Summers M F, South T L, Kim B, Hare D R
Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21228.
Biochemistry. 1990 Jan 16;29(2):329-40. doi: 10.1021/bi00454a005.
A new method is described for determining molecular structures from NMR data. The approach utilizes 2D NOESY back-calculations to generate simulated spectra for structures obtained from distance geometry (DG) computations. Comparison of experimental and back-calculated spectra, including analysis of cross-peak buildup and auto-peak decay with increasing mixing time, provides a quantitative measure of the consistence between the experimental data and generated structures and allows for use of tighter interproton distance constraints. For the first time, the "goodness" of the generated structures is evaluated on the basis of their consistence with the actual experimental data rather than on the basis of consistence with other generated structures. This method is applied to the structure determination of an 18-residue peptide with an amino acid sequence comprising the first zinc fingerlike domain from the gag protein p55 of HIV. This is the first structure determination to atomic resolution for a retroviral zinc fingerlike complex. The peptide [Zn(p55F1)] exhibits a novel folding pattern that includes type I and type II NH-S tight turns and is stabilized both by coordination of the three Cys and one His residues to zinc and by extensive internal hydrogen bonding. The backbone folding is significantly different from that of a "classical" DNA-binding zinc finger. Residues C(1)-F(2)-N(3)-C(4)-G(5)-K(6) fold in a manner virtually identical with the folding observed by X-ray crystallography for related residues in the iron domain of rubredoxin; superposition of all main-chain and Cys side-chain atoms of residues C(1)-K(6) of Zn(p55F1) onto residues C(6)-Y(11) and C(39)-V(44) of rubredoxin gives RMSDs of 0.46 and 0.35 A, respectively. The side chains of conservatively substituted Phe and Ile residues implicated in genomic RNA recognition form a hydrophobic patch on the peptide surface.
本文描述了一种从核磁共振（NMR）数据确定分子结构的新方法。该方法利用二维核欧沃豪斯效应光谱（NOESY）反计算，为从距离几何（DG）计算获得的结构生成模拟光谱。将实验光谱与反计算光谱进行比较，包括分析随着混合时间增加交叉峰的积累和自峰衰减，可提供实验数据与生成结构之间一致性的定量度量，并允许使用更严格的质子间距离约束。首次基于生成结构与实际实验数据的一致性而非与其他生成结构的一致性来评估生成结构的“优劣”。该方法应用于具有18个残基的肽的结构测定，其氨基酸序列包含来自HIV gag蛋白p55的首个锌指样结构域。这是首次对逆转录病毒锌指样复合物进行原子分辨率的结构测定。该肽[Zn(p55F1)]呈现出一种新颖的折叠模式，包括I型和II型NH-S紧密转角，并且通过三个半胱氨酸（Cys）和一个组氨酸（His）残基与锌的配位以及广泛的内部氢键作用得以稳定。其主链折叠与“经典”DNA结合锌指的折叠显著不同。残基C(1)-F(2)-N(3)-C(4)-G(5)-K(6)的折叠方式与通过X射线晶体学观察到的红氧还蛋白铁结构域中相关残基的折叠几乎相同；将Zn(p55F1)中残基C(1)-K(6)的所有主链和半胱氨酸侧链原子叠加到红氧还蛋白的残基C(6)-Y(11)和C(39)-V(44)上，均方根偏差（RMSD）分别为0.46 Å和0.35 Å。参与基因组RNA识别的保守取代苯丙氨酸（Phe）和异亮氨酸（Ile）残基的侧链在肽表面形成一个疏水斑块。
