Holak T A, Kearsley S K, Kim Y, Prestegard J H
Department of Chemistry, Yale University, New Haven, Connecticut 06511.
Biochemistry. 1988 Aug 9;27(16):6135-42. doi: 10.1021/bi00416a046.
Distance constraints from two-dimensional NMR cross-relaxation data are used to derive a three-dimensional structure for acyl carrier protein from Escherichia coli. Several approaches to structure determination are explored. The most successful proves to be an approach that combines the early stages of a distance geometry program with energy minimization in the presence of NMR constraints represented as pseudopotentials. Approximately 450 proton to proton distance constraints including 50 long-range constraints were included in these programs. Starting structures were generated at random by the distance geometry program and energies minimized by a molecular mechanics module to give final structures. Seven of the structures were deemed acceptable on the basis of agreement with experimentally determined distances. Root-mean-square deviations from the mean of these structures for backbone atoms range from 2 to 3 A. All structures show three roughly parallel helices with hydrophobic residues facing inward and hydrophilic residues facing outward. A hydrophobic cleft is recognizable and is identified as a likely site for acyl chain binding.
利用二维核磁共振交叉弛豫数据的距离约束来推导大肠杆菌酰基载体蛋白的三维结构。探索了几种结构测定方法。最成功的方法是将距离几何程序的早期阶段与在以伪势表示的核磁共振约束存在下的能量最小化相结合。这些程序中包括大约450个质子到质子的距离约束，其中有50个长程约束。起始结构由距离几何程序随机生成，并通过分子力学模块使能量最小化以得到最终结构。根据与实验确定的距离的一致性，其中七个结构被认为是可接受的。这些结构主链原子相对于其平均值的均方根偏差在2到3埃之间。所有结构都显示出三条大致平行的螺旋，疏水残基向内，亲水残基向外。可识别出一个疏水裂缝，并将其确定为酰基链结合的可能位点。
