Department of Computer Science, Western Washington University, 516 High Street, Bellingham, WA 98225, USA.
Department of Computer Science and Engineering, Lehigh University, 19 Memorial Drive West, Bethlehem, PA 18015, USA.
Molecules. 2018 Feb 7;23(2):351. doi: 10.3390/molecules23020351.
The geometry of cavities in the surfaces of proteins facilitates a variety of biochemical functions. To better understand the biochemical nature of protein cavities, the shape, size, chemical properties, and evolutionary nature of functional and nonfunctional surface cavities have been exhaustively surveyed in protein structures. The rigidity of surface cavities, however, is not immediately available as a characteristic of structure data, and is thus more difficult to examine. Using rigidity analysis for assessing and analyzing molecular rigidity, this paper performs the first survey of the relationships between cavity properties, such as size and residue content, and how they correspond to cavity rigidity. Our survey measured a variety of rigidity metrics on 120,323 cavities from 12,785 sequentially non-redundant protein chains. We used VASP-E, a volume-based algorithm for analyzing cavity geometry. Our results suggest that rigidity properties of protein cavities are dