Study of Conformation of Actin Monomer by Molecular Mechanics Calculation

• Published in: Nihon Kikai Gakkai ronbunshū. A Vol. 60; no. 580; pp. 2915 - 2920
• Main Authors: Nakamachi, Eiji, Iwamoto, Masami
• Format: Journal Article
• Language: English; Japanese
• Published: The Japan Society of Mechanical Engineers 1994
• Subjects: Calculations; Clarification; Computer simulation; Continuum mechanics; G-Actin; Hydrolysis; Mechanical properties; Minimum-Energy Conformation; Molecular dynamics; Molecular Mechanics; Molecular structure; Molecules; Numerical Analysis; Optimization; Proteins
• ISSN: 0387-5008; 1884-8338
• DOI: 10.1299/kikaia.60.2915

In this paper, the 3-D molecular structure of actin monomer (G-actin) is studied by using the molecular mechanics analysis code, AMBER, which was developed by Kollman et al. . Actin and myosin molecules come together to construct the actomyosin system, which generates the motility assay to induce the whole muscle contraction. Several constitutive models for the muscle material exist under the theoretical basis of continuum mechanics, but the contraction process model is still incomplete. Therefore, we focus the investigation on the clarification of the contraction mechanism at the microlevel, because, in this decade there has been great progress in computational chemistry and protein engineering at the molecular level. The conformation of the actin molecule in vivo should take the optimum structure to generate the relative sliding between actin and myosin filaments under ATPase hydrolysis. At this moment the molecular structure of actin may be optimized in the molecular mechanics sense. We employ the molecular structure data of G-actin determined experimentally by Holmes et al. in 1990. The minimum-energy conformations of G-actin in four cases, e. g., with ATP or without ATP, and proK-actin-cut off between Met-47 and Gly-48- or normal actin, were determined by the steepest-descent method and the conjugate-gradient method in the molecular mechanics calculation. We investigate the differences of the conformation and potential energies among these four cases to characterize the atom structure and mechanical properties.