Bridging from molecular simulation to biochemical networks

被引：39

作者：

Stein, Matthias

Gabdoulline, Razif R.

Wade, Rebecca C.

机构：

[1] EML Res, Mol & Cellular Modeling Grp, D-69118 Heidelberg, Germany

[2] Heidelberg Univ, BIOMS, Ctr Modeling & Simulat Biosci, D-69120 Heidelberg, Germany

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2007年 / 17卷 / 02期

关键词：

CHROMATOPHORE VESICLES; DYNAMICS SIMULATIONS; SYSTEMS BIOLOGY; HISTONE TAILS; PROTEIN; MODEL; CELL; MECHANISMS; PREDICTION; KINETICS;

D O I：

10.1016/j.sbi.2007.03.014

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

How can we make the connection between the three-dimensional structures of individual proteins and understanding how complex biological systems involving many proteins work? The modelling and simulation of protein structures can help to answer this question for systems ranging from multi macromolecular complexes to organelles and cells. On one hand, multiscale modelling and simulation techniques are advancing to permit the spatial and temporal properties of large systems to be simulated using atomic-detail structures. On the other hand, the estimation of kinetic parameters for the mathematical modelling of biochemical pathways using protein structure information provides a basis for iterative manipulation of biochemical pathways guided by protein structure. Recent advances include the structural modelling of protein complexes on the genomic level, novel coarse-graining strategies to increase the size of the system and the time span that can be simulated, and comparative molecular field analyses to estimate enzyme kinetic parameters.

引用

收藏

页码：166 / 172

页数：7

相关论文

共 52 条

[31] Molecular dynamics and protein function [J].

Karplus, M ;

Kuriyan, J .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (19) :6679-6685

[32]

Klipp E, 2005, SYSTEMS BIOLOGY IN PRACTICE: CONCEPTS, IMPLEMENTATION AND APPLICATION, P1, DOI 10.1002/3527603603

[33] Space as the final frontier in stochastic simulations of biological systems [J].

Lemerle, C ;

Di Ventura, B ;

Serrano, L .

FEBS LETTERS, 2005, 579 (08) :1789-1794

[34] Atomically detailed simulations of concentrated protein solutions: The effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems [J].

McGuffee, Sean R. ;

Elcock, Adrian H. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (37) :12098-12110

[35] Reaction diffusion modeling of calcium dynamics with realistic ER geometry [J].

Means, Shawn ;

Smith, Alexander J. ;

Shepherd, Jason ;

Shadid, John ;

Fowler, John ;

Wojcikiewicz, Richard J. H. ;

Mazel, Tomas ;

Smith, Gregory D. ;

Wilson, Bridget S. .

BIOPHYSICAL JOURNAL, 2006, 91 (02) :537-557

[36] Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway [J].

Orton, RJ ;

Sturm, OE ;

Vyshemirsky, V ;

Calder, M ;

Gilbert, DR ;

Kolch, W .

BIOCHEMICAL JOURNAL, 2005, 392 :249-261

[37] Multiscale modeling of protein transport in silicon membrane nanochannels. Part 1. Derivation of molecular parameters from computer simulations [J].

Pricl, Sabrina ;

Ferrone, Marco ;

Fermeglia, Maurizio ;

Amato, Francesco ;

Cosentino, Carlo ;

Cheng, Mark Ming-Cheng ;

Walczak, Robert ;

Ferrari, Mauro .

BIOMEDICAL MICRODEVICES, 2006, 8 (04) :277-290

[38] Simulating movement of tRNA into the ribosome during decoding [J].

Sanbonmatsu, KY ;

Joseph, S ;

Tung, CS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (44) :15854-15859

[39] BRENDA, the enzyme database: updates and major new developments [J].

Schomburg, I ;

Chang, A ;

Ebeling, C ;

Gremse, M ;

Heldt, C ;

Huhn, G ;

Schomburg, D .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D431-D433

[40] Coarse grained protein-lipid model with application to lipoprotein particles [J].

Shih, AY ;

Arkhipov, A ;

Freddolino, PL ;

Schulten, K .

JOURNAL OF PHYSICAL CHEMISTRY B, 2006, 110 (08) :3674-3684

← 1 2 3 4 5 6 →