CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.
CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.
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DOI：
10.1021/jp905496e
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发表时间：
2009-09-17
期刊：
影响因子：
--
通讯作者：
Mackerell AD
中科院分区：
文献类型：
--
作者：
Hatcher E;Guvench O;Mackerell AD
一个添加剂的全原子经验力场aldopentofuranoses，甲基aldopentofuranosides（Me-aldopentofuranosides）和fructofuranose碳水化合物，兼容现有的CHARMM碳水化合物参数，提出。基于从环醚和吡喃己糖转移的现有参数，使用完全呋喃糖碳水化合物以及O-甲基四氢呋喃的目标数据进一步开发参数。调整键和角平衡参数以从呋喃糖晶体结构的调查再现目标几何形状，并且二面角参数拟合到超过1700个量子力学（QM）MP2/cc-pVTZ//MP2/6- 31 G（d）构象能。各种完整的呋喃糖单糖的构象能，并包括二维环褶皱能量表面。键合参数优化导致了对大量呋喃糖化合物的环褶皱的正确描述，而呋喃糖-水相互作用能和距离再现了许多呋喃糖单糖的QM HF/6- 31 G（d）结果，从而验证了非键合参数。晶格晶胞参数和体积，水相密度，和水NMR环起皱和exocyclic数据被用来验证在凝聚相环境中的参数。构象采样分析的环褶皱和环外基团表现出良好的协议与实验NMR数据，表明在水溶液中的构象能准确地描述了优化力场。总的来说，参数再现可用的实验数据以及预计将在未来的碳水化合物的计算研究，包括在蛋白质，核酸和/或脂质的情况下，与现有的CHARMM生物分子力场相结合的实用程序。
An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields.
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影响因子：
15
作者：
ALTONA, C;SUNDARALINGAM, M
通讯作者：
SUNDARALINGAM, M
影响因子：
2.9
作者：
HOOVER, WG
通讯作者：
HOOVER, WG
影响因子：
5.5
作者：
Hatcher, Elizabeth R.;Guvench, Olgun;MacKerell, Alexander D., Jr.
通讯作者：
MacKerell, Alexander D., Jr.
影响因子：
3.6
作者：
Gordon, MT;Lowary, TL;Hadad, CM
通讯作者：
Hadad, CM
影响因子：
3
作者：
Guvench, Olgun;Greene, Shannon N.;Kamath, Ganesh;Brady, John W.;Venable, Richard M.;Pastor, Richard W.;Mackerell, Alexander D., Jr.
通讯作者：
Mackerell, Alexander D., Jr.