Sodium-induced population shift drives activation of thrombin

[1]  J. Fenton.  Thrombin , 2019, Reactions Weekly.

[2]  E. Di Cera,et al.  Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin , 2019, Scientific Reports.

[3]  F. Salsbury,et al.  Na+-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling. , 2019, Physical chemistry chemical physics : PCCP.

[4]  K. Liedl,et al.  Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties , 2019, Front. Immunol..

[5]  Gregory R Bowman,et al.  Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding , 2018, bioRxiv.

[6]  Anu R. Melge,et al.  Structure-function studies of prothrombin Amrita, a dysfunctional prothrombin characterized by point mutation at Arg553 → Gln. , 2018, International journal of biological macromolecules.

[7]  E. Komives,et al.  Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. , 2018, Biochemistry.

[8]  Gerhard Stock,et al.  Metadynamics Enhanced Markov Modeling of Protein Dynamics. , 2018, The journal of physical chemistry. B.

[9]  Ryan L. Melvin,et al.  Mechanistic insights into thrombin's switch between "slow" and "fast" forms. , 2017, Physical chemistry chemical physics : PCCP.

[10]  Brian Fuglestad,et al.  NMR reveals a dynamic allosteric pathway in thrombin , 2017, Scientific Reports.

[11]  Sangwook Wu.  Loop-driven conformational transition between the alternative and collapsed form of prethrombin-2: targeted molecular dynamics study , 2017, Journal of biomolecular structure & dynamics.

[12]  Kathryn M Hart,et al.  supplementary figures , 2018 .

[13]  M. Zerbetto,et al.  Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin. , 2016, Biochemistry.

[14]  Julian E. Fuchs,et al.  Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD , 2016, Journal of chemical theory and computation.

[15]  Christian Kramer,et al.  Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin , 2015, PloS one.

[16]  Frank Noé,et al.  PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. , 2015, Journal of chemical theory and computation.

[17]  E. Di Cera,et al.  Kinetic Dissection of the Pre-existing Conformational Equilibrium in the Trypsin Fold* , 2015, The Journal of Biological Chemistry.

[18]  C. Simmerling,et al.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. , 2015, Journal of chemical theory and computation.

[19]  F. Noé,et al.  Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models , 2015, Nature Communications.

[20]  Bruce Bartholow Duncan,et al.  Prevalence, Awareness, Treatment and Influence of Socioeconomic Variables on Control of High Blood Pressure: Results of the ELSA-Brasil Study , 2015, PloS one.

[21]  Carsten Kutzner,et al.  Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS , 2015, EASC.

[22]  M. Nagaoka,et al.  Toward understanding allosteric activation of thrombin: a conjecture for important roles of unbound Na(+) molecules around thrombin. , 2015, The journal of physical chemistry. B.

[23]  Frank Noé,et al.  Markov state models of biomolecular conformational dynamics. , 2014, Current opinion in structural biology.

[24]  Massimiliano Bonomi,et al.  PLUMED 2: New feathers for an old bird , 2013, Comput. Phys. Commun..

[25]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.

[26]  J. Andrew McCammon,et al.  Correlated Motions and Residual Frustration in Thrombin , 2013, The journal of physical chemistry. B.

[27]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[28]  Vijay S Pande,et al.  Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. , 2013, Journal of chemical theory and computation.

[29]  Toni Giorgino,et al.  Identification of slow molecular order parameters for Markov model construction. , 2013, The Journal of chemical physics.

[30]  J. Mccammon,et al.  Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities , 2012, Proceedings of the National Academy of Sciences.

[31]  Frank Noé,et al.  Kinetic characterization of the critical step in HIV-1 protease maturation , 2012, Proceedings of the National Academy of Sciences.

[32]  S. Freund,et al.  An ensemble view of thrombin allostery , 2012, Biological chemistry.

[33]  E. Di Cera,et al.  Conformational selection in trypsin-like proteases. , 2012, Current opinion in structural biology.

[34]  J Andrew McCammon,et al.  The dynamic structure of thrombin in solution. , 2012, Biophysical journal.

[35]  E. Di Cera,et al.  Crystal structures of prethrombin-2 reveal alternative conformations under identical solution conditions and the mechanism of zymogen activation. , 2011, Biochemistry.

