A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa)

[1]  J. Bae,et al.  Protein Z-dependent Protease Inhibitor Binds to the C-terminal Domain of Protein Z* , 2008, Journal of Biological Chemistry.

[2]  D. Case,et al.  Homology Modeling of NR2B Modulatory Domain of NMDA Receptor and Analysis of Ifenprodil Binding , 2007, ChemMedChem.

[3]  J. C. Rau,et al.  Serpins in thrombosis, hemostasis and fibrinolysis , 2007, Journal of thrombosis and haemostasis : JTH.

[4]  L. Pedersen,et al.  A proposed structural model of human protein Z , 2007, Journal of thrombosis and haemostasis : JTH.

[5]  B. Olgemöller,et al.  Hybridization probe genotyping of the R67X nonsense polymorphism in the protein Z-dependent protease inhibitor reveals a new R67Q mutation. , 2007, Clinical chemistry.

[6]  Steven W. Muchmore,et al.  Rapid Estimation of Relative Protein-Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA , 2007, J. Chem. Inf. Model..

[7]  J. Corral,et al.  Protein Z/Z‐dependent protease inhibitor (PZ/ZPI) anticoagulant system and thrombosis , 2007, British journal of haematology.

[8]  A. Folsom,et al.  Prospective study of polymorphisms of the protein Z-dependent protease inhibitor and risk of venous thromboembolism , 2007, Thrombosis and Haemostasis.

[9]  G. Damante,et al.  Mutations R67X and W303X of the protein Z-dependent protease inhibitor gene and venous thromboembolic disease: a case–control study in Italian subjects , 2007, Journal of Thrombosis and Thrombolysis.

[10]  J. Whisstock,et al.  An overview of the serpin superfamily , 2006, Genome Biology.

[11]  J. Huntington,et al.  Antithrombin–S195A factor Xa‐heparin structure reveals the allosteric mechanism of antithrombin activation , 2006, The EMBO journal.

[12]  I. Martinelli,et al.  Polymorphisms of the protein Z-dependent protease inhibitor (ZPI) gene and the risk of venous thromboembolism , 2006, Thrombosis and Haemostasis.

[13]  Martin Almlöf,et al.  Probing the effect of point mutations at protein-protein interfaces with free energy calculations. , 2006, Biophysical journal.

[14]  A. Kornberg,et al.  Protein Z levels and central retinal vein or artery occlusion , 2005, European journal of haematology.

[15]  K. M. Cabral,et al.  Down-regulation of Factor IXa in the Factor Xase Complex by Protein Z-dependent Protease Inhibitor* , 2005, Journal of Biological Chemistry.

[16]  A. Rezaie,et al.  Identification of Factor Xa Residues Critical for Interaction with Protein Z-dependent Protease Inhibitor , 2005, Journal of Biological Chemistry.

[17]  R. Eckert,et al.  Reformable intramolecular cross-linking of the N-terminal domain of heparin cofactor II: effects on enzyme inhibition. , 2004, European journal of biochemistry.

[18]  P. Browett,et al.  Mutations within the protein Z‐dependent protease inhibitor gene are associated with venous thromboembolic disease: a new form of thrombophilia , 2004, British journal of haematology.

[19]  C. Esmon,et al.  Structure of the antithrombin–thrombin–heparin ternary complex reveals the antithrombotic mechanism of heparin , 2004, Nature Structural &Molecular Biology.

[20]  Lisa D. Cabrita,et al.  How do proteins avoid becoming too stable? Biophysical studies into metastable proteins , 2004, European Biophysics Journal.

[21]  S. Olson,et al.  Serpin-ligand interactions. , 2004, Methods.

[22]  Holger Gohlke,et al.  Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf , 2004, J. Comput. Chem..

[23]  P. Gettins Serpin structure, mechanism, and function. , 2002, Chemical reviews.

[24]  A. Paganini-Hill,et al.  Low protein Z levels and risk of ischemic stroke: differences by diabetic status and gender. , 2002, Blood cells, molecules & diseases.

[25]  R. Carrell,et al.  Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  B. Lämmle,et al.  Frequency of protein Z deficiency in patients with ischaemic stroke , 2001, The Lancet.

[27]  G. Broze Protein Z-Dependent Regulation of Coagulation , 2001, Thrombosis and Haemostasis.

[28]  G. Broze,et al.  Protein Z Circulates in Plasma in a Complex with Protein Z-Dependent Protease Inhibitor , 2001, Thrombosis and Haemostasis.

[29]  X. Han,et al.  Characterization of the protein Z-dependent protease inhibitor. , 2000, Blood.

[30]  J. Whisstock,et al.  Conformational changes in serpins: II. The mechanism of activation of antithrombin by heparin. , 2000, Journal of molecular biology.

[31]  A. Rezaie Identification of Basic Residues in the Heparin-binding Exosite of Factor Xa Critical for Heparin and Factor Va Binding* , 2000, The Journal of Biological Chemistry.

[32]  X. Han,et al.  The protein Z-dependent protease inhibitor is a serpin. , 1999, Biochemistry.

[33]  Xiongwu Wu,et al.  Self-Guided Molecular Dynamics Simulation for Efficient Conformational Search , 1998 .

[34]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[35]  J. Whisstock,et al.  The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site. , 1997, Journal of molecular biology.

[36]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[37]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[38]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

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

[40]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[41]  D. Eisenberg,et al.  Assessment of protein models with three-dimensional profiles , 1992, Nature.

[42]  D. Tollefsen,et al.  The N-terminal acidic domain of heparin cofactor II mediates the inhibition of alpha-thrombin in the presence of glycosaminoglycans. , 1991, The Journal of biological chemistry.

[43]  H. Ragg,et al.  Glycosaminoglycan-mediated leuserpin-2/thrombin interaction. Structure-function relationships. , 1990, The Journal of biological chemistry.

[44]  J. Tainer,et al.  Elucidating the structural chemistry of glycosaminoglycan recognition by protein C inhibitor. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

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

[46]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[47]  D. Lomas,et al.  Topography of a 2.0 Å structure of α1‐antitrypsin reveals targets for rational drug design to prevent conformational disease , 2000, Protein science : a publication of the Protein Society.

[48]  P A Kollman,et al.  Continuum solvent studies of the stability of RNA hairpin loops and helices. , 1998, Journal of biomolecular structure & dynamics.

[49]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[50]  D. Eisenberg,et al.  A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.

[51]  M. Caron,et al.  Structure-Function Relationships , 1991 .

[52]  J. Miletich,et al.  Human plasma protein Z antigen: range in normal subjects and effect of warfarin therapy. , 1987, Blood.