Bonvin A M, Rullmann J A, Lamerichs R M, Boelens R, Kaptein R
Bijvoet Center, University of Utrecht, The Netherlands.
Proteins. 1993 Apr;15(4):385-400. doi: 10.1002/prot.340150406.
The structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an "ensemble" approach is proposed and compared to the more standard initial rate analysis approach and a "single structure" relaxation matrix approach. The effects of fast local motions are included and R-factor calculations are performed on NOE build-ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 A on backbone atoms and 1.1 A on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr-29 which is determined in solution by both J-coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found in the solution structure, in particular for the loop between the two helices (Gly-20 to Pro-22).
胰凝乳蛋白酶抑制剂（一种由46个残基组成的小蛋白）在溶液中的结构，已通过二维核磁共振数据，使用迭代弛豫矩阵方法（IRMA）结合距离几何、距离约束驱动动力学、分子动力学和能量最小化来确定。提出了一种基于“系综”方法的新方案，并与更标准的初始速率分析方法和“单一结构”弛豫矩阵方法进行了比较。考虑了快速局部运动的影响，并对核Overhauser效应（NOE）积累进行了R因子计算，以描述理论与实验之间的吻合质量。一种基于理论和实验NOE强度比较的前手性基团立体专一性归属新方法已得到应用。胰凝乳蛋白酶抑制剂的溶液结构在主链原子上的精度（相对于平均结构的均方根偏差）为0.7 Å，在所有重原子上为1.1 Å，并且与晶体结构在很大程度上相似，只是在Tyr-29侧链位置上观察到有小差异，该位置在溶液中由J耦合和NOE数据共同确定。在溶液结构中发现了结构变异性较高（表明流动性较高）的区域，特别是在两个螺旋之间的环（Gly-20至Pro-22）。
