Whole-Cell Models and Simulations in Molecular Detail

被引:42
作者
Feig, Michael [1 ,2 ]
Sugita, Yuji [2 ,3 ]
机构
[1] Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA
[2] RIKEN Ctr Biosyst Dynam Res, Lab Biomol Funct Simulat, Kobe, Hyogo 6500047, Japan
[3] RIKEN Cluster Pioneering Res, Theoret Mol Sci Lab, Wako, Saitama 3510198, Japan
来源
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 35 | 2019年 / 35卷
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
crowding; systems biology; protein structure; molecular dynamics simulation; network models; PROTEIN-STRUCTURE DETERMINATION; BROWNIAN DYNAMICS SIMULATIONS; ENHANCED SAMPLING ALGORITHMS; LIQUID PHASE-SEPARATION; FORCE-FIELD; HYDRODYNAMIC INTERACTIONS; MEMBRANE-PROTEINS; BIOLOGICAL-MEMBRANES; DISORDERED PROTEINS; HYBRID-PARALLEL;
D O I
10.1146/annurev-cellbio-100617-062542
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Comprehensive data about the composition and structure of cellular components have enabled the construction of quantitative whole-cell models. While kinetic network-type models have been established, it is also becoming possible to build physical, molecular-level models of cellular environments. This review outlines challenges in constructing and simulating such models and discusses near- and long-term opportunities for developing physical whole-cell models that can connect molecular structure with biological function.
引用
收藏
页码:191 / 211
页数:21
相关论文
共 50 条
  • [31] Pharmacophore Models Derived From Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study
    Wieder, Marcus
    Perricone, Ugo
    Seidel, Thomas
    Langer, Thieny
    NATURAL PRODUCT COMMUNICATIONS, 2016, 11 (10) : 1499 - 1504
  • [32] Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off-switchable whole-cell cancer diagnostics
    Putri, Athika Darumas
    Murti, Bayu Tri
    Kanchi, Suvardhan
    Sabela, Myalowenkosi I.
    Bisetty, Krishna
    Tiwari, Ashutosh
    Inamuddin
    Asiri, Abdullah M.
    SCIENTIFIC REPORTS, 2019, 9 (1)
  • [34] FFLUX molecular simulations driven by atomic Gaussian process regression models
    Manchev, Yulian T.
    Popelier, Paul L. A.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2024, 45 (15) : 1235 - 1246
  • [35] Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step
    Jung, Jaewoon
    Kobayashi, Chigusa
    Sugita, Yuji
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (01) : 84 - 94
  • [36] First order melting transitions of highly ordered dipalmitoyl phosphatidylcholine gel phase membranes in molecular dynamics simulations with atomistic detail
    Schubert, Thomas
    Schneck, Emanuel
    Tanaka, Motomu
    JOURNAL OF CHEMICAL PHYSICS, 2011, 135 (05)
  • [37] Whole-cell biosensor engineering based on the transcription factor XylS/Pm for sensitive detection of PCB intermediate chlorobenzoic acid
    Xian, Yufan
    Zhang, Faying
    Wang, Meixing
    Zhao, Xiang
    Sun, Xuting
    Lu, Zhenghui
    Zhang, Guimin
    BIOCHEMICAL ENGINEERING JOURNAL, 2024, 202
  • [38] SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations
    Yu, Isseki
    Mori, Takaharu
    Matsuoka, Daisuke
    Surblys, Donatas
    Sugita, Yuji
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2024, 45 (08) : 498 - 505
  • [39] Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface
    Ensign, Daniel L.
    Webb, Lauren J.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 (12) : 3511 - 3524
  • [40] Bending characteristics of carbon nanotubes: Micropolar elasticity models and molecular dynamics simulations
    Izadi, Razie
    Tuna, Meral
    Trovalusci, Patrizia
    Fantuzzi, Nicholas
    MECHANICS OF ADVANCED MATERIALS AND STRUCTURES, 2021, 30 (01) : 189 - 206