Kurochkina N, Privalov G
Applied Thermodynamics, Hunt Valley, Maryland 21031-0157, USA.
Protein Sci. 1998 Apr;7(4):897-905. doi: 10.1002/pro.5560070407.
Analysis of the heterogeneity of packing in proteins showed that different groups of the protein preferentially contribute to low- or high-density regions. Statistical distribution reveals the two preferable values for packing density in the form of two peaks. One peak occurs in the range of densities 0.55-0.65, the other occurs in the range 0.75-0.8. The high-density peak is originated primarily by high packing inside the hydrogen bonded backbone and to some extent by side chains. Polar/charged and apolar side chains both contribute to the low-density peak. The average packing density values of individual atomic groups significantly vary for backbone atoms as well as for side chain atoms. The carbonyl oxygen atoms of protein backbone and the end groups of side chains show lower packing density than the rest of the protein. The side-chain atomic groups of a secondary structure element when packed against the neighboring secondary structure element form stronger contacts with the side chains of this element than with its backbone. Analysis of the low-density regions around each buried peptide group was done for the set of proteins with different types of packing, including alpha-alpha, alpha-beta, and beta-beta packing. It was shown that cavities are regularly situated in the groove of secondary structure element packed against neighboring elements for all types of packing. Low density in the regions surrounding the peptide groups and the end groups of side chains can be explained by their positioning next to a cavity formed upon the association of secondary structure elements. The model proposed can be applied to the analysis of protein internal motions, mechanisms of cellular signal transduction, diffusion through protein matrix, and other events.
对蛋白质中堆积异质性的分析表明，蛋白质的不同基团优先对低密度或高密度区域有贡献。统计分布以两个峰的形式揭示了堆积密度的两个优选值。一个峰出现在密度为0.55 - 0.65的范围内，另一个峰出现在0.75 - 0.8的范围内。高密度峰主要源于氢键主链内部的高堆积，并在一定程度上源于侧链。极性/带电侧链和非极性侧链都对低密度峰有贡献。单个原子基团的平均堆积密度值对于主链原子和侧链原子都有显著差异。蛋白质主链的羰基氧原子和侧链的末端基团显示出比蛋白质其他部分更低的堆积密度。当一个二级结构元件的侧链原子基团与相邻的二级结构元件堆积时，与该元件的侧链形成的接触比与主链形成的接触更强。对具有不同堆积类型（包括α - α、α - β和β - β堆积）的蛋白质组，分析了每个埋藏肽基团周围的低密度区域。结果表明，对于所有类型的堆积，空腔规则地位于与相邻元件堆积的二级结构元件的凹槽中。肽基团和侧链末端基团周围区域的低密度可以通过它们位于二级结构元件缔合形成的空腔旁边来解释。所提出的模型可应用于蛋白质内部运动、细胞信号转导机制、通过蛋白质基质的扩散以及其他事件的分析。
