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Simulations suggest double sodium binding induces unexpected conformational changes in thrombin

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Abstract

Thrombin is a Na\(^+\)-activated serine protease existing in two forms targeted to procoagulant and anticoagulant activities, respectively. There is one Na\(^+\)-binding site that has been the focus of the study of the thrombin. However, molecular dynamics (MD) simulations suggest that there might be actually two Na\(^+\)-binding sites in thrombin and that Na\(^+\) ions can even bind to two sites simultaneously. In this study, we performed 12 independent 2-µs all-atom MD simulations for the wild-type (WT) thrombin and we studied the effects of the different Na\(^+\) binding modes on thrombin. From the root-mean-square fluctuations (RMSF) for the \(\alpha\)-carbons, we see that the atomic fluctuations mainly change in the 60s, 170s, and 220s loops, and the connection (residue 167 to 170). The correlation matrices for different binding modes suggest regions that may play an important role in thrombin’s allosteric response and provide us a possible allosteric pathway for the sodium binding. Amorim-Hennig (AH) clustering tells us how the structure of the regions of interest changes on sodium binding. Principal component analysis (PCA) shows us how the different regions of thrombin change conformation together with sodium binding. Solvent-accessible surface area (SASA) exposes the conformational change in exosite I and catalytic triad. Finally, we argue that the double binding mode might be an inactive mode and that the kinetic scheme for the Na\(^+\) binding to thrombin might be a multiple-step mechanism rather than a 2-step mechanism.

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Acknowledgements

The authors wish to acknowledge the support of the Wake Forest Baptist Comprehensive Cancer Center Crystallography & Computational Biosciences Shared Resource, supported by the National Cancer Institute’s Cancer Center Support Grant award number P30CA012197. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute. Some computations were performed on the Wake Forest University DEAC Cluster, a centrally managed resource with support provided in part by the University. FRS would also like to thank the Scott Family for the Scott Family Fellowship.

Funding

Partial support by NIH P30CA012197, Scott Family Fellowship.

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Authors and Affiliations

  1. Department of Physics, Wake Forest University, Winston-Salem, 27106, NC, USA

    Dizhou Wu & Freddie R. Salsbury Jr

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  1. Dizhou Wu
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  2. Freddie R. Salsbury Jr
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Contributions

DW performed the calculations, FRS oversaw the project, and DW and FRS conceived of the project and developed the analyses.

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Correspondence to Freddie R. Salsbury Jr.

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The authors declare no competing interests.

Supplementary Information

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Supplementary information

Supplementary information

The following format should be used: Supporting Information Available: [Sodium ion coordinated by TYR184 and five water molecules; RMSF with standard errors for unbound, double binding, outer binding, and inner binding, respectively; IMWKRescaled clustering visualization for the \(\gamma\) loop; IMWKRescaled clustering visualization for the catalytic triad; Time series plots of the alpha carbons’ root-mean-square deviation (RMSD) referring to the initial structure of the thrombin; The probability of the closest mean distance between Na\(^+\) ions and the 220s loop; Sodium ion coordinated by O\(_1\)-O\(_5\); Correlation coefficients for Figure 4e–g.]

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Wu, D., Salsbury, F.R. Simulations suggest double sodium binding induces unexpected conformational changes in thrombin. J Mol Model 28, 120 (2022). https://doi.org/10.1007/s00894-022-05076-0

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