[36]  E. Di Cera,et al.  Allostery in trypsin-like proteases suggests new therapeutic strategies. , 2011, Trends in biotechnology.

[37]  Fatima Zapata,et al.  Crystallographic and kinetic evidence of allostery in a trypsin-like protease. , 2011, Biochemistry.

[38]  S. Freund,et al.  NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation , 2010, Proceedings of the National Academy of Sciences.

[39]  Klaus R Liedl,et al.  Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa. , 2010, The journal of physical chemistry. B.

[40]  J. A. Guimarães,et al.  Thrombin allosteric modulation revisited: a molecular dynamics study , 2010, Journal of molecular modeling.

[41]  E. Di Cera,et al.  Crystal Structure of Thrombin Bound to the Uncleaved Extracellular Fragment of PAR1* , 2010, The Journal of Biological Chemistry.

[42]  R. Nussinov,et al.  The role of dynamic conformational ensembles in biomolecular recognition. , 2009, Nature chemical biology.

[43]  P. Labute.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Protonate3D: Assignment of ionization , 2013 .

[44]  J. Huntington.  How Na+ activates thrombin – a review of the functional and structural data , 2008, Biological chemistry.

[45]  T. Cheatham,et al.  Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations , 2008, The journal of physical chemistry. B.

[46]  F. S. Mathews,et al.  Structural identification of the pathway of long-range communication in an allosteric enzyme , 2008, Proceedings of the National Academy of Sciences.

[47]  D. Kern,et al.  Dynamic personalities of proteins , 2007, Nature.

[48]  E. Di Cera,et al.  Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics. , 2007, Biophysical chemistry.

[49]  Jianyin Shao,et al.  Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. , 2007, Journal of chemical theory and computation.

[50]  E. Di Cera,et al.  Rapid Kinetics of Na+ Binding to Thrombin* , 2006, Journal of Biological Chemistry.

[51]  E. Davie,et al.  An Overview of the Structure and Function of Thrombin , 2006, Seminars in thrombosis and hemostasis.

[52]  W. Bode.  The structure of thrombin: a janus-headed proteinase. , 2006, Seminars in thrombosis and hemostasis.

[53]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[54]  V. De Filippis,et al.  Effect of Na+ binding on the conformation, stability and molecular recognition properties of thrombin. , 2005, The Biochemical journal.

[55]  E. Di Cera,et al.  Kinetic Pathway for the Slow to Fast Transition of Thrombin , 1997, The Journal of Biological Chemistry.

[56]  A. Tulinsky,et al.  The molecular environment of the Na+ binding site of thrombin. , 1997, Biophysical chemistry.

[57]  E. Di Cera,et al.  The Na+ Binding Site of Thrombin (*) , 1995, The Journal of Biological Chemistry.

[58]  E. Di Cera,et al.  An allosteric switch controls the procoagulant and anticoagulant activities of thrombin. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[59]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[60]  E. Di Cera,et al.  Thrombin is a Na(+)-activated enzyme. , 1992, Biochemistry.

[61]  K Fujikawa,et al.  The coagulation cascade: initiation, maintenance, and regulation. , 1991, Biochemistry.

[62]  R. Huber,et al.  The refined 1.9 A crystal structure of human alpha‐thrombin: interaction with D‐Phe‐Pro‐Arg chloromethylketone and significance of the Tyr‐Pro‐Pro‐Trp insertion segment. , 1989, The EMBO journal.

[63]  Giovanni Ciccotti,et al.  Molecular dynamics simulation of rigid molecules , 1986 .

[64]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[65]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[66]  C. Orthner,et al.  Evidence that human alpha-thrombin is a monovalent cation-activated enzyme. , 1980, Archives of biochemistry and biophysics.

[67]  S. Adelman.  Quantum generalized Langevin equation approach to gas/solid collisions , 1976 .

[68]  Diwakar Shukla,et al.  Activation pathway of Src kinase reveals intermediate states as targets for drug design , 2014 .

[69]  J. Huntington.  Thrombin plasticity. , 2012, Biochimica et biophysica acta.

[70]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..