Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
暂无分享,去创建一个
Didier Devaurs | Lydia E. Kavraki | Mark Moll | John D. Lambris | Daniel Ricklin | John D Lambris | Dinler A. Antunes | Malvina Papanastasiou | L. Kavraki | Mark Moll | D. Antunes | Didier Devaurs | D. Ricklin | J. Lambris | M. Papanastasiou | Malvina Papanastasiou | Daniel Ricklin
[1] Didier Devaurs,et al. Characterizing Energy Landscapes of Peptides Using a Combination of Stochastic Algorithms , 2015, IEEE Transactions on NanoBioscience.
[2] Adelene Y. L. Sim,et al. Modeling and design by hierarchical natural moves , 2012, Proceedings of the National Academy of Sciences.
[3] Michele Vendruscolo,et al. Prediction of local structural stabilities of proteins from their amino acid sequences. , 2007, Structure.
[4] L Mayne,et al. Primary structure effects on peptide group hydrogen exchange. , 1972, Proteins.
[5] Daniel Ricklin,et al. A structural basis for complement inhibition by Staphylococcus aureus , 2007, Nature Immunology.
[6] Peter G Wolynes,et al. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. , 2011, Journal of the American Chemical Society.
[7] Yawen Bai,et al. Primary structure effects on peptide group hydrogen exchange , 1993, Biochemistry.
[8] Didier Devaurs,et al. MoMA-LigPath: a web server to simulate protein–ligand unbinding , 2013, Nucleic Acids Res..
[9] John R Engen,et al. Conformational insight into multi-protein signaling assemblies by hydrogen-deuterium exchange mass spectrometry. , 2016, Current opinion in structural biology.
[10] Ole N Jensen,et al. Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry. , 2009, Analytical chemistry.
[11] Elizabeth A Komives,et al. Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry , 2006, Journal of the American Society for Mass Spectrometry.
[12] Yang Li,et al. KINARI-Web: a server for protein rigidity analysis , 2011, Nucleic Acids Res..
[13] Kresten Lindorff-Larsen,et al. PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure , 2013, J. Comput. Chem..
[14] T. Oas,et al. A statistical thermodynamic model of the protein ensemble. , 2006, Chemical reviews.
[15] R. Nussinov,et al. Polymorphic Triple β-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid β42 Peptide* , 2011, The Journal of Biological Chemistry.
[16] Ernst-Walter Knapp,et al. Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study , 2005, JBIC Journal of Biological Inorganic Chemistry.
[17] S. Hazen,et al. Congruency between biophysical data from multiple platforms and molecular dynamics simulation of the double-super helix model of nascent high-density lipoprotein. , 2010, Biochemistry.
[18] Guodong Chen,et al. Higher order structure characterization of protein therapeutics by hydrogen/deuterium exchange mass spectrometry , 2014, Analytical and Bioanalytical Chemistry.
[19] T. Oas,et al. A Statistical Thermodynamic Model of the Protein Ensemble , 2006 .
[20] John D Lambris,et al. Hydrogen/deuterium exchange mass spectrometry: potential for investigating innate immunity proteins. , 2007, Advances in experimental medicine and biology.
[21] B. Nagar,et al. X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2. , 1998, Science.
[22] Adrian G Turjanski,et al. Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments. , 2013, Journal of chemical theory and computation.
[23] Nicholas P. Schafer,et al. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. , 2012, Journal of Physical Chemistry B.
[24] D. LeMaster,et al. Peptide Conformer Acidity Analysis of Protein Flexibility Monitored by Hydrogen Exchange† , 2009, Biochemistry.
[25] James O. Wrabl,et al. The role of protein conformational fluctuations in allostery, function, and evolution. , 2011, Biophysical chemistry.
[26] Michail Yu. Lobanov,et al. A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange , 2013, Bioinform..
[27] S. Englander,et al. Protein dynamics viewed by hydrogen exchange , 2012, Protein science : a publication of the Protein Society.
[28] M. Levitt. A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.
[29] Robert L. Baldwin,et al. Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added , 2009, Proceedings of the National Academy of Sciences.
[30] S Walter Englander,et al. Protein hydrogen exchange: Testing current models , 2012, Protein science : a publication of the Protein Society.
[31] Lars Konermann,et al. Hydrogen exchange mass spectrometry for studying protein structure and dynamics. , 2011, Chemical Society reviews.
[32] Michele Vendruscolo,et al. Structural interpretation of hydrogen exchange protection factors in proteins: characterization of the native state fluctuations of CI2. , 2006, Structure.
