Journal of Molecular Modeling

, Volume 18, Issue 6, pp 2717–2725

Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations

  • Jing-Fang Wang
  • Pei Hao
  • Yi-Xue Li
  • Jian-Liang Dai
  • Xuan Li
Original Paper


Human coagulation Factor X (FX), a member of the vitamin K-dependent serine protease family, is a crucial component of the human coagulation cascade. Activated FX (FXa) participates in forming the prothrombinase complex on activated platelets to convert prothrombin to thrombin in coagulation reactions. In the current study, 30-ns MD simulations were performed on both the open and closed states of human FXa. Root mean squares (RMS) fluctuations showed that structural fluctuations concentrated on the loop regions of FXa, and the presence of a ligand in the closed system resulted in larger fluctuations of the gating residues. The open system had a gating distance from 9.23 to 11.33 Å, i.e., significantly larger than that of the closed system (4.69–6.35 Å), which allows diversified substrates of variable size to enter. Although the solvent accessible surface areas (SASA) of FXa remained the same in both systems, the open system generally had a larger total SASA or hydrophobic SASA (or both) for residues surrounding the S4 pocket. Additionally, more hydrogen bonds were formed in the closed state than in the open state of FXa, which is believed to play a significant role in maintaining the closed confirmation of the aryl-binding site. Based on the results of MD simulations, we propose that an induced-fit mechanism governs the functioning of human coagulation FX, which helps provide a better understanding of the interactions between FXa and its substrate, and the mechanism of the conformational changes involved in human coagulation.


Human coagulation Factor X Serine-protease domain Structural transition Molecular dynamics simulation 


