A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests.
A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests.
复制标题
肽的 CHARMM、AMBER 和 ECEPP 潜力的比较。
DOI：
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发表时间：
1989
影响因子：
4.4
通讯作者：
H. Scheraga
中科院分区：
文献类型：
--
作者：
I. Roterman;M. Lambert;K. Gibson;H. Scheraga
用CHARMM势、全原子AMBER势和ECEPP/2势计算了N-乙酰丙氨酸N ′-甲酰胺绝热弛豫前后的φ-psi图。使用CHARMM和AMBER电位的地图被确定为具有1.0和4.0的介电常数ε的值，并且具有依赖于距离的介电常数。绝热松弛进行了灵活的几何形状的CHARMM和琥珀电位，并使用刚性几何的琥珀和ECEPP电位。在所有情况下，在C7eq区域发现最低能量（phi约为-70度，psi约为70度）。CHARMM和AMBER的图（λ = 4.0）和ECEPP的图（无绝热弛豫）大致相似，但分配给图中高能区域的相对能量不同。在刚性几何绝热弛豫后，ECEPP图和AMBER图使用距离依赖的介电常数，除了α R，α L和C7ax区域的相对能量的差异外，一致性相当好。在使用柔性几何结构进行绝热弛豫之后，CHARMM和AMBER的图变得非常相似;在C7eq区域、C5区域（phi约为-150度，psi约为150度）和C7ax区域（phi约为70度，psi约为-70度）中观察到最低能量。绝热弛豫后能量分解为静电能、非键能和几何能结果表明：（1）在几何构型固定的情况下，非键和扭转对ECEPP和AMBER势能的贡献非常相似，但静电作用的贡献明显不同;（2）在弹性几何条件下，非键对CHARMM势和AMBER势的贡献在整个图上变化不大。phi-psi图与实验进行了三次简单的比较。(1)用该图谱预测聚-L-丙氨酸的特征比，并将结果与实验结果（D.A.Brant和P.J.Flory，J. Amer.Chem.Soc.87，2788 - 2791，1965）进行比较。ECEPP和CHARMM绝热弛豫后与实验符合较好，AMBER绝热弛豫后与实验符合较差，而CHARMM和AMBER绝热弛豫后与实验不符合。(2)从他们的平衡值，在能量最小化的构象键角的偏差进行了比较，从晶体的末端封闭的氨基酸推导出的值。使用灵活的几何形状的CHARMM和AMBER势，在C7ax局部最小值中观察到一个或多个过度偏差。（400字处截断摘要）
phi-psi maps of N-acetyl alanine N'-methyl amide have been computed using the CHARMM potential, the all-atom AMBER potential, and the ECEPP/2 potential, before and after adiabatic relaxation. Maps using the CHARMM and AMBER potentials were determined with values of 1.0 and 4.0 for the dielectric constant epsilon, and with a distance dependent dielectric constant. Adiabatic relaxation was carried out using flexible geometry for the CHARMM and AMBER potentials, and using rigid geometry for the AMBER and ECEPP potentials. In all cases, the lowest energy was found in the C7eq region (phi approximately -70 degrees, psi approximately 70 degrees). The maps with CHARMM and AMBER with epsilon = 4.0 and with ECEPP, without adiabatic relaxation, were broadly similar but differed in the relative energies allotted to high-energy regions of the map. After adiabatic relaxation with rigid geometry, the map with ECEPP, and the map with AMBER using a distance-dependent dielectric constant, agreed fairly well apart from differences in the relative energies of the alpha R, alpha L, and C7ax regions. After adiabatic relaxation with flexible geometry, the maps with CHARMM and AMBER became very similar; the lowest energies were observed in the C7eq region, the C5 region (phi approximately -150 degrees, psi approximately 150 degrees) and the C7ax region (phi approximately 70 degrees, psi approximately -70 degrees). Breakdown of the energies, after adiabatic relaxation, into electrostatic, nonbonded, and geometric (including torsional) contributions, showed that (1) with fixed geometry, the nonbonded and torsional contribution to the ECEPP and AMBER potentials were very similar, but the electrostatic contributions were markedly different; (2) with flexible geometry, the nonbonded contribution to the CHARMM and AMBER potentials did not vary greatly over the whole map. The phi-psi maps were subjected to three simple comparisons with experiment. (1) The maps were used to predict the characteristic ratio for poly-L-alanine, and the results were compared with experimental findings (D.A. Brant and P.J. Flory, J. Amer. Chem. Soc. 87, 2788-2791, 1965). The agreement with experiment was acceptable for ECEPP, and for CHARMM after adiabatic relaxation, marginal for AMBER after adiabatic relaxation, and unsatisfactory for CHARMM or AMBER without adiabatic relaxation. (2) Deviations of bond angles from their equilibrium values, in energy-minimized conformations, were compared with values deduced from crystals of terminally-blocked amino acids. With both the CHARMM and AMBER potentials using flexible geometry, one or more excessive deviations was observed in the C7ax local minimum.(ABSTRACT TRUNCATED AT 400 WORDS)
DOI：
10.1146/annurev.bb.17.060188.002315
发表时间：
1988
期刊：
Annual review of biophysics and biophysical chemistry
影响因子：
--
作者：
H. Frauenfelder;F. Parak;R. Young
通讯作者：
H. Frauenfelder;F. Parak;R. Young
影响因子：
56.9
作者：
BASH, PA;SINGH, UC;KOLLMAN, PA
通讯作者：
KOLLMAN, PA