The PT1-Ca2+ Gla domain binds to a membrane through two dipalmitoylphosphatidylserines. A computational study

Biochemistry

Volumn 47, Issue 50, 2008, Pages 13267-13278

  Rodríguez, Yoel ^a,b   Mezei, Mihaly ^a   Osman, Roman ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b HOSTOS COMMUNITY COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; CALCIUM; CALCIUM ALLOYS; CELL MEMBRANES; COAGULATION; CRYSTAL STRUCTURE; CYTOLOGY; FREE ENERGY; GLYCOPROTEINS; IONS; LIPIDS; MEMBRANES; PHOSPHOLIPIDS; PLATELETS; PROTEINS;

ACTIVATED PLATELETS; ANIONIC LIPIDS; ANIONIC PHOSPHOLIPIDS; BILAYER MEMBRANES; BLOOD COAGULATIONS; CALCIUM IONS; CARBOXYGLUTAMIC ACIDS; COFACTOR; COMPUTATIONAL STUDIES; CRYSTALLOGRAPHIC STUDIES; DIPALMITOYL PHOSPHATIDYLCHOLINE; DO-MAINS; ENERGY SIMULATIONS; ENTROPIC EFFECTS; FREE ENERGY OF BINDINGS; LIPID MEMBRANES; MD SIMULATIONS; PHOSPHATIDYL SERINES; PROTHROMBINASE; SERINE PROTEASES;

BINDING SITES;

4 CARBOXYGLUTAMIC ACID; CALCIUM ION; DIPALMITOYLPHOSPHATIDYLCHOLINE; LIPID; PROTEIN; PROTHROMBIN FRAGMENT 1; SERINE; SERINE DERIVATIVE; UNCLASSIFIED DRUG; CALCIUM; DIPALMITOYLPHOSPHATIDYLSERINE; PEPTIDE FRAGMENT; PHOSPHATIDYLSERINE; PROTEIN PRECURSOR; PROTHROMBIN;

ARTICLE; BILAYER MEMBRANE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENTROPY; LIPID MEMBRANE; PRIORITY JOURNAL; PROTEIN DOMAIN; SIMULATION; ANIMAL; BIOLOGY; CATTLE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; HUMAN; LIPID BILAYER; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; 1-CARBOXYGLUTAMIC ACID; ANIMALS; CALCIUM; CATTLE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HUMANS; LIPID BILAYERS; PEPTIDE FRAGMENTS; PHOSPHATIDYLSERINES; PROTEIN BINDING; PROTEIN PRECURSORS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTHROMBIN; THERMODYNAMICS;

EID: 57649121583     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801199v     Document Type: Article

References (42)

