A mixed molecular modeling‐robotics approach to investigate lipase large molecular motions
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Thierry Siméon | Juan Cortés | Magali Remaud-Siméon | Sophie Barbe | Isabelle André | Pierre Monsan | T. Siméon | Juan Cortés | I. André | P. Monsan | M. Remaud-Siméon | S. Barbe
[1] Jürgen Pleiss,et al. Solvent‐induced lid opening in lipases: A molecular dynamics study , 2010, Protein science : a publication of the Protein Society.
[2] L. Mourey,et al. Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase. , 2010, Biophysical journal.
[3] Thierry Siméon,et al. Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method. , 2010, Physical chemistry chemical physics : PCCP.
[4] Ying Wang,et al. Molecular Dynamics Studies on T1 Lipase: Insight into a Double-Flap Mechanism , 2010, J. Chem. Inf. Model..
[5] Lydia Tapia,et al. A Motion Planning Approach to Studying Molecular Motions , 2010, Commun. Inf. Syst..
[6] Thierry Siméon,et al. Control of Lipase Enantioselectivity by Engineering the Substrate Binding Site and Access Channel , 2009, Chembiochem : a European journal of chemical biology.
[7] I. André,et al. Insights into lid movements of Burkholderia cepacia lipase inferred from molecular dynamics simulations , 2009, Proteins.
[8] L. Kavraki,et al. Multiscale characterization of protein conformational ensembles , 2009, Proteins.
[9] Thierry Siméon,et al. Encoding molecular motions in voxel maps , 2009, 2009 IEEE International Conference on Robotics and Automation.
[10] G. Chirikjian,et al. Iterative cluster‐NMA: A tool for generating conformational transitions in proteins , 2009, Proteins.
[11] R. Fernández-Lafuente,et al. Activation of Bacterial Thermoalkalophilic Lipases Is Spurred by Dramatic Structural Rearrangements* , 2009, Journal of Biological Chemistry.
[12] J. Pleiss,et al. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase , 2009, BMC Structural Biology.
[13] C. Cambillau,et al. Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation. , 2008, Biochemistry.
[14] Thierry Siméon,et al. A Structure‐Controlled Investigation of Lipase Enantioselectivity by a Path‐Planning Approach , 2008, Chembiochem : a European journal of chemical biology.
[15] Jung-Kee Lee,et al. Structural basis for the cold adaptation of psychrophilic M37 lipase from Photobacterium lipolyticum , 2008, Proteins.
[16] Cecilia Clementi,et al. Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.
[17] T. Siméon,et al. An NMA‐guided path planning approach for computing large‐amplitude conformational changes in proteins , 2007, Proteins.
[18] Thierry Siméon,et al. Disassembly Path Planning for Complex Articulated Objects , 2007, IEEE Transactions on Robotics.
[19] A. Seshasayee,et al. Activation of Candida rugosa lipase at alkane–aqueous interfaces: A molecular dynamics study , 2007, FEBS letters.
[20] Jean-Claude Latombe,et al. Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values , 2007, J. Comput. Biol..
[21] Lydia Tapia,et al. Kinetics analysis methods for approximate folding landscapes , 2007, ISMB/ECCB.
[22] Manfred J. Sippl,et al. Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..
[23] R. Verger,et al. Probing the opening of the pancreatic lipase lid using site-directed spin labeling and EPR spectroscopy. , 2007, Biochemistry.
[24] Dan Halperin,et al. Prediction and simulation of motion in pairs of transmembrane alpha-helices , 2007, Bioinform..
[25] D. Boehr,et al. The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis , 2006, Science.
[26] Steven M. LaValle,et al. Planning algorithms , 2006 .
[27] Lydia Tapia,et al. Simulating Protein Motions with Rigidity Analysis , 2006, RECOMB.
[28] T. Ha,et al. Bridging conformational dynamics and function using single-molecule spectroscopy. , 2006, Structure.
[29] PRINCIPLES OF ROBOT MOTION, Theory, Algorithms and Implementations, by Howie Choset et al., MIT Press, 2005. xix + 603 pp., index, ISBN 0-262-03327-5, 433 references (Hb. £38.95) , 2006, Robotica.
[30] Guang Song,et al. Protein folding by motion planning , 2005, Physical biology.
