A multiscale modeling approach for biomolecular systems

被引:2
|
作者
Bowling, Alan [1 ]
Haghshenas-Jaryani, Mahdi [1 ]
机构
[1] Univ Texas Arlington, Dept Mech & Aerosp Engn, Arlington, TX 76019 USA
基金
美国国家科学基金会;
关键词
Multibody; Dynamics; Motor protein; Multiscale; Modeling; Myosin V; Contact; MOLECULAR-DYNAMICS SIMULATION; MOTOR PROTEINS; KINETIC-MODEL; CONFORMATIONAL DYNAMICS; ENERGY TRANSDUCTION; BROWNIAN DYNAMICS; STEPPING KINETICS; STOCHASTIC-MODEL; ATP HYDROLYSIS; KINESIN;
D O I
10.1007/s11044-014-9431-x
中图分类号
O3 [力学];
学科分类号
08 ; 0801 ;
摘要
This paper presents a new multiscale molecular dynamic model for investigating the effects of external interactions, such as contact and impact, during stepping and docking of motor proteins and other biomolecular systems. The model retains the mass properties ensuring that the result satisfies Newton's second law. This idea is presented using a simple particle model to facilitate discussion of the rigid body model; however, the particle model does provide insights into particle dynamics at the nanoscale. The resulting three-dimensional model predicts a significant decrease in the effect of the random forces associated with Brownian motion. This conclusion runs contrary to the widely accepted notion that the motor protein's movements are primarily the result of thermal effects. This work focuses on the mechanical aspects of protein locomotion; the effect ATP hydrolysis is estimated as internal forces acting on the mechanical model. In addition, the proposed model can be numerically integrated in a reasonable amount of time. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of myosin V.
引用
收藏
页码:333 / 365
页数:33
相关论文
共 50 条
  • [1] A multiscale modeling approach for biomolecular systems
    Alan Bowling
    Mahdi Haghshenas-Jaryani
    [J]. Multibody System Dynamics, 2015, 33 : 333 - 365
  • [2] Multiscale modeling of biomolecular systems
    Bennun, Sandra V.
    Dickey, Allison N.
    Faller, Roland
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2006, 231
  • [3] Multiscale modeling of biomolecular systems: in serial and in parallel
    Ayton, Gary S.
    Noid, Will G.
    Voth, Gregory A.
    [J]. CURRENT OPINION IN STRUCTURAL BIOLOGY, 2007, 17 (02) : 192 - 198
  • [4] The multiscale challenge for biomolecular systems: coarse-grained modeling
    Chu, J. -W.
    Izvekov, S.
    Voth, G. A.
    [J]. MOLECULAR SIMULATION, 2006, 32 (3-4) : 211 - 218
  • [5] Multiscale modeling of the nanomechanics of biomolecular filaments
    Dima, Ruxandra
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012, 244
  • [6] Multiscale theory and simulation of biomolecular systems
    Voth, Gregory A.
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2010, 240
  • [7] Emerging methods for multiscale simulation of biomolecular systems
    Chu, J. -W.
    Ayton, G. S.
    Izvekov, S.
    Voth, G. A.
    [J]. MOLECULAR PHYSICS, 2007, 105 (2-3) : 167 - 175
  • [8] Overcoming the Multiscale Simulation Challenge for Biomolecular Systems
    Voth, G.
    [J]. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2019, 48 : S33 - S33
  • [10] MODELING SOLVENT IN BIOMOLECULAR SYSTEMS
    SMITH, PE
    PETTITT, BM
    [J]. JOURNAL OF PHYSICAL CHEMISTRY, 1994, 98 (39): : 9700 - 9711