1. Jesty, J., and Nemerson, Y. (1995)The pathways of blood coagulation. In Williams Hematology (Beutler, E., Lichtman, M. A., Coller, B. S., and Kipps, T. J., Eds.) 5th ed., pp 1227-1238, MacGraw-Hill, New York.
2. Lentz, B. R. (2003) Exposure of platelet membrane phosphatidylserine regulates blood coagulation. Prog. Lipid Res. 42, 423-438.
3. Furie, B., and Furie, B. C. (1990) Molecular basis of vitamin K-dependent γ-carboxylation. Blood 75, 1753-1762.
4. Rosing, J., Tans, G., Goversriemslag, J. W. P., Zwaal, R. F. A., and Hemker, H. C. (1980) Role of phospholipids and factor-Va in the prothrombinase complex. J. Biol. Chem. 255, 274-283.
5. Huang, M., Rigby, A. C., Morelli, X., Grant, M. A., Huang, G., Furie, B., Seaton, B., and Furie, B. C. (2003) Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins. Nat. Struct. Biol. 10, 751-756.
6. Kulman, J. D., Harris, J. E., Xie, L., and Davie, E. W. (2001) Identification of two novel transmembrane γ-carboxyglutamic acid proteins expressed broadly in fetal and adult tissues. Proc. Natl. Acad. Sci. U.S.A. 98, 1370-1375.
7. Luo, G. B., Ducy, P., McKee, M. D., Pinero, G. J., Loyer, E., Behringer, R. R., and Karsenty, G. (1997) Spontaneous calcification of arteries and cartilage in mice lacking matrix GLA protein. Nature 386, 78-81.
8. Zhai, X., Srivastava, A., Drummond, D. C., Daleke, D., and Lentz, B. R. (2002) Phosphatidylserine binding alters the conformation and specifically enhances the cofactor activity of bovine factor Va. Biochemistry 41, 5675-5684.
9. Koppaka, V., Wang, J. F., Banerjee, M., and Lentz, B. R. (1996) Soluble phospholipids enhance factor X(a)-catalyzed prothrombin activation in solution. Biochemistry 35, 7482-7491.
10. Srivastava, A., Wang, J. F., Majumder, R., Rezaie, A. R., Stenflo, J., Esmon, C. T., and Lentz, B. R. (2002) Localization of phosphatidylserine binding sites to structural domains of factor X-a. J. Biol. Chem. 277, 1855-1863.
11. Mizuno, H., Fujimoto, Z., Atoda, H., and Morita, T. (2001) Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X. Proc. Natl. Acad. Sci. U.S.A. 98, 7230-7234.
12. 2+ ion and membrane binding structure of the Gla domain of Ca-prothrombin fragment 1. Biochemistry 31, 2554-2566.
13. Falls, L. A., Furie, B. C., Jacobs, M., Furie, B., and Rigby, A. C. (2001) The ω-loop region of the human prothrombin γ-carboxyglutamic acid domain penetrates anionic phospholipid membranes. J. Biol. Chem. 276, 23895-23902.
14. McDonald, J. F., Shah, A. M., Schwalbe, R. A., Kisiel, W., Dahlback, B., and Nelsestuen, G. L. (1997) Comparison of naturally occurring vitamin K-dependent proteins: Correlation of amino acid sequences and membrane binding properties suggests a membrane contact site. Biochemistry 36, 5120-5127.
15. Roux, B. Building a configuration for a membrane/protein system. http://thallium.bsd.uchicago.edu/RouxLab/method.html.
16. De Loof, H., Harvey, S. C., Segrest, J. P., and Pastor, R. W. (1991) Mean Field Stochastic Boundary Molecular-Dynamics Simulation of a Phospholipid in a Membrane. Biochemistry 30, 2099-2113.
17. Pastor, R. W., Venable, R. M., and Karplus, M. (1991) Model for the structure of the lipid bilayer. Proc. Natl. Acad. Sci. U.S.A. 88, 892-896.
18. Venable, R. M., Zhang, Y., Hardy, B. J., and Pastor, R. W. (1993) Molecular dynamics simulations of a lipid bilayer and of hexadecane: An investigation of membrane fluidity. Science 262, 223-226.
19. Rodríguez, Y., Mezei, M., and Osman, R. (2006) Association free energy of dipalmitoylphosphatidylserines in a mixed dipalmitoylphosphatidylcholine membrane. Biophys. J. 92, 3071-3080.
20. Jedlovszky, P., and Mezei, M. (1999) Grand canonical ensemble Monte Carlo simulation of a lipid bilayer using extension biased rotations. J. Chem. Phys. 111, 10770-10773.
21. Feller, S. E., and MacKerell, A. D. (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J. Phys. Chem. B 104, 7510-7515.
22. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
23. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of cartesian equations of motion of a system with constraints molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341.
24. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187-217.
25. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802.
26. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593.
27. Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald: An N.Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
28. Pearlman, D. A. (1994) A comparison of alternative approaches to free-energy calculations. J. Phys. Chem. 98, 1487-1493.
29. Mezei, M., and Beveridge, D. L. (1986) Free energy simulations. Ann. N.Y. Acad. Sci. 482, 1-23.
30. Resat, H., and Mezei, M. (1993) Studies on Free-Energy Calculations. 1. Thermodynamic Integration Using a Polynomial Path. J. Chem. Phys. 99, 6052-6061.
31. Boresch, S., and Karplus, M. (1999) The role of bonded terms in free energy simulations: 1. Theoretical analysis. J. Phys. Chem. A 103, 103-118.
32. Boresch, S., and Karplus, M. (1999) The role of bonded terms in free energy simulations. 2. Calculation of their influence on free energy differences of solvation. J. Phys. Chem. A 103, 119-136.
33. Tidor, B., and Karplus, M. (1991) Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry 30, 3217-3228.
34. Simonson, T., Archontis, G., and Karplus, M. (1997) Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding. J. Phys. Chem. B 101, 8349-8362.
35. Michielin, O., and Karplus, M. (2002) Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: A simulation analysis. J. Mol. Biol. 324, 547-569.
36. Zeng, J., Fridman, M., Maruta, H., Treutlein, H. R., and Simonson, T. (1999) Protein-protein recognition: An experimental and computational study of the R89K mutation in Raf and its effect on Ras binding. Protein Sci. 8, 50-64.
37. Archontis, G., Simonson, T., Moras, D., and Karplus, M. (1998) Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. J. Mol. Biol. 275, 823 846.
38. White, S. H., and Wiener, M. C. (1996)The liquid-crystallographic structure of fluid lipid bilayer membranes. In Biological Membranes: A Molecular Perspective from Computation and Experiment (Merz, K. M., and Roux, B., Eds.) pp 127-144, Birkhäuser, Boston.
39. Mezei, M. (2008)MMC: Monte Carlo program for simulation of molecular assemblies. http://inka.mssm.edu/~mezei/mmc.
40. May, S., Harries, D., and Ben-Shaul, A. (2000) Lipid demixing and protein-protein interactions in the adsorption of charged proteins on mixed membranes. Biophys. J. 79, 1747-1760.
41. Boas, F. E., and Harbury, P. B. (2007) Potential energy functions for protein design. Curr. Opin. Struct. Biol. 17, 199-204.
42. Ji, C., Mei, Y., and Zhang, J. Z. (2008) Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin. Biophys. J. 95, 1080-1088.