通过核磁共振化学屏蔽各向异性（CSA）参数确定肽和蛋白质的二级结构。

Secondary structures of peptides and proteins via NMR chemical-shielding anisotropy (CSA) parameters.

作者信息

Czinki Eszter, Császár Attila G, Magyarfalvi Gábor, Schreiner Peter R, Allen Wesley D

机构信息

Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, H-1518 Budapest 112, P.O. Box 32, Hungary.

出版信息

J Am Chem Soc. 2007 Feb 14;129(6):1568-77. doi: 10.1021/ja065461k.

DOI:10.1021/ja065461k

PMID:17284001

Abstract

Complete nuclear magnetic resonance (NMR) chemical-shielding tensors, sigma, have been computed at different levels of density-functional theory (DFT), within the gauge-including atomic orbital (GIAO) formalism, for the atoms of the peptide model For-L-Ala-NH2 as a function of the backbone dihedral angles phi and psi by employing a dense grid of 10 degrees. A complete set of rigorously orthogonal symmetric tensor invariants, {sigma iso, rho, tau}, is introduced, where sigma iso is the usual isotropic chemical shielding, while the newly introduced rho and tau parameters describe the magnitude and the orientation/shape of the chemical-shielding anisotropy (CSA), respectively. The set {sigma iso, rho, tau} is unaffected by unitary transformations of the symmetric part of the shielding tensor. The mathematically and physically motivated {rho, tau} anisotropy pair is easily connected to more traditional shielding anisotropy measures, like span (Omega) and skew (kappa). The effectiveness of the different partitions of the CSA information in predicting conformations of peptides and proteins has been tested throughout the Ramachandran space by generating theoretical NMR anisotropy surfaces for our For-L-Ala-NH2 model. The CSA surfaces, including Omega(phi, psi), kappa(phi, psi), rho(phi, psi), and tau(phi, psi) are highly structured. Individually, none of these surfaces is able to distinguish unequivocally between the alpha-helix and beta-strand secondary structural types of proteins. However, two- and three-dimensional correlated plots, including Omega versus kappa, rho versus tau, and sigma iso versus rho versus tau, especially for 13Calpha, have considerable promise in distinguishing among all four of the major secondary structural elements.

摘要

在包含规范的原子轨道（GIAO）形式体系内，利用10度的密集网格，针对肽模型For-L-Ala-NH2的原子，在不同密度泛函理论（DFT）水平下计算了完整的核磁共振（NMR）化学屏蔽张量σ，其作为主链二面角φ和ψ的函数。引入了一组严格正交的对称张量不变量{σiso, ρ, τ}，其中σiso是通常的各向同性化学屏蔽，而新引入的ρ和τ参数分别描述化学屏蔽各向异性（CSA）的大小和取向/形状。集合{σiso, ρ, τ}不受屏蔽张量对称部分的酉变换影响。从数学和物理角度出发的{ρ, τ}各向异性对很容易与更传统的屏蔽各向异性度量（如展度（Ω）和偏斜度（κ））联系起来。通过为我们的For-L-Ala-NH2模型生成理论NMR各向异性表面，在整个拉马钱德兰空间中测试了CSA信息的不同划分在预测肽和蛋白质构象方面的有效性。CSA表面，包括Ω(φ, ψ)、κ(φ, ψ)、ρ(φ, ψ)和τ(φ, ψ)，具有高度的结构。单独来看，这些表面都无法明确区分蛋白质的α螺旋和β链二级结构类型。然而，二维和三维相关图，包括Ω对κ、ρ对τ以及σiso对ρ对τ，特别是对于13Cα，在区分所有四种主要二级结构元素方面具有很大的潜力。