On nonequivalent intermolecular stagger states in collagen fibrils.
On nonequivalent intermolecular stagger states in collagen fibrils.
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关于胶原原纤维中非等价分子间交错状态。
DOI：
10.1002/bip.1977.360160615
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发表时间：
1977
期刊：
影响因子：
2.9
通讯作者：
E. P. Katz
中科院分区：
文献类型：
--
作者：
E. Golub;E. P. Katz
最近的研究试图从原生结构的角度阐明天然胶原蛋白670-A周期性的物理化学基础。研究表明，假设Hodge-Petruska模型适用于胶原蛋白的分子包装，那么原纤维的染色模式可以通过胶原蛋白多肽的氨基酸序列来定量解释。2;以及分子间的成对吸引相互作用的数量：静电侧链@；疏水基团”;和dipole-dipoles4。当相邻分子纵向交错的距离为n X D时，会达到相对最大值，其中n为整数（0-4），D为分子间交错距离的值。这些关于侧链相互作用的研究是有限的，因为结果是定性的，因此不能与实验结果进行比较；它们也不允许在同等基础上对不同的交错状态进行比较。我们已经开发了一种计算方法来进行这些比较，并且还获得了一些实验证据来支持它的准确性。我们在这里报告了由011~胶原多肽组成的假想原纤维中不同可能的分子间交错状态的计算相互作用参数。我们的起点是由Hulmes等人描述的几何模型；假设相邻三螺旋分子之间的相互作用只能用两个a链之间的相互作用模式来解释，当每个分子都考虑轴向投影时。如果考虑的一对残基的位置在相当于胶原分子残基重复距离的三倍（即3 X 2.86 a）的距离内，则认为分子间具有相反电荷的基团（“静电键”）之间的成对相互作用是可能的；如果各自残基的位置在螺旋重复距离的两倍距离内，则认为具有大疏水基的残基之间的成对相互作用是可能的。我们描述侧链相互作用的过程与该模型在以下四个方面有所不同：1)考虑到分子内和分子间侧链相互作用之间的竞争，因为当分子间键以牺牲分子内键为代价形成时，结构的稳定能量没有净收益。另一方面，这种交换会产生有利的熵效应。2)分析了阵列分子之间的相互作用，而不是孤立的分子对之间的相互作用。这是为了确保在比较不同错开状态的结果时使用相同的基础。（在双分子计算中，可以参与分子间相互作用的残基的绝对数量随着错开距离的增加而逐渐减少，因为在这种情况下，接触的分子的比例也会减少。）3)考虑了给定交错状态下可能存在的侧链相互作用模式的多样性。生成给定交错态的所有可能的相互作用模式，并确定包含最大数量的分子内键（“总键”），以避免因任意选择一种侧链相互作用模式而使结果产生偏差。4)在制表过程中严格保持质量守恒，避免了涉及相同残基的键形成的多次计数。
Recent studies have attempted to elucidate the physical-chemical basis for the 670-A periodicity of native collagen from considerations of the primary structure.” It has been shown that the staining pattern of fibrils can be quantitatively accounted for by the amino-acid sequence of a polypeptide of collagen assuming that the Hodge-Petruska modelX for the molecular packing of collagen applies’. 2; and that the numbers of intermolecular pairwise attractive interactions between: electrostatic side chain@; hydrophobic groups’; and dipole-dipoles4.’go through relative maxima when adjacent molecules are longitudinally staggered with respect to one another by distances of n X D, where n is an integer (0-4), and D is the value of the intermolecular stagger distance. These studies of side chain interactions, how€ xr, were limited in that the results were qualitative, and thus could not be compared to experimental findings; they also did not permit a comparison of different stagger states on an equivalent basis. We have developed a method of calculation that permits these comparisons, and moreover have obtained some experimental evidence supporting its accura~ y.~,~~ We report here calculated interaction parameters for different possible intermolecular stagger states in hypothetical fibrils comprised of 011~ collagen polypeptides. Our starting point was the geometric model described by Hulmes et al.;’which assumes that interactions between adjacent triple-helical molecules can be accounted for in terms of the interaction pattern between two a chains only, when each is considered in axial projection. Intermolecular, pairwise interactions between oppositely charged groups (“electrostatic bonds”) are deemed possible if the positions of the pair of residues under consideration are within a distance equivalent to three times the residue repeat distance of a collagen molecule (ie, 3 X 2.86 A), and between residues having large hydrophobic groups (hydrophobic bonds) if the positions of respective residues are within a distance of two times the helical repeat distance. Our procedure for characterizing side chain interactions differs from this model in the following four ways: 1) The competition between intra-and intermolecular side chain interactions is taken into account since there is no net gain in the stabilizing energy of a structure when an intermolecular bond is formed at the expense of an intramolecular bond. On the other hand there would be a favorable entropy effect associated with such an interchange. 2) Interactions between molecules in an array rather than between an isolated pair of molecules were analyzed. This is to ensure that the same basis is used when comparing results for different stagger states.(In a two-molecule calculation the absolute number of residues which can participate in intermolecular interactions progressively decreases with increasing stagger distance, as the portion of the molecules in contact also decreases in this situation.) 3) The multiplicity of side chain interaction patterns which is possible for a given stagger state was taken into account. All possible interaction patterns for a given stagger state were generated and the ones containing the maximum number of inter-plus intramolecular bonds (“total bonds”) were determined to avoid biasing the results by arbitrarily choosing one pattern of side chain interactions. 4) Conservation of mass was strictly maintained in the tabulation procedures to avoid multiple counting of bond formation involving the same residues.