Structure and behavior of human α-thrombin upon ligand recognition: thermodynamic and molecular dynamics studies

• Published in: PloS one Vol. 6; no. 9; p. e24735
• Main Authors: Silva, Vivian de Almeira, Cargnelutti, Maria Thereza, Giesel, Guilherme M, Palmieri, Leonardo C, Monteiro, Robson Q, Verli, Hugo, Lima, Luis Mauricio T R
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 14.09.2011; Public Library of Science (PLoS)
• Subjects: Amino Acid Chloromethyl Ketones - chemistry; Amino Acid Chloromethyl Ketones - metabolism; Binding Sites; Biochemistry; Biology; Catalysis; Chloromethyl ketone; Circular dichroism; Coagulation; Computer Science; Conformation; Crystal structure; Crystallography; Dichroism; Dynamic structural analysis; Enzymes; Human behavior; Humans; Ligands; Molecular dynamics; Molecular Dynamics Simulation; Molecular structure; Molecular weight; Pharmacy; Protein structure; Proteinase; Proteinase inhibitors; Proteins; Recognition; Scattering, Small Angle; Secondary structure; Sensors; Serine; Serine proteinase; Small angle X ray scattering; Studies; Thermodynamics; Thrombin; Thrombin - chemistry; Thrombin - metabolism; X ray scattering; X-Rays; Brazil; Rio Grande do Sul Brazil; Rio de Janeiro Brazil
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0024735

Thrombin is a serine proteinase that plays a fundamental role in coagulation. In this study, we address the effects of ligand site recognition by alpha-thrombin on conformation and energetics in solution. Active site occupation induces large changes in secondary structure content in thrombin as shown by circular dichroism. Thrombin-D-Phe-Pro-Arg-chloromethyl ketone (PPACK) exhibits enhanced equilibrium and kinetic stability compared to free thrombin, whose difference is rooted in the unfolding step. Small-angle X-ray scattering (SAXS) measurements in solution reveal an overall similarity in the molecular envelope of thrombin and thrombin-PPACK, which differs from the crystal structure of thrombin. Molecular dynamics simulations performed with thrombin lead to different conformations than the one observed in the crystal structure. These data shed light on the diversity of thrombin conformers not previously observed in crystal structures with distinguished catalytic and conformational behaviors, which might have direct implications on novel strategies to design direct thrombin inhibitors.