Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
J Biomol NMR. 2011 Jul;50(3):267-76. doi: 10.1007/s10858-011-9517-1. Epub 2011 Jun 28.
We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unassigned signals, and assignment gaps. Examination of a set of high-scoring assignments from a large number of independent runs allows one to determine whether a unique assignment exists for the entire sequence or parts thereof. We demonstrate the MCSA algorithm using two-dimensional (2D) and three-dimensional (3D) solid state NMR spectra of several model protein samples (α-spectrin SH3 domain and protein G/B1 microcrystals, HET-s(218-289) fibrils), obtained with magic-angle spinning and standard polarization transfer techniques. The MCSA algorithm and MCASSIGN2 program can accommodate arbitrary combinations of NMR spectra with arbitrary dimensionality, and can therefore be applied in many areas of solid state and solution NMR.
我们描述了一种基于简单蒙特卡罗/模拟退火（MCSA）算法的通用计算方法，用于对均（15）N，（13）C 标记的生物聚合物的多维 NMR 研究中的特定位置进行共振分配，该算法包含在程序 MCASSIGN2 中。MCASSIGN2 的输入包括 NMR 光谱中多维信号及其可能的残基类型分配列表（不必唯一），生物聚合物序列以及描述将一个信号列表与另一个信号列表相关联的连接的表。作为输出，MCASSIGN2 使用奖励良好连接（即不同信号列表中相关化学位移集之间的一致性）和惩罚不良连接，未分配的信号和分配间隙的评分函数，对多维信号进行高分序列分配。从大量独立运行中检查一组高分分配，可以确定整个序列或其部分是否存在唯一分配。我们使用二维（2D）和三维（3D）固态 NMR 光谱来演示 MCSA 算法，这些光谱来自几个模型蛋白样品（α- spectrin SH3 结构域和蛋白 G/B1 微晶，HET-s（218-289）原纤维），采用魔角旋转和标准极化传递技术获得。MCSA 算法和 MCASSIGN2 程序可以适应任意维度的任意 NMR 光谱组合，因此可应用于固态和溶液 NMR 的许多领域。
