Armen Roger, Alonso Darwin O V, Daggett Valerie
Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA.
Protein Sci. 2003 Jun;12(6):1145-57. doi: 10.1110/ps.0240103.
The conformational equilibrium between 3(10)- and alpha-helical structure has been studied via high-resolution NMR spectroscopy by Millhauser and coworkers using the MW peptide Ac-AMAAKAWAAKA AAARA-NH2. Their 750-MHz nuclear Overhauser effect spectroscopy (NOESY) spectra were interpreted to reflect appreciable populations of 3(10)-helix throughout the peptide, with the greatest contribution at the N and C termini. The presence of simultaneous alphaN(i,i + 2) and alphaN(i,i + 4) NOE cross-peaks was proposed to represent conformational averaging between 3(10)- and alpha-helical structures. In this study, we describe 25-nsec molecular dynamics simulations of the MW peptide at 298 K, using both an 8 A and a 10 A force-shifted nonbonded cutoff. The ensemble averages of both simulations are in reasonable agreement with the experimental helical content from circular dichroism (CD), the (3)J(HNalpha) coupling constants, and the 57 observed NOEs. Analysis of the structures from both simulations revealed very little formation of contiguous i --> i + 3 hydrogen bonds (3(10)-helix); however, there was a large population of bifurcated i --> i + 3 and i --> i + 4 alpha-helical hydrogen bonds. In addition, both simulations contained considerable populations of pi-helix (i --> i + 5 hydrogen bonds). Individual turns formed over residues 1-9, which we predict contribute to the intensities of the experimentally observed alphaN(i,i + 2) NOEs. Here we show how sampling of both folded and unfolded structures can provide a structural framework for deconvolution of the conformational contributions to experimental ensemble averages.
米尔豪泽及其同事使用MW肽Ac-AMAAKAWAAKA AAARA-NH2，通过高分辨率核磁共振光谱研究了3(10)-螺旋结构和α-螺旋结构之间的构象平衡。他们对750兆赫的核Overhauser效应光谱（NOESY）进行了解释，以反映整个肽中3(10)-螺旋的可观比例，在N端和C端贡献最大。同时存在的αN(i,i + 2)和αN(i,i + 4) NOE交叉峰被认为代表了3(10)-螺旋结构和α-螺旋结构之间的构象平均。在本研究中，我们描述了MW肽在298 K下的25纳秒分子动力学模拟，使用了8埃和10埃的力移非键截止。两个模拟的系综平均值与圆二色性（CD）实验得到的螺旋含量、(3)J(HNα)耦合常数以及57个观察到的NOE合理一致。对两个模拟得到的结构分析表明，几乎没有形成连续的i --> i + 3氢键（3(10)-螺旋）；然而，有大量的分叉i --> i + 3和i --> i + 4α-螺旋氢键。此外，两个模拟都包含相当数量的π-螺旋（i --> i + 5氢键）。在残基1-9上形成了单个转角，我们预测这有助于实验观察到的αN(i,i + 2) NOE的强度。在这里，我们展示了对折叠和未折叠结构的采样如何为构象对实验系综平均值的贡献解卷积提供一个结构框架。