  1. 1.
    Davie EW, Fujikawa K, Kisiel W (1991) The coagulation cascade: initiation, maintenance, and regulation. Biochemistry 30:10363–10370CrossRefGoogle Scholar
  2. 2.
    Mann KG, Nesheim ME, Church WR, Haley P, Krishnaswamy S (1990) Surface-dependent reactions of the vitamin K-dependent enzyme complexes. Blood 76:1–16Google Scholar
  3. 3.
    Caldwell SH, Hoffman M, Lisman T, Macik BG, Northup PG, Reddy KR, Tripodi A, Sanyal AJ (2006) Coagulation disorders and hemostasis in liver disease: pathophysiology and critical assessment of current management. Hepatology 44:1039–1046CrossRefGoogle Scholar
  4. 4.
    Kozek-Langenecker S (2007) Management of massive operative blood loss. Minerva Anestesiol 73:401–415Google Scholar
  5. 5.
    Soliman DE, Broadman LM (2006) Coagulation defects. Anesthesiol Clin 24:549–578, viiCrossRefGoogle Scholar
  6. 6.
    Telfer TP, Denson KW, Wright DR (1956) A new coagulation defect. Br J Haematol 2:308–316CrossRefGoogle Scholar
  7. 7.
    Graham JB, Barrow EM, Hougie C (1957) Stuart clotting defect. II. Genetic aspects of a new hemorrhagic state. J Clin Invest 36:497–503CrossRefGoogle Scholar
  8. 8.
    Bode W, Mayr I, Baumann U, Huber R, Stone SR, Hofsteenge J (1989) 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. EMBO J 8:3467–3475Google Scholar
  9. 9.
    Katz BA, Elrod K, Luong C, Rice MJ, Mackman RL, Sprengeler PA, Spencer J, Hataye J, Janc J, Link J, Litvak J, Rai R, Rice K, Sideris S, Verner E, Young W (2001) A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J Mol Biol 307:1451–1486CrossRefGoogle Scholar
  10. 10.
    Bode W, Turk D, Karshikov A (1992) The refined 1.9-A X-ray crystal structure of d-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. Protein Sci 1:426–471CrossRefGoogle Scholar
  11. 11.
    Katz BA, Elrod K, Verner E, Mackman RL, Luong C, Shrader WD, Sendzik M, Spencer JR, Sprengeler PA, Kolesnikov A, Tai VW, Hui HC, Breitenbucher JG, Allen D, Janc JW (2003) Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. J Mol Biol 329:93–120CrossRefGoogle Scholar
  12. 12.
    Katz BA, Mackman R, Luong C, Radika K, Martelli A, Sprengeler PA, Wang J, Chan H, Wong L (2000) Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator. Chem Biol 7:299–312CrossRefGoogle Scholar
  13. 13.
    Katz BA, Spencer JR, Elrod K, Luong C, Mackman RL, Rice M, Sprengeler PA, Allen D, Janc J (2002) Contribution of multicentered short hydrogen bond arrays to potency of active site-directed serine protease inhibitors. J Am Chem Soc 124:11657–11668CrossRefGoogle Scholar
  14. 14.
    Parker ET, Pohl J, Blackburn MN, Lollar P (1997) Subunit structure and function of porcine factor Xa-activated factor VIII. Biochemistry 36:9365–9373CrossRefGoogle Scholar
  15. 15.
    Padmanabhan K, Padmanabhan KP, Tulinsky A, Park CH, Bode W, Huber R, Blankenship DT, Cardin AD, Kisiel W (1993) Structure of human des(1–45) factor Xa at 2.2 A resolution. J Mol Biol 232:947–966CrossRefGoogle Scholar
  16. 16.
    Singh N, Briggs JM (2008) Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites. Biopolymer 89:1104–1113CrossRefGoogle Scholar
  17. 17.
    Wang JF, Wei DQ, Li L, Zheng SY, Li YX, Chou KC (2007) 3D structure modeling of cytochrome P450 2 C19 and its implication for personalized drug design. Biochem Biophys Res Commun 355:513–519CrossRefGoogle Scholar
  18. 18.
    Wang JF, Wei DQ, Lin Y, Wang YH, Du HL, Li YX, Chou KC (2007) Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem Biophys Res Commun 359:323–329CrossRefGoogle Scholar
  19. 19.
    Wang JF, Wei DQ, Chen C, Li Y, Chou KC (2008) Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Protein Peptide Lett 15:27–32CrossRefGoogle Scholar
  20. 20.
    Wang JF, Gong K, Wei DQ, Li YX, Chou KC (2009) Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one. Protein Eng Des Sel 22:349–355CrossRefGoogle Scholar
  21. 21.
    Wang JF, Wei DQ, Chou KC (2009) Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem Biophys Res Commun 388:413–417CrossRefGoogle Scholar
  22. 22.
    Zeng QK, Du HL, Wang JF, Wei DQ, Wang XN, Li YX, Lin Y (2009) Reversal of coenzyme specificity and improvement of catalytic efficiency of Pichia stipitis xylose reductase by rational site-directed mutagenesis. Biotechnol Lett 31:1025–1029CrossRefGoogle Scholar
  23. 23.
    Wang Y, Wei DQ, Wang JF (2010) Molecular dynamics studies on T1 lipase: insight into a double-flap mechanism. J Chem Inf Model 50:875–878CrossRefGoogle Scholar
  24. 24.
    Guo X, Wang JF, Zhu Y, Wei DQ (2010) Recent progress on computer-aided inhibitor design of H5N1 influenza A virus. Curr Comput Aided Drug Des 6:139–146CrossRefGoogle Scholar
  25. 25.
    Wang JF, Wei DQ (2009) Role of structural bioinformatics and traditional Chinese medicine databases in pharmacogenomics. Pharmacogenomics 10:1213–1215CrossRefGoogle Scholar
  26. 26.
    Wang JF, Chou KC (2010) Molecular modeling of cytochrome P450 and drug metabolism. Curr Drug Metab 11:342–346CrossRefGoogle Scholar
  27. 27.
    Wang JF, Chou KC (2010) Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics. Protein Eng Des Sel 23:663–666CrossRefGoogle Scholar
  28. 28.
    Li L, Wei DQ, Wang JF, Chou KC (2007) Computational studies of the binding mechanism of calmodulin with chrysin. Biochem Biophys Res Commun 358:1102–1107CrossRefGoogle Scholar
  29. 29.
    Wang JF, Wei DQ, Chou KC (2008) Drug candidates from traditional chinese medicines. Curr Top Med Chem 8:1656–1665CrossRefGoogle Scholar
