PROTEIN MODELING Protein storytelling through physics

被引:52
作者
Brini, Emiliano [1 ]
Simmerling, Carlos [1 ,2 ]
Dill, Ken [1 ,2 ,3 ]
机构
[1] SUNY Stony Brook, Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA
[2] SUNY Stony Brook, Dept Chem, Stony Brook, NY 11794 USA
[3] SUNY Stony Brook, Dept Phys & Astron, Stony Brook, NY 11794 USA
关键词
MOLECULAR-DYNAMICS SIMULATIONS; SOLVATION FREE-ENERGIES; SLOW-ONSET INHIBITION; FORCE-FIELD; MACROMOLECULAR ENERGY; NUCLEIC-ACIDS; HYDROGEN-BOND; WEB SERVER; PREDICTION; PEPTIDES;
D O I
10.1126/science.aaz3041
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Every protein has a story how it folds, what it binds, its biological actions, and how it misbehaves in aging or disease. Stories are often inferred from a protein's shape (i.e., its structure). But increasingly, stories are told using computational molecular physics (CMP). CMP is rooted in the principled physics of driving forces and reveals granular detail of conformational populations in space and time. Recent advances are accessing longer time scales, larger actions, and blind testing, enabling more of biology's stories to be told in the language of atomistic physics.
引用
收藏
页码:1056 / +
页数:9
相关论文
共 135 条
[41]   ENERGY FUNCTIONS FOR PEPTIDES AND PROTEINS .1. DERIVATION OF A CONSISTENT FORCE-FIELD INCLUDING HYDROGEN-BOND FROM AMIDE CRYSTALS [J].
HAGLER, AT ;
HULER, E ;
LIFSON, S .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1974, 96 (17) :5319-5327
[42]   Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent [J].
Hai Nguyen ;
Maier, James ;
Huang, He ;
Perrone, Victoria ;
Simmerling, Carlos .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2014, 136 (40) :13959-13962
[43]   OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins [J].
Harder, Edward ;
Damm, Wolfgang ;
Maple, Jon ;
Wu, Chuanjie ;
Reboul, Mark ;
Xiang, Jin Yu ;
Wang, Lingle ;
Lupyan, Dmitry ;
Dahlgren, Markus K. ;
Knight, Jennifer L. ;
Kaus, Joseph W. ;
Cerutti, David S. ;
Krilov, Goran ;
Jorgensen, William L. ;
Abel, Robert ;
Friesner, Richard A. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2016, 12 (01) :281-296
[44]   The Free Energy Landscape of Small Molecule Unbinding [J].
Huang, Danzhi ;
Caflisch, Amedeo .
PLOS COMPUTATIONAL BIOLOGY, 2011, 7 (02)
[45]  
Huang J, 2017, NAT METHODS, V14, P71, DOI [10.1038/NMETH.4067, 10.1038/nmeth.4067]
[46]   Weighted-ensemble Brownian dynamics simulations for protein association reactions [J].
Huber, GA ;
Kim, S .
BIOPHYSICAL JOURNAL, 1996, 70 (01) :97-110
[47]   Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity [J].
Huggins, David J. ;
Biggin, Philip C. ;
Damgen, Marc A. ;
Essex, Jonathan W. ;
Harris, Sarah A. ;
Henchman, Richard H. ;
Khalid, Syma ;
Kuzmanic, Antonija ;
Laughton, Charles A. ;
Michel, Julien ;
Mulholland, Adrian J. ;
Rosta, Edina ;
Sansom, Mark S. P. ;
van der Kamp, Marc W. .
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2019, 9 (03)
[48]   A multiscale coarse-graining method for biomolecular systems [J].
Izvekov, S ;
Voth, GA .
JOURNAL OF PHYSICAL CHEMISTRY B, 2005, 109 (07) :2469-2473
[49]  
Jarvis L. M., 2019, C EN, V97
[50]   Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis [J].
Jia, Xiwen ;
Lynch, Allyson ;
Huang, Yuheng ;
Danielson, Matthew ;
Lang'at, Immaculate ;
Milder, Alexander ;
Ruby, Aaron E. ;
Wang, Hao ;
Friedler, Sorelle A. ;
Norquist, Alexander J. ;
Schrier, Joshua .
NATURE, 2019, 573 (7773) :251-+