GLYCAM06: A generalizable biomolecular force field. Carbohydrates

Journal of Computational Chemistry - Tập 29 Số 4 - Trang 622-655 - 2008
Karl N. Kirschner1, Austin B. Yongye1, Sarah M. Tschampel1, Jorge González‐Outeiriño1, Charlisa R. Daniels1, B. Lachele Foley1, Robert J. Woods1
1Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602

Tóm tắt

AbstractA new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small‐molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both α‐ and β‐anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas‐phase properties of an array of small test molecules, condensed‐phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Từ khóa


Tài liệu tham khảo

10.1074/jbc.M511097200

10.1073/pnas.94.26.14683

10.1146/annurev.biochem.73.011303.074043

10.1128/JVI.76.14.7293-7305.2002

10.1093/glycob/10.3.329

10.1074/jbc.M500119200

10.1093/glycob/3.2.97

10.1021/cr940283b

10.1021/cr990343j

10.1074/jbc.M109919200

10.1021/bi0261387

10.1016/j.sbi.2003.08.001

10.1002/bip.10188

10.1016/S0006-3495(02)75610-5

10.1021/cr990368i

10.1021/bi00241a003

10.1021/bk-2006-0930.ch013

10.1016/0008-6215(90)80041-Z

10.1021/jo00391a036

10.1016/j.carres.2004.12.034

10.1021/j100011a061

10.1016/j.carres.2003.11.024

10.1016/S0008-6215(98)00305-X

10.1073/pnas.191362798

10.1002/jcc.10405

10.1002/jcc.540070216

10.1093/glycob/cwg031

10.1139/v06-036

Umemura M., 2005, J Mol Struct (THEOCHEM), 130, 1, 10.1016/j.theochem.2005.05.034

10.1021/ja9835180

10.1016/S0166-1280(00)00487-5

Woods R. J., 1998, Eur J Biochem, 158, 372, 10.1046/j.1432-1327.1998.2580372.x

10.1074/jbc.M507643200

10.1002/prot.10428

10.1073/pnas.0602815103

10.1021/ja061216p

10.1002/prot.10590

10.1074/jbc.M403421200

10.1107/S0907444901011957

10.1063/1.445869

10.1016/0022-2860(94)87017-9

10.1016/S0166-1280(97)00149-8

10.1021/ja0496266

10.1021/jp045171v

Chevalier F., 2005, Eur J Org Chem, 16, 3489, 10.1002/ejoc.200500171

10.1016/S0006-3495(02)75630-0

10.1002/jcc.1155

10.1016/S0006-3495(03)74984-4

10.1021/jp004413y

10.1002/(SICI)1096-987X(19991130)20:15<1593::AID-JCC1>3.0.CO;2-A

10.1016/S0008-6215(00)00043-4

10.1016/S0008-6215(00)00042-2

Frisch M. J. T., G. W., 2002, Gaussian '98

Case D. A., 2002, AMBER 7

Case D. A., 2004, AMBER 8

10.1103/PhysRev.159.98

10.1080/00268977700102571

10.1002/jcc.540130812

10.1016/0010-4655(95)00053-I

10.1021/j100142a004

10.1002/jcc.1072

Case D. A., 2006, AMBER 9

10.1107/S0567740879004374

Korolevich M., 1994, J Mol Struct, 306, 261, 10.1016/0166-1280(94)80046-4

Korolevich M., 1992, J Appl Spectrosc, 56, 217, 10.1007/BF00659098

10.1016/0022-2860(90)80120-9

10.1002/jcc.540140303

10.1002/jcc.10119

10.1016/0022-2860(81)80029-4

10.1080/07328309908544041

10.1016/0022-2860(90)87031-R

Prima A., 1967, J Struct Chem, 5, 783, 10.1007/BF00744230

10.1021/ja00214a001

10.1002/jcc.540110304

10.1002/jcc.540110311

10.1063/1.481505

10.1002/(SICI)1096-987X(199602)17:3<367::AID-JCC11>3.0.CO;2-H

Juaristi E., 1995, Conformational Behavior of Six‐Membered Rings: Analysis, Dynamics and Stereochemical Effects

10.1016/j.carres.2003.10.014

10.1016/S0008-6215(00)82752-4

10.1021/ja00470a003

10.1016/0008-6215(90)84003-D

Dinur U., 1991, Reviews in Computational Chemistry

10.1002/jcc.540040211

10.1002/bip.360230807

10.1021/jp973084f

10.1002/jcc.20082

10.1021/bi00136a012

10.1016/S0008-6215(00)83531-4

10.1039/p29720000324

10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F

10.1021/j100463a018

10.1063/1.444864

10.1063/1.448683

10.1021/j100577a009

van Alsenoy C., 1982, J Mol Struct, 86, 365, 10.1016/0166-1280(82)80027-4

10.1016/0166-1280(82)80026-2

10.1063/1.1700280

Sasada Y., 1988, J Mol Struct, 190, 93, 10.1016/0022-2860(88)80274-6

10.1021/jp0550311

10.1021/ja00063a040

10.1016/0304-4165(75)90218-4

10.1021/bi00399a055

10.1007/BF01875524

10.1107/S0567740873005698

10.1107/S0108270189007134

10.1016/0166-1280(92)80073-U

10.1063/1.1536163

10.3891/acta.chem.scand.03-0415

10.1080/00268978800101651

10.1021/ja00088a027

10.1002/(SICI)1099-1395(199704)10:4<196::AID-POC889>3.0.CO;2-O

10.1021/jp048921

10.1021/jp046715w

10.1063/1.462947

Nagy P. I., 1992, J Am Chem Soc, 113, 6719, 10.1021/ja00018a002

10.1016/0022-2860(70)90029-3

10.1063/1.1340605

Fateley W. G., 1962, Spectrochim Acta, 18, 977

10.1021/jp981009e

Liu H., 1995, J Chem Phys, 1042, 1722, 10.1063/1.468699

10.1021/ja00106a061

10.1039/a703436i

10.1021/jp001340

10.1016/S0032-3861(96)00497-1

10.1021/ja9529652

Lemieux R. U., 1979, Anomeric Effect, Origin and Consequences

10.1021/jp963765v

10.1021/jp014426r

10.1021/j150656a049

10.1046/j.1432-1033.2003.03927.x

10.1016/0022-2852(80)90265-9

10.1016/0009-2614(81)80342-9

10.1107/S0567740873006631

10.1016/S0021-9258(17)41867-9

Mobli M., 2007, Org Biomol Chem, 4, 2243, 10.1039/b705761j

Smondyrev A. M., 1999, J Comput Chem, 25, 531, 10.1002/(SICI)1096-987X(19990415)20:5<531::AID-JCC5>3.0.CO;2-3

10.1111/j.1432-1033.1989.tb14504.x

10.1002/1096-987X(200010)21:13<1204::AID-JCC9>3.0.CO;2-F

10.1021/jo010985i

10.1002/bip.1981.360200610

10.1080/07328309408011662

10.1080/07328308808058917

10.1016/S0040-4039(01)90014-0

10.1021/ja00839a011

10.1107/S0567740877004567

10.1107/S0567740879005148

10.1016/0008-6215(88)80078-8

10.1002/jcc.540141104

10.1021/ja00315a051

Thông tin
Thông tin xuất bản

Journal of Computational Chemistry

Tập 29 Số 4

622-655

Thông tin tác giả