Peptide Dynamics Investigated by 13C- & 15N-NMR Relaxation & Modeling

为了系统地研究短线性肽的主链和侧链旋转动力学，将测定Mayo 13C-和15n偶极自相关和互相关光谱密度和noe。亚甲基和甲基中的13C-多重弛豫将提供独特的运动信息。侧链运动将在没有大多数空间阻碍的情况下得到更好的理解，例如，“展开”的溶剂暴露状态。像G-G- x - G-G- g这样的五肽将被研究以帮助分离由于相关的内部旋转和整体分子翻滚而产生的松弛效应。为了推导出合理的能垒，我们将研究所有弛豫参数的温度依赖性。测量将在水中和有机溶剂中进行，例如二甲基亚砜。在水中，pH值的影响和离子强度的变化将有助于理解静电对内部旋转的贡献。受限制和不受限制的旋转扩散、势阱内的旋转波动、跳跃模型、包含内部旋转关联等，以及“无模型”方法将用于分析弛豫数据，并计算分子动力学模拟和F，Y，C键旋转能量分布图，以深入了解哪些键旋转可能对这些弛豫现象贡献最大。蛋白质由以重复聚合阵列排列的主链原子和按特定顺序排列的特定侧链基团组成。例如，这20个常见侧链的序列特异性排列告诉蛋白质如何折叠以及它将具有什么功能。在这项研究中，核磁共振波谱和计算机建模将用于研究蛋白质的小部分如何在溶液中移动和行为的基本过程。这反过来将提供一个更好的理解蛋白质的主链和侧链的内部运动和他们的运动相互影响。此外，由于蛋白质中相关运动的本质，这项研究将为更好地理解蛋白质折叠，即所谓的“第二遗传密码”奠定基础。* * *

9420203 Mayo 13C- and 15N-dipolar auto-and cross-correlation spectral densities and NOEs will be determined to systematically investigate backbone and side-chain rotational dynamics in short linear peptides. 13C- multiplet relaxation in methylene and methyl groups will provide unique motional information. Side-chain motions then will be better understood in the absence of most steric hinderences, e.g., the "unfolded," solvent-exposed state. Penta-peptides like G-G-X- G-G will be studied to assist in separating relaxation effects due to correlated internal rotations and overall molecular tumbling. The temperature dependence of all relaxation parameters will be investigated in order to derive rational energy barriers. Measurements will be done in water and in organic solvent, e.g., DMSO. In water, the effect of pH and varying ionic strength will assist in understanding electrostatic contributions to internal rotations. Restricted and unrestricted rotational diffusion, rotational fluctuation within potential wells, jump models, inclusion of internal rotational correlations, etc., and "model free" approaches will be used to analyze relaxation data, and molecular dynamics simulations and F,Y,C bond rotation energy profiles will be calculated for insight into which bond rotations may contribute most to these relaxation phenomena. %%% Proteins are composed of backbone atoms arranged in a repetitious polymeric array and specific side-chain groups that are arranged in a specific sequence. This sequence-specific arrangement of the twenty common side-chains tells, for example, a protein how to fold and what function it will have. In this study, NMR spectroscopy and computer modeling will be used to investigate fundamental processes of how small parts of proteins move and behave in solution. This in turn will provide a better understanding of protein backbone and side-chain internal motions and the influence of their motions on each other. In addition, due to the very nature of correlated motions in proteins, this study will set the stage for a better understanding of protein folding, the so-called "second genetic code." ***