Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities.
ABSTRACT The serine protease α-thrombin is a dual-action protein that mediates the blood-clotting cascade. Thrombin alone is a procoagulant, cleaving fibrinogen to make the fibrin clot, but the thrombin-thrombomodulin (TM) complex initiates the anticoagulant pathway by cleaving protein C. A TM fragment consisting of only the fifth and sixth EGF-like domains (TM56) is sufficient to bind thrombin, but the presence of the fourth EGF-like domain (TM456) is critical to induce the anticoagulant activity of thrombin. Crystallography of the thrombin-TM456 complex revealed no significant structural changes in thrombin, suggesting that TM4 may only provide a scaffold for optimal alignment of protein C for its cleavage by thrombin. However, a variety of experimental data have suggested that the presence of TM4 may affect the dynamic properties of the active site loops. In the present work, we have used both conventional and accelerated molecular dynamics simulation to study the structural dynamic properties of thrombin, thrombin:TM56, and thrombin:TM456 across a broad range of time scales. Two distinct yet interrelated allosteric pathways are identified that mediate both the pro- and anticoagulant activities of thrombin. One allosteric pathway, which is present in both thrombin:TM56 and thrombin:TM456, directly links the TM5 domain to the thrombin active site. The other allosteric pathway, which is only present on slow time scales in the presence of the TM4 domain, involves an extended network of correlated motions linking the TM4 and TM5 domains and the active site loops of thrombin.
SourceAvailable from: Xianqiang Sun[Show abstract] [Hide abstract]
ABSTRACT: Experiments have revealed that in the beta(2) adrenergic receptor (beta(2)AR)-Gs protein complex the a subunit (G alpha s) of the Gs protein can adopt either an open conformation or a closed conformation. In the open conformation the Gs protein prefers to bind to the beta(2)AR, while in the closed conformation an uncoupling of the Gs protein from the beta(2)AR occurs. However, the mechanism that leads to such different behaviors of the Gs protein remains unclear. Here, we report results from microsecond molecular dynamics simulations and community network analysis of the beta(2)AR-Gs complex with G alpha s in the open and closed conformations. We observed that the complex is stabilized differently in the open and closed conformations. The community network analysis reveals that in the closed conformation there exists strong allosteric communication between the beta(2)AR and G beta gamma, mediated by G alpha s. We suggest that such high information flows are necessary for the Gs protein uncoupling from the beta(2)AR.The Journal of Physical Chemistry B 12/2014; 118(51). DOI:10.1021/jp506579a · 3.38 Impact Factor
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ABSTRACT: Allostery connects subtle changes in a protein's potential energy surface, induced by perturbations like ligand-binding, to significant changes in its function. Understanding this phenomenon and predicting its occurrence are major goals of current research in biophysics and molecular biology. In this paper we introduce a novel approach for studying complex structural transformations such as those typical for allostery. We show that the calculation and analysis of atomic elastic constants of a known allosterically regulated protein, lac repressor, highlights regions that are particularly prone to suffer structural deformation and are experimentally linked to allosteric function. The calculations are based on a high resolution, all-atom description of the protein. We also show that, for the present system, modifying the description of the system from an all-atom forcefield to an elastic network model yields qualitatively different results, indicating the importance of adequately describing the local environment surrounding the different parts of the protein. Copyright © 2015 Elsevier Inc. All rights reserved.Journal of Molecular Graphics and Modelling 02/2015; 57C. DOI:10.1016/j.jmgm.2015.01.013 · 2.02 Impact Factor
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ABSTRACT: Understanding how allosteric proteins respond to changes in their environment is a major goal of current biological research. We show that these responses can be quantified by analyzing protein energy networks using a method recently developed in our group. Based on this method, we introduce here a quantity named energetic coupling, which we show is able to discriminate allosterically active mutants of the lactose repressor (LacI) protein, and of the catabolite activator protein (CAP), a dynamically-driven allosteric protein. Our method assumes that allostery and signal transmission can be more accurately described as efficient energy propagation, and not as the more widely-used atomic motion correlations. We demonstrate the validity of this assumption by performing energy-propagation simulations. Finally, we present results from energy-propagation simulations performed on folded and fully-extended conformations of the postsynaptic density protein 95 (PSD-95). They show that the protein backbone provides a more efficient route for energy transfer, when compared to secondary or tertiary contacts. Based on this, we propose energy propagation through the backbone as a possible explanation for the observation that intrinsically disordered proteins can efficiently transmit signals while lacking a well-defined tertiary structure.The Journal of Physical Chemistry B 01/2015; 119(5). DOI:10.1021/jp509906m · 3.38 Impact Factor