title: Na+Binding Is Ineffective in Forming a Primary Substrate Pocket of Thrombin.
abstract: Thrombin is a serine protease involved in the blood coagulation reaction, and it shows maximum enzymatic activity in the presence of Na+. It has been supposed that Na+binding promotes conversion from the inactive form, with a collapsed primary substrate pocket (S1 pocket), to the active form, with a properly formed S1 pocket. However, the evidence supporting this activation mechanism was derived from the X-ray crystallographic structures solved under nonphysiological conditions and using thrombin mutants; thus, it still remains elusive whether the activation mechanism is actually attributed to Na+binding. To address the problem, we employed all-atom molecular dynamics simulations for both active and inactive forms of thrombin in the presence and absence of Na+binding and examined the effect of Na+binding on S1-pocket formation. In contrast to the conventional supposition, we revealed that Na+binding does not prevent S1-pocket collapse virtually, but rather, the bound Na+can move to the S1 pocket, thus blocking substrate access directly. Additionally, it was clarified that Na+binding does not promote S1-pocket formation. According to these insights, we concluded that Na+binding is irrelevant to the interconversion between the inactive and active forms of thrombin.
authors: Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.|Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan.
authors: Ikuo
authors: I
authors: Kurisaki
authors: Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.|Core Research for Evolutional Science and Technology, Japan Science and Technology Agency , Honmachi, Kawaguchi 332-0012, Japan.
authors: Masataka
authors: M
authors: Nagaoka
mesh_terms: D001665:Binding Sites; D056004:Molecular Dynamics Simulation; D055550:Protein Stability; D012964:Sodium / Q000737:chemistry* / Q000378:metabolism; D013379:Substrate Specificity; D013917:Thrombin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012964:Sodium; D013917:Thrombin