[33] Rajeev Motwani,et al. Path planning in expansive configuration spaces , 1997, Proceedings of International Conference on Robotics and Automation.
[34] David Baker,et al. Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.
[35] Lydia E. Kavraki,et al. Kinodynamic Motion Planning by Interior-Exterior Cell Exploration , 2008, WAFR.
[36] Sheila S Jaswal,et al. Biological insights from hydrogen exchange mass spectrometry. , 2013, Biochimica et biophysica acta.
[37] S. Radford,et al. Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[38] Virgil L. Woods,et al. Quantitative Assessment of Protein Structural Models by Comparison of H/D Exchange MS Data with Exchange Behavior Accurately Predicted by DXCOREX , 2011, Journal of The American Society for Mass Spectrometry.
[39] Guodong Chen,et al. Hydrogen/Deuterium Exchange Mass Spectrometry for Protein Higher-Order Structure Characterization , 2013 .
[40] Derek J. Wilson,et al. Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development - A review. , 2016, Analytica chimica acta.
[41] S. Hazen,et al. Double Superhelix Model of High Density Lipoprotein* , 2009, The Journal of Biological Chemistry.
[42] Daniel Ricklin,et al. Structural Implications for the Formation and Function of the Complement Effector Protein iC3b , 2017, The Journal of Immunology.
[43] Scott A. Lesley,et al. Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis , 2015, J. Chem. Inf. Model..
[44] John R. Engen,et al. Applications of Hydrogen/Deuterium Exchange MS from 2012 to 2014 , 2014, Analytical chemistry.
[45] P. Chacón,et al. New generation of elastic network models. , 2016, Current opinion in structural biology.
[46] T. Sosnick,et al. Hydrogen exchange: The modern legacy of Linderstrøm‐Lang , 1997, Protein science : a publication of the Protein Society.
[47] D. LeMaster,et al. A billion-fold range in acidity for the solvent-exposed amides of Pyrococcus furiosus rubredoxin. , 2008, Biochemistry.
[48] Thierry Siméon,et al. Motion planning algorithms for molecular simulations: A survey , 2012, Comput. Sci. Rev..
[49] A. Fersht,et al. Hydrogen exchange in chymotrypsin inhibitor 2 probed by mutagenesis. , 1997, Journal of molecular biology.
[50] E. Paci,et al. Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation , 2014, Biophysical journal.
[51] Bo Nilsson,et al. Rare Loss-of-Function Mutation in Complement Component C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity , 2015, The Journal of Immunology.
[52] A. Fersht,et al. Hydrogen exchange in chymotrypsin inhibitor 2 probed by denaturants and temperature. , 1997, Journal of molecular biology.
[53] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[54] G. Morris,et al. Residue-specific NH exchange rates studied by NMR diffusion experiments. , 2007, Journal of magnetic resonance.
[55] Xiaomeng Shi,et al. Hydrogen Exchange Mass Spectrometry for Conformational Analysis of Proteins , 2011 .
[56] S Walter Englander,et al. Protein hydrogen exchange at residue resolution by proteolytic fragmentation mass spectrometry analysis , 2013, Proceedings of the National Academy of Sciences.
[57] Derek J. Wilson,et al. Probing protein ensemble rigidity and hydrogen–deuterium exchange , 2013, Physical biology.
[58] Leland Mayne,et al. Hydrogen Exchange Mass Spectrometry. , 2016, Methods in enzymology.
[59] S W Englander,et al. Isotope effects in peptide group hydrogen exchange , 1993, Proteins.
[60] M. Y. Lobanov,et al. Prediction of amino acid residues protected from hydrogen-deuterium exchange in a protein chain , 2009, Biochemistry (Moscow).
[61] L. Kavraki,et al. SIMS: A Hybrid Method for Rapid Conformational Analysis , 2013, PloS one.
[62] T. Burzykowski,et al. Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry. , 2017, Mass spectrometry reviews.
[63] Didier Devaurs,et al. Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling. , 2018, International journal of computational biology and drug design.
[64] Samuel L. DeLuca,et al. Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You , 2010, Biochemistry.
[65] Lydia E Kavraki,et al. Computational models of protein kinematics and dynamics: beyond simulation. , 2012, Annual review of analytical chemistry.
[66] Michele Vendruscolo,et al. Rare fluctuations of native proteins sampled by equilibrium hydrogen exchange. , 2003, Journal of the American Chemical Society.
[67] S. Radford,et al. Equilibrium hydrogen exchange reveals extensive hydrogen bonded secondary structure in the on-pathway intermediate of Im7. , 2004, Journal of molecular biology.