Dynamic properties of the native free antithrombin from molecular dynamics simulations: computational evidence for solvent- exposed Arg393 side chain

Abstract

While antithrombin (AT) has small basal inhibitory activity, it reaches its full inhibitory potential against activated blood coagulation factors, FXa, FIXa, and FIIa (thrombin), via an allosteric and/or template (bridging) mechanism by the action of heparin, heparan sulfate, or heparin-mimetic pentasaccharides (PS). From the numerous X-ray structures available for different conformational states of AT, only indirect and incomplete conclusions can be drawn on the inherently dynamic properties of AT. As a typical example, the basal inhibitory activity of AT cannot be interpreted on the basis of “non-activated” free antithrombin X-ray structures since the Arg393 side chain, playing crucial role in antithrombin-proteinase interaction, is not exposed. In order to reveal the intrinsic dynamic properties and the reason of basal inhibitory activity of antithrombin, 2 μs molecular dynamics simulations were carried out on its native free-forms. It was shown from the simulation trajectories that the reactive center loop which is functioning as “bait” for proteases, even without any biasing potential can populate conformational state in which the Arg393 side chain is solvent exposed. It is revealed from the trajectory analysis that the peptide sequences correspond to the helix D extension, and new helix P formation can be featured with especially large root-mean-square fluctuations. Mutual information analyses of the trajectory showed remarkable (generalized) correlation between those regions of antithrombin which changed their conformations as the consequence of AT–PS complex formation. This suggests that allosteric information propagation pathways are present even in the non-activated native form of AT.

Keywords:

• antithrombin
• molecular dynamics simulation
• serpin structure
• reactive center loop
• generalized correlation
• allostery
• fluctuation
• principal component analysis

Acknowledgments

We are thankful to Dr Arpad Somogyi (CCIC Mass Spectrometry and Proteomics Facility, Ohio State University, Columbus, OH) for his useful comments and suggestions.

Additional information

Funding

This work was supported by the Hungarian Scientific Research Fund (OTKA K-106294, K-105459, PD101120), NIIF-1057, TÁMOP-4.2.2.A-11/1/KONV-2012-0045, TÁMOP 4.2.4.A/2-11-1-2012-0001, and TAMOP-4.2.2.C-11/1/KONV-2012-0010.1.