Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization

被引：6

作者：

Aronica, Pietro G. A. ^{[1
]}

Fox, Stephen J. ^{[1
]}

Verma, Chandra S. ^{[1
,2
,3
]}

机构：

[1] Bioinformat Inst A STAR, 30 Biopolis St,07-01 Matrix, Singapore 138671, Singapore

[2] Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr, Singapore 117558, Singapore

[3] Nanyang Technol Univ, Sch Biol Sci, 60 Nanyang Dr, Singapore 637551, Singapore

来源：

ACS OMEGA | 2018年 / 3卷 / 04期

关键词：

ATOMIC CHARGES; FORCE-FIELD; MOLECULAR-DYNAMICS; LIGAND-BINDING; FREE-ENERGIES; SIDE-CHAIN; PROTEIN; FF99SB; MODEL; WATER;

D O I：

10.1021/acsomega.8b00438

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new species. As there are many variables in the charge derivation process, an investigation was devised to compare different approaches and determine their effect on simulations. This was done with the purpose to identify the methods which produced results compatible with the existing parameters. It was found in this study that all analyzed charge derivation methods reproduce with sufficient accuracy the literature values and can be used with confidence when parameterizing novel species.

引用

页码：4664 / 4673

页数：10

共 42 条

[1] A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL [J].

BAYLY, CI ;

CIEPLAK, P ;

CORNELL, WD ;

KOLLMAN, PA .

JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (40) :10269-10280

[2] GROMACS - A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION [J].

BERENDSEN, HJC ;

VANDERSPOEL, D ;

VANDRUNEN, R .

COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) :43-56

[3]

Bowen J.P., 1991, REV COMPUTATIONAL CH, V2, P81, DOI DOI 10.1002/9780470125793.CH3

[4] CHARMM: The Biomolecular Simulation Program [J].

Brooks, B. R. ;

Brooks, C. L., III ;

Mackerell, A. D., Jr. ;

Nilsson, L. ;

Petrella, R. J. ;

Roux, B. ;

Won, Y. ;

Archontis, G. ;

Bartels, C. ;

Boresch, S. ;

Caflisch, A. ;

Caves, L. ;

Cui, Q. ;

Dinner, A. R. ;

Feig, M. ;

Fischer, S. ;

Gao, J. ;

Hodoscek, M. ;

Im, W. ;

Kuczera, K. ;

Lazaridis, T. ;

Ma, J. ;

Ovchinnikov, V. ;

Paci, E. ;

Pastor, R. W. ;

Post, C. B. ;

Pu, J. Z. ;

Schaefer, M. ;

Tidor, B. ;

Venable, R. M. ;

Woodcock, H. L. ;

Wu, X. ;

Yang, W. ;

York, D. M. ;

Karplus, M. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (10) :1545-1614

[5]

Case DAD., 2017, AMBER 2017 Reference Manual

[6] APPLICATION OF THE MULTIMOLECULE AND MULTICONFORMATIONAL RESP METHODOLOGY TO BIOPOLYMERS - CHARGE DERIVATION FOR DNA, RNA, AND PROTEINS [J].

CIEPLAK, P ;

CORNELL, WD ;

BAYLY, C ;

KOLLMAN, PA .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (11) :1357-1377

[7] APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN-BOND ENERGIES, AND FREE-ENERGIES OF SOLVATION [J].

CORNELL, WD ;

CIEPLAK, P ;

BAYLY, CI ;

KOLLMAN, PA .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (21) :9620-9631

[8] The R.ED. tools: advances in RESP and ESP charge derivation and force field library building [J].

Dupradeau, Francois-Yves ;

Pigache, Adrien ;

Zaffran, Thomas ;

Savineau, Corentin ;

Lelong, Rodolphe ;

Grivel, Nicolas ;

Lelong, Dimitri ;

Rosanski, Wilfried ;

Cieplak, Piotr .

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2010, 12 (28) :7821-7839

[9] NATURAL HYBRID ORBITALS [J].

FOSTER, JP ;

WEINHOLD, F .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1980, 102 (24) :7211-7218

[10] The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities [J].

Genheden, Samuel ;

Ryde, Ulf .

EXPERT OPINION ON DRUG DISCOVERY, 2015, 10 (05) :449-461

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