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首页> 外文期刊>Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological >Improved Treatment of Cyclic #beta#-Amino Acids and Succesful Prediction of #beta#-Pepptide Secondary Structure Using a Modified Force Field: AMBER~*C
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Improved Treatment of Cyclic #beta#-Amino Acids and Succesful Prediction of #beta#-Pepptide Secondary Structure Using a Modified Force Field: AMBER~*C

机译:改进的力场:AMBER〜* C对环状#beta#-氨基酸的改良处理和成功预测#beta#-肽的二级结构

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摘要

We added parameters to the AMBER~* force field to model cyclic #beta#-amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformation preference,s carbon-carbon torsional parametes were modified and incorporated into a force field we call AMBER~8C. Simulation of trans-2-aminocyclohexanecarboxylic acid (trans-ACHC) and trans-2-aminocyclopentanecarboxylic acid (trans-ACPC) derivatives using AMBER~*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformatorial conformations than does simulation using AMBER~*. AMBER~*C molecular dynamics simulations more accurately reproduce the experimental hydrogen-bonding tendencies of simple diamide derivatives of trans-ACHC and trans-ACPC than do simulations using the AMGBER~* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by #beta#-amino acid homo-oligomers.
机译:我们将参数添加到AMBER〜*力场中,以便在常用的MacroModel程序中更精确地模拟环状#β#-氨基酸衍生物。为了产生对环己烷和环戊烷构象偏好的改进处理,对碳-碳扭转参数进行了修改,并将其纳入我们称为AMBER〜8C的力场中。使用AMBER〜* C模拟反式-2-氨基环己烷羧酸(trans-ACHC)和反式-2-氨基环戊烷羧酸(trans-ACPC)衍生物在(伪)双轴和(伪)赤道构象构象之间产生的能量差比实际的差得多。使用AMBER〜*进行仿真。与使用AMGBER〜*力场进行的模拟相比,AMBER〜* C分子动力学模拟更准确地再现了反式ACHC和反式ACPC的简单二酰胺衍生物的氢键键合实验趋势。更重要的是,这种改进的力场可以准确定性地预测#beta#-氨基酸均聚物所采用的螺旋二级结构。

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