A polarizable force field for computing the infrared spectra of the polypeptide backbone.
A polarizable force field for computing the infrared spectra of the polypeptide backbone.
复制标题
用于计算多肽主链的红外光谱的极化力场。
DOI：
10.1021/jp8013767
复制
发表时间：
2008
期刊：
影响因子：
--
通讯作者：
P. Tavan
中科院分区：
文献类型：
--
作者：
Verena Schultheis;Rudolf Reichold;B. Schropp;P. Tavan
蛋白质和肽的红外（IR）光谱中酰胺带的形状是由多肽骨架内的静电耦合振动引起的，并编码这些生物聚合物的结构。酰胺带的结构解码必须求助于简化的模型，因为这些大分子的巨大尺寸阻止了精确的量子力学方法如密度泛函理论（DFT）的应用。以前的模型采用过渡偶极耦合的方法是有限的精度。在这里，我们提出了一个概念的蛋白质红外光谱的计算，它描述了分子力学（MM）的多肽骨架的极化力场的“II型”。通过扩展传统的可极化MM力场的概念，这样的PMM/II方法采用场依赖的参数不仅用于分子组分的静电签名，而且用于局部电位建模化学键相对于伸长、角度变形和扭转的刚度。使用PMM/II力场，多肽主链的IR光谱可以从短（例如，100 ps）通过傅立叶变换的MD模拟。PMM/II参数推导出谐波键合电位的酰胺基团在多肽从一系列的DFT计算模型分子N-甲基乙酰胺（NMA）暴露于均匀的外电场。酰胺力常数的变化高达20%，相关的磁场强度。作为一个证明的原则，它示出的NMA的红外光谱中观察到的大的溶剂化变色效应后，从气相转移到水溶液中，不仅出色地再现由DFT/MM模拟，但也很好地建模的PMM/II方法。指定了实践证明剩余的任务。
The shapes of the amide bands in the infrared (IR) spectra of proteins and peptides are caused by electrostatically coupled vibrations within the polypeptide backbone and code the structures of these biopolymers. A structural decoding of the amide bands has to resort to simplified models because the huge size of these macromolecules prevents the application of accurate quantum mechanical methods such as density functional theory (DFT). Previous models employed transition-dipole coupling methods that are of limited accuracy. Here we propose a concept for the computation of protein IR spectra, which describes the molecular mechanics (MM) of polypeptide backbones by a polarizable force field of "type II". By extending the concepts of conventional polarizable MM force fields, such a PMM/II approach employs field-dependent parameters not only for the electrostatic signatures of the molecular components but also for the local potentials modeling the stiffness of chemical bonds with respect to elongations, angle deformations, and torsions. Using a PMM/II force field, the IR spectra of the polypeptide backbone can be efficiently calculated from the time dependence of the backbone's dipole moment during a short (e.g., 100 ps) MD simulation by Fourier transformation. PMM/II parameters are derived for harmonic bonding potentials of amide groups in polypeptides from a series of DFT calculations on the model molecule N-methylacetamide (NMA) exposed to homogeneous external electric fields. The amide force constants are shown to vary by as much as 20% for relevant field strengths. As a proof of principle, it is shown that the large solvatochromic effects observed in the IR spectra of NMA upon transfer from the gas phase into aqueous solution are not only excellently reproduced by DFT/MM simulations but are also nicely modeled by the PMM/II approach. The tasks remaining for a proof of practice are specified.
影响因子：
--
作者：
J. Ponder;D. Case
通讯作者：
J. Ponder;D. Case