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

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Abstract

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.

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Acknowledgments

This work was supported by the grants from the National Basic Research Program of China (973 Program, No. 2011CB910204 and 2012CB316501), Research Program of CAS (KSCX2-EW-R-04), National Natural Science Foundation of China (No. 30900272), Shanghai Natural Science Foundation (No. 10ZR1421500), China Postdoctoral Science Foundation (No. 20110490068), and in part by Shanghai Pujiang Scholarship Program (No. 10PJ1408000). The authors gratefully acknowledge the support of SA-SIBS scholarship program.

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Authors and Affiliations

  1. Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, 200240, China

    Jing-Fang Wang & Yi-Xue Li

  2. Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Pei Hao & Xuan Li

  3. Shanghai Center for Bioinformation Technology, Shanghai, 200235, China

    Jing-Fang Wang, Pei Hao, Yi-Xue Li & Xuan Li

  4. School of Life Sciences, Fudan University, Shanghai, 200433, China

    Jing-Fang Wang & Jian-Liang Dai

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  1. Jing-Fang Wang
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Correspondence to Jing-Fang Wang.

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Wang, JF., Hao, P., Li, YX. et al. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 18, 2717–2725 (2012). https://doi.org/10.1007/s00894-011-1295-x

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  • DOI: https://doi.org/10.1007/s00894-011-1295-x

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