PACKING OF ALPHA-HELICES - GEOMETRICAL CONSTRAINTS AND CONTACT AREAS
PACKING OF ALPHA-HELICES - GEOMETRICAL CONSTRAINTS AND CONTACT AREAS
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DOI：
10.1016/0022-2836(78)90201-2
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发表时间：
1978-01-01
影响因子：
5.6
通讯作者：
RICHARDS, FM
中科院分区：
文献类型：
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作者：
RICHMOND, TJ;RICHARDS, FM
检查了抹香鲸肌红蛋白的螺旋堆积。依次使用基于每个螺旋轴的柱坐标，螺旋的侧链原子与结构其他部分的周围原子的重叠为2.3°，但分布完全不均匀，并且每个螺旋至少在1个位置发生严重重叠。自然结构中任何螺旋的简单轴向平移或旋转都是不允许的运动。沿至少 1 个方向垂直于螺旋轴的平移不受互锁侧链的限制。 2 个螺旋沿连接其轴的接触法线接近，在约 6 埃的距离处产生溶剂排斥效应。从最终位置。在这种相互作用位点中发现的溶剂排除区域相当于对缔合自由能的巨大疏水贡献。 6 个主要地点本身相当于从扩展香肠模型到原生结构的总面积变化的 40%。这些位点的平均原子堆积密度和这些值的 SD 相似，并且等于整个蛋白质的值。密堆积球体的螺旋与实际的肽螺旋形成有用的近似。索引号4的螺旋与α-螺旋密切对应。所需的球体尺寸在体积上与亮氨酸或蛋氨酸等残基相对应。此类螺旋的预测堆积方案对应于实际看到的 3 种通用相互作用类别。利用密堆积球螺旋所暗示的几何形状，提出了一种算法，用于在已知序列的肽链中挑选潜在的强螺旋-螺旋相互作用位点。当与初步二级结构预测相结合时，该算法可能会有效地限制在通用折叠程序的对接部分中对这些特定类型的接触的搜索。
The helical packing in sperm whale myoglobin was examined. Using cylindrical co-ordinates based on each helix axis in turn, the overlap of the side-chain atoms of a helix with the surrounding atoms from other parts of the structure was 2.3 .ANG., but the distribution was not at all uniform and severe overlap occurred in at least 1 location for each helix. Simple axial translations or rotations of any helix in the native structure are not permitted motions. Translation perpendicular to the helix axis in at least 1 direction is not restricted by interlocking side-chains. The approach of 2 helices along the contact normal connecting their axes produces solvent exclusion effects at a distance of about 6 .ANG. from the final position. The solvent-excluded area found in such interaction sites is equivalent to a large hydrophobic contribution to the free energy of association. The 6 principal sites correspond by themselves to 40% of the total area change in going from the extended sausage model to the native structure. The mean atom-packing densities for these sites and the SD of these values are similar and are equal to that found for the protein as a whole. Helices of close-packed spheres form useful approximations to actual peptide helices. The helix of index number 4 corresponds closely to an .alpha.-helix. The required sphere size corresponds in volume to residues such as leucine or methionine. The predicted packing scheme for such helices corresponds to the 3 general classes of interactions actually seen. Making use of the geometry implied by the close-packed sphere helix, an algorithm is proposed for picking potentially strong helix-helix interaction sites in peptide chains of known sequence. When combined with preliminary secondary structure predictions, this algorithm might usefully restrict the search for these specific types of contact in the docking portion of a general folding program.