[31] L. Kay,et al. Intrinsic dynamics of an enzyme underlies catalysis , 2005, Nature.
[32] Subbulakshmi Latha Cherukuvada,et al. Evidence of a Double-Lid Movement in Pseudomonas aeruginosa Lipase: Insights from Molecular Dynamics Simulations , 2005, PLoS Comput. Biol..
[33] Robert L Jernigan,et al. Rigid-cluster models of conformational transitions in macromolecular machines and assemblies. , 2005, Biophysical journal.
[34] Thierry Siméon,et al. BioCD : An Efficient Algorithm for Self-collision and Distance Computation between Highly Articulated Molecular Models , 2005, Robotics: Science and Systems.
[35] J. Schrag,et al. Mirror-image packing in enantiomer discrimination molecular basis for the enantioselectivity of B.cepacia lipase toward 2-methyl-3-phenyl-1-propanol. , 2005, Chemistry & biology.
[36] Nancy M. Amato,et al. Using motion planning to study RNA folding kinetics , 2004, J. Comput. Biol..
[37] Thierry Siméon,et al. A path planning approach for computing large-amplitude motions of flexible molecules , 2005, ISMB.
[38] A. Salleh,et al. Structure and dynamics of Candida rugosa lipase: the role of organic solvent , 2004, Journal of molecular modeling.
[39] Teresa Mitchell,et al. Engineering of an artificial glycosylation pathway blocked in core oligosaccharide assembly in the yeast Pichia pastoris: production of complex humanized glycoproteins with terminal galactose. , 2004, Glycobiology.
[40] Georgia Hadjipavlou,et al. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair , 2004, Nature Structural &Molecular Biology.
[41] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[42] A. Palmer,et al. NMR characterization of the dynamics of biomacromolecules. , 2004, Chemical reviews.
[43] Thierry Siméon,et al. Geometric algorithms for the conformational analysis of long protein loops , 2004, J. Comput. Chem..
[44] S. Benkovic,et al. Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[45] P. Kangueane,et al. Insights from molecular dynamics simulations into pH-dependent enantioselective hydrolysis of ibuprofen esters by Candida rugosa lipase. , 2003, Protein engineering.
[46] J. Hermoso,et al. Structural insights into the lipase/esterase behavior in the Candida rugosa lipases family: crystal structure of the lipase 2 isoenzyme at 1.97A resolution. , 2003, Journal of molecular biology.
[47] R. S. Goody,et al. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[48] Martin Karplus,et al. Catalysis and specificity in enzymes: a study of triosephosphate isomerase and comparison with methyl glyoxal synthase. , 2003, Advances in protein chemistry.
[49] W. Eaton,et al. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy , 2002, Nature.
[50] Jean-Claude Latombe,et al. Stochastic roadmap simulation for the study of ligand-protein interactions , 2002, ECCB.
[51] O. G. Mouritsen,et al. Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations. , 2002, Biophysical journal.
[52] Jean-Claude Latombe,et al. Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion , 2002, RECOMB '02.
[53] Nancy M. Amato,et al. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures , 2002, RECOMB '02.
[54] Nancy M. Amato,et al. Using motion planning to study protein folding pathways , 2001, J. Comput. Biol..
[55] R. Bywater,et al. Influence of a lipid interface on protein dynamics in a fungal lipase. , 2001, Biophysical journal.
[56] S. Tomić,et al. Complex of Burkholderia cepacia lipase with transition state analogue of 1-phenoxy-2-acetoxybutane: biocatalytic, structural and modelling study. , 2001, European journal of biochemistry.
[57] B. Dijkstra,et al. The Crystal Structure of Bacillus subtilis Lipase : A Minimal α/β Hydrolase Fold Enzyme , 2001 .
[58] B. Dijkstra,et al. The crystal structure of Bacillus subtilis lipase: a minimal alpha/beta hydrolase fold enzyme. , 2001, Journal of molecular biology.
[59] Nancy M. Amato,et al. Ligand binding with OBPRM and user input , 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).
[60] Jean-Claude Latombe,et al. Capturing molecular energy landscapes with probabilistic conformational roadmaps , 2001, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164).
[61] Nancy M. Amato,et al. Ligand Binding with OBPRM and Haptic User Input: Enhancing Automatic Motion Planning with Virtual Touch , 2000 .