  30. 30.
    Lian P, Wei DQ, Wang JF, Chou KC (2011) An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One 6:e18587CrossRefGoogle Scholar
  31. 31.
    Wang JF, Wei DQ, Chou KC (2008) Pharmacogenomics and personalized use of drugs. Curr Top Med Chem 8:1573–1579CrossRefGoogle Scholar
  32. 32.
    Gong K, Li L, Wang JF, Cheng F, Wei DQ, Chou KC (2009) Binding mechanism of H5N1 influenza virus neuraminidase with ligands and its implication for drug design. Med Chem 5:242–249CrossRefGoogle Scholar
  33. 33.
    Wang JF, Chou KC (2011) Insights from modeling the 3D structure of New Delhi metallo-β-lactamse and its binding interactions with antibiotic drugs. PLoS One 6:e18414CrossRefGoogle Scholar
  34. 34.
    Gu RX, Gu H, Xie ZY, Wang JF, Arias HR, Wei DQ, Chou KC (2009) Possible drug candidates for Alzheimer’s disease deduced from studying their binding interactions with alpha7 nicotinic acetylcholine receptor. Med Chem 5:250–262CrossRefGoogle Scholar
  35. 35.
    Wang JF, Yan JY, Wei DQ, Chou KC (2009) Binding of CYP2C9 with diverse drugs and its implications for metabolic mechanism. Med Chem 5:263–270CrossRefGoogle Scholar
  36. 36.
    Wang JF, Zhang CC, Chou KC, Wei DQ (2009) Structure of cytochrome p450s and personalized drug. Curr Med Chem 16:232–244CrossRefGoogle Scholar
  37. 37.
    Chen Q, Zhang T, Wang JF, Wei DQ (2011) Advances in human cytochrome P450 and personalized medicine. Curr Drug Metab 12:436–444CrossRefGoogle Scholar
  38. 38.
    Daura X, Haaksma E, van Gunsteren WF (2000) Factor Xa: simulation studies with an eye to inhibitor design. J Comput Aided Mol Des 14:507–529CrossRefGoogle Scholar
  39. 39.
    Venkateswarlu D, Perera L, Darden T, Pedersen LG (2002) Structure and dynamics of zymogen human blood coagulation factor X. Biophys J 82:1190–1206CrossRefGoogle Scholar
  40. 40.
    Corte JR, Fang T, Pinto DJ, Han W, Hu Z, Jiang XJ, Li YL, Gauuan JF, Hadden M, Orton D, Rendina AR, Luettgen JM, Wong PC, He K, Morin PE, Chang CH, Cheney DL, Knabb RM, Wexler RR, Lam PY (2008) Structure-activity relationships of anthranilamide-based factor Xa inhibitors containing piperidinone and pyridinone P4 moieties. Bioorg Med Chem Lett 18:2845–2849CrossRefGoogle Scholar
  41. 41.
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242CrossRefGoogle Scholar
  42. 42.
    Underwood MC, Zhong D, Mathur A, Heyduk T, Bajaj SP (2000) Thermodynamic linkage between the S1 stie, the Na + site, and the Ca2+ site in the protease domain of human coagulation factor xa. J Biol Chem 275:36876–36884CrossRefGoogle Scholar
  43. 43.
    Griffon N, Di Stasio E (2001) Thermodynamics of Na + binding to coagulation serine proteases. Biophys Chem 90:89–96CrossRefGoogle Scholar
  44. 44.
    Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718CrossRefGoogle Scholar
  45. 45.
    Scott WRP, Hüenenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Krueger P, van Gunsteren WF (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596–3607CrossRefGoogle Scholar
  46. 46.
    Aalten DM van, Bywater R, Findlay JB, Hendlich M, Hooft RW, Vriend G (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des 10:255–262Google Scholar
  47. 47.
    Matter H, Nazaré M, Güssregen S, Will DW, Schreuder H, Bauer A, Urmann M, Ritter K, Wagner M, Wehner V (2009) Evidence for C-Cl/C-Br…pi interactions as an important contribution to protein-ligand binding affinity. Angew Chem Int Edn Engl 48:2911–2916CrossRefGoogle Scholar
  48. 48.
    Wallnoefer HG, Fox T, Liedl KR, Tautermann CS (2010) Dispersion dominate halogen-π interactions: energies and locations of minima. Phys Chem Chem Phys 12:14941–14949CrossRefGoogle Scholar
  49. 49.
    Sreenivasan U, Axelsen PH (1992) Buried water in homologous serine proteases. Biochemistry 31:12785–12791CrossRefGoogle Scholar
  50. 50.
    Guvench O, Price DJ, Brooks CL III (2005) Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins 58:407–417CrossRefGoogle Scholar
  51. 51.
    Lesk AM, Fordham WD (1996) Conservation and variability in the structures of serine proteinases of the chymotrypsin family. J Mol Biol 258:501–537CrossRefGoogle Scholar
  52. 52.
    Wallnoefer HG, Handschuh S, Liedl KR, Fox T (2010) Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa. J Phys Chem B 114:7405–7412CrossRefGoogle Scholar
  53. 53.
    Miller CA, Gellman SH, Abbott NL, de Pablo JJ (2009) Association of helical beta-peptides and their aggregation behavior from the potential of mean force in explicit solvent. Biophys J 96:4349–4362CrossRefGoogle Scholar
  54. 54.
    Hlevnjak M, Zitkovic G, Zagrovic B (2010) Hydrophilicity matching: a potential prerequisite for the formation of protein-protein complexes in the cell. PLoS One 5:e11169CrossRefGoogle Scholar
  55. 55.
    Lee C, Ham SJ (2011) Characterizing amyloid-beta protein misfolding from molecular dynamics simulations with explicit water. J Comput Chem 32:349–355CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Jing-Fang Wang
    • 1
    • 3
    • 4
  • Pei Hao
    • 2
    • 3
  • Yi-Xue Li
    • 1
    • 3
  • Jian-Liang Dai
    • 4
  • Xuan Li
    • 2
    • 3
  1. 1.Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems BiomedicineShanghai Jiaotong UniversityShanghaiChina
  2. 2.Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
  3. 3.Shanghai Center for Bioinformation TechnologyShanghaiChina
  4. 4.School of Life SciencesFudan UniversityShanghaiChina

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