Abstract
Binding of platelet receptor glycoprotein Ibα (GPIbα) to the A1 domain of von Willebrand factor (vWF) is a critical step in both physiologic hemostasis and pathologic thrombosis, for initiating platelet adhesion to subendothelium of blood vessels at sites of vascular injury. Gain-of-function mutations in GPIbα contribute to an abnormally high-affinity binding of platelets to vWF and can lead to thrombosis, an accurate complication causing heart attack and stroke. Of various antithrombotic monoclonal antibodies (mAbs) targeting human GPIbα, 6B4 is a potent one to inhibit the interaction between GPIbα and vWF-A1 under static and flow conditions. Mapping paratope to epitope with mutagenesis experiments, a traditional route in researches of these antithrombotic mAbs, is usually expensive and time-consuming. Here, we suggested a novel computational procedure, which combines with homology modeling, rigid body docking, free and steered molecular dynamics (MD) simulations, to identify key paratope residues on 6B4 and their partners on GPIbα, with hypothesis that the stable hydrogen bonds and salt bridges are the important linkers between paratope and epitope residues. Based on a best constructed model of 6B4 bound with GPIbα, the survival ratios and rupture times of all detected hydrogen bonds and salt bridges in binding site were examined via free and steered MD simulations and regarded as indices of thermal and mechanical stabilizations of the bonds, respectively. Five principal paratope residues with their partners were predicted with their high survival ratios and/or long rupture times of involved hydrogen bonds, or with their hydrogen bond stabilization indices ranked in top 5. Exciting, the present results were in good agreement with previous mutagenesis experiment data, meaning a wide application prospect of our novel computational procedure on researches of molecular of basis of ligand-receptor interactions, various antithrombotic mAbs and other antibodies as well as theoretically design of biomolecular drugs.
Highlights
As a crucial step in a cascade of adhesion and signaling events in physiological hemostatic process, blood platelet adhesion to subendothelium of injured blood vessels is initiated by interaction of platelet glycoprotein Iba (GPIba) with its ligand von Willebrand factor [1]
Less information of paratope residues and their partners are provided by Docking results Through homology modeling, we built a model of 6B4-ScFv (Fig. 2 A), in which six complementarity determining regions (CDRs), distributed on the top of both lightand heavy- chains, will contribute to binding of 6B4 to GPIba
With PSAIA software [33], we found that, 29 residues on GPIba were involved in 57 interactions of von Willebrand factor (vWF)-A1 and GPIba
Summary
As a crucial step in a cascade of adhesion and signaling events in physiological hemostatic process, blood platelet adhesion to subendothelium of injured blood vessels is initiated by interaction of platelet glycoprotein Iba (GPIba) with its ligand von Willebrand factor (vWF) [1]. Under pathological conditions, this interaction can lead to thrombosis, an accurate complication causing heart attack and stroke [2]. The resolved crystal structure of globular N-terminal domain of GPIba is characterized by eight leucine-rich repeats (LRRs), a protruding flexible loop b-switch and a b-hairpin on the bottom [5]. Antibody AK2, 24G10 and 6B4 can occupy completely the binding site of vWF-A1 domain on GPIba [11,12], whereas SZ-123 and SZ-125 compete with each other in targeting A3 domain of vWF [13]
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