Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

被引:131
作者
Monti, Susanna [1 ]
Corozzi, Alessandro [2 ]
Fristrup, Peter [2 ]
Joshi, Kaushik L. [3 ]
Shin, Yun Kyung [3 ]
Oelschlaeger, Peter [4 ]
van Duin, Adri C. T. [3 ]
Barone, Vincenzo [5 ]
机构
[1] UOS Pisa, Inst Chem Organometall Cpds, CNR, Area Ric, I-56124 Pisa, Italy
[2] Tech Univ Denmark, Dept Chem, DK-2800 Lyngby, Denmark
[3] Penn State Univ, Dept Mech & Nucl Engn, University Pk, PA 16802 USA
[4] Western Univ Hlth Sci, Coll Pharm, Dept Pharmaceut Sci, Pomona, CA 91766 USA
[5] Scuola Normale Super Pisa, I-56126 Pisa, Italy
关键词
METALLO-BETA-LACTAMASES; ELASTIC BAND METHOD; DENSITY-FUNCTIONAL THEORY; MINIMUM-ENERGY PATHS; MOLECULAR-DYNAMICS; AB-INITIO; POTENTIAL FUNCTIONS; PROTON-TRANSFER; GAS-PHASE; THERMAL-DECOMPOSITION;
D O I
10.1039/c3cp51931g
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained.
引用
收藏
页码:15062 / 15077
页数:16
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