Levy R M, Bassolino D A, Kitchen D B, Pardi A
Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08903.
Biochemistry. 1989 Nov 28;28(24):9361-72. doi: 10.1021/bi00450a017.
The structure of neutrophil peptide 5 in solution has recently been reported (Pardi et al., 1988). The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distance constraints obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small (approximately 2.4 A). In this paper we report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures (approximately 5.0 A). The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. For small proteins, the problem of distinguishing the correct structure among pseudo mirror images is likely to be greater than previously recognized. When a set of test distance constraints constructed from a novel Monte Carlo structure is used as input in the distance geometry algorithm, the fold of the resulting structure does not correspond to that of the target. The results also demonstrate that the previously accepted criteria (the magnitude of the rms deviation between multiple solutions of the distance geometry equations) for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data. An alternative fold corresponding to structures with low energies and small total distance violations is ruled out because for this fold predicted NOEs are not observed experimentally.
中性粒细胞肽5在溶液中的结构最近已有报道（帕尔迪等人，1988年）。结构测定是通过使用距离几何算法和从二维核磁共振数据获得的107个质子间距离约束来完成的。在距离几何方程的八个独立解中，多肽主链的总体折叠是相同的，叠加结构主链原子之间的均方根（rms）偏差很小（约2.4埃）。在本文中，我们报告了通过使用一种新的结构生成算法获得的额外NP-5结构：在扭转角空间中的蒙特卡罗搜索。这些结构与距离几何结构的主链均方根偏差较大（约5.0埃）。主链拓扑结构在重要方面与距离几何结构以及彼此之间都有所不同。发现了一些结构，它们是与最初通过距离几何程序获得的折叠部分或全部对应的伪镜像。对于小蛋白质，在伪镜像中区分正确结构的问题可能比以前认识到的更大。当将从新的蒙特卡罗结构构建的一组测试距离约束用作距离几何算法的输入时，所得结构的折叠与目标结构不对应。结果还表明，先前用于定义从核磁共振数据生成的肽结构的准确性和精度的标准（距离几何方程多个解之间的均方根偏差大小）是不充分的。已经对与不同折叠拓扑对应的结构进行了能量分析。通过最小化和分子动力学细化获得的分子力学能量提供了足够的信息来排除某些替代结构。在仔细比较不同的试验结构与实验数据的基础上，得出结论，最初报道的NP-5肽折叠与数据最一致。排除了一种对应于低能量和小总距离违反结构的替代折叠，因为对于这种折叠，预测的核Overhauser效应（NOE）在实验中未观察到。