[62] Seokmin Shin,et al. Computational Studies of Essential Dynamics of Pseudomonas cepacia Lipase , 2000, Journal of biomolecular structure & dynamics.
[63] Steven M. LaValle,et al. Rapidly-Exploring Random Trees: Progress and Prospects , 2000 .
[64] R. Bywater,et al. Computational analysis of chain flexibility and fluctuations in Rhizomucor miehei lipase. , 1999, Protein engineering.
[65] Jean-Claude Latombe,et al. A Motion Planning Approach to Flexible Ligand Binding , 1999, ISMB.
[66] P. Kinnunen,et al. Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase. , 1998, Biochemistry.
[67] R. Hubbard,et al. Conformational change in the activation of lipase: An analysis in terms of low‐frequency normal modes , 1998, Protein science : a publication of the Protein Society.
[68] B. Dijkstra,et al. University of Groningen Structural basis of the chiral selectivity of Pseudomonas cepacia lipase , 2017 .
[69] Y Li,et al. The open conformation of a Pseudomonas lipase. , 1997, Structure.
[70] S. Suh,et al. The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor. , 1997, Structure.
[71] D. V. van Aalten,et al. Essential dynamics of lipase binding sites: the effect of inhibitors of different chain length. , 1997, Protein engineering.
[72] R. Verger. ‘Interfacial activation’ of lipases: facts and artifacts , 1997 .
[73] L. Sarda,et al. A critical reevaluation of the phenomenon of interfacial activation. , 1997, Methods in enzymology.
[74] D. V. van Aalten,et al. Dynamics of proteins in different solvent systems: analysis of essential motion in lipases. , 1996, Biophysical journal.
[75] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[76] O. Olsen,et al. Theoretical investigation of the dynamics of the active site lid in Rhizomucor miehei lipase. , 1996, Biophysical journal.
[77] D. Schomburg,et al. Crystal structure of a bacterial lipase from Chromobacterium viscosum ATCC 6918 refined at 1.6 angstroms resolution. , 1996, Journal of molecular biology.
[78] A. Klibanov,et al. On the issue of interfacial activation of lipase in nonaqueous media , 1996, Biotechnology and bioengineering.
[79] G J Kleywegt,et al. Crystallographic and molecular-modeling studies of lipase B from Candida antarctica reveal a stereospecificity pocket for secondary alcohols. , 1995, Biochemistry.
[80] H. van Tilbeurgh,et al. The 2.46 A resolution structure of the pancreatic lipase-colipase complex inhibited by a C11 alkyl phosphonate. , 1994, Biochemistry.
[81] J. Schrag,et al. Analogs of reaction intermediates identify a unique substrate binding site in Candida rugosa lipase. , 1995, Biochemistry.
[82] M. Haas,et al. Conformational lability of lipases observed in the absence of an oil-water interface: crystallographic studies of enzymes from the fungi Humicola lanuginosa and Rhizopus delemar. , 1995, Journal of lipid research.
[83] O. Edholm,et al. Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent. , 1994, Biophysical journal.
[84] T A Jones,et al. The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica. , 1994, Structure.
[85] Z. Derewenda,et al. Structure and function of lipases. , 1994, Advances in protein chemistry.
[86] M. Haas,et al. An unusual buried polar cluster in a family of fungal lipases , 1994, Nature Structural Biology.
[87] B Rubin,et al. Insights into interfacial activation from an open structure of Candida rugosa lipase. , 1994, The Journal of biological chemistry.
[88] L. Johnson,et al. The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate , 1993, FEBS letters.
[89] J. Schrag,et al. 1.8 A refined structure of the lipase from Geotrichum candidum. , 1993, Journal of molecular biology.
[90] L. Norskov,et al. A serine protease triad forms the catalytic centre of a triacylglycerol lipase , 1990, Nature.
[91] T. Thuren. A model for the molecular mechanism of interfacial activation of phospholipase A2 supporting the substrate theory , 1988, FEBS letters.
[92] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[93] N. Go,et al. Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three‐dimensional lattice model of lysozyme , 1978 .
[94] J. H. Law,et al. Catalysis by adsorbed enzymes. The hydrolysis of tripropionin by pancreatic lipase adsorbed to siliconized glass beads. , 1973, The Journal of biological chemistry.