-cadherin dimersFabien Cailliez
Laboratoire de Biochimie Theorique, CNRS UPR 9080, Institut de Biologie Physico Chimique, Paris, France
Biophys J 91:3964-71. 2006.... - Recognizing DNARichard Lavery
Laboratoire de Biochimie Theorique, CNRS UPR 9080, Institut de Biologie Physico Chimique, Paris, France
Q Rev Biophys 38:339-44. 2005..I present here some recent results from our group and their consequences for improving our understanding of protein-DNA binding, and their potential for predicting, and eventually modulating, protein-DNA binding... - Investigating the local flexibility of functional residues in hemoproteinsSophie Sacquin-Mora
, UMR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris, France
Biophys J 90:2706-17. 2006..We note, however, that residues other than those in the active site can also have high force constants, as in the case of residues belonging to the folding nucleus of c-type hemoproteins... - Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) stepsDavid L Beveridge
Chemistry Department, Molecular Biology and Biochemistry Department, and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
Biophys J 87:3799-813. 2004.... - Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide stepsSurjit B Dixit
Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA
Biophys J 89:3721-40. 2005..The results in general provide new insight into MD on DNA and the sequence-dependent dynamical structural characteristics of DNA... - Probing protein mechanics: residue-level properties and their use in defining domainsIsabelle Navizet
, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris 75005, France
Biophys J 87:1426-35. 2004..It is also shown that the mechanical information obtained by residue-level probing opens a new route for defining so-called dynamical domains within protein structures... - Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stackingStephen C Harvey
Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294 0005, USA
J Comput Chem 24:1-9. 2003..Test cases are presented to show the utility of the method. The restraints could be adapted for implementation in other molecular mechanics packages...