Braun W
Institut für Molekularbiologie u. Biophysik, Eidgenössische Technische Hochschule, Zürich, Switzerland.
Q Rev Biophys. 1987 May;19(3-4):115-57. doi: 10.1017/s0033583500004108.
Computational tools have been developed in the last few years, to allow a direct determination of protein structures from NMR data. Numerical calculations with simulated and experimental NMR constraints for distances and torsional angles show that data sets available with present NMR techniques carry enough information to determine reliably the global fold of a small protein. The maximum size of a protein for which the direct method can be applied is not limited by the computational tools but rather by the resolution of the two-dimensional spectra. A general estimate of the maximum size would be a molecular weight of about 10,000 (Markley et al. 1984), but parts of larger proteins might be accessible with the method. Effort for improvement of the NMR structures should be concentrated more on the local conformation rather than the global features. The r.m.s. D values for variations of the polypeptide backbone fold are on the order of 1.5-2 A for several of the studied proteins, indicating that the global structure is well determined by the present NMR data and their interpretation. The local structures are sometimes rather poor, with standard deviations for the backbone torsion angles of about 50 degrees. Possible improvements would be stereospecific resonance assignments of individual methylene protons and individual assignments of the methyl groups of the branched side-chains. Accurate estimates of the short-range NOE distance constraints by calibrating the distance constraints, including segmental flexibility effects, and combined use of distance geometry, energy minimization and molecular dynamics calculations, are further tools for improving the structures.
在过去几年中已经开发出了计算工具，以便能直接根据核磁共振（NMR）数据确定蛋白质结构。利用模拟的和实验得到的距离及扭转角的NMR约束进行数值计算表明，现有NMR技术所提供的数据集携带了足够的信息来可靠地确定小蛋白质的整体折叠情况。可应用直接法的蛋白质的最大尺寸并非受计算工具的限制，而是受二维谱分辨率的限制。最大尺寸的一般估计是分子量约为10,000（Markley等人，1984年），但该方法可能可用于较大蛋白质的部分结构。改善NMR结构的努力应更多地集中在局部构象而非整体特征上。对于几种所研究的蛋白质，多肽主链折叠变化的均方根偏差值在1.5 - 2埃的量级，这表明目前的NMR数据及其解释能很好地确定整体结构。局部结构有时相当差，主链扭转角的标准偏差约为50度。可能的改进包括对单个亚甲基质子进行立体专一性共振归属以及对分支侧链的甲基进行单个归属。通过校准距离约束（包括片段柔性效应）来准确估计短程核Overhauser效应（NOE）距离约束，以及联合使用距离几何、能量最小化和分子动力学计算，是改善结构的进一步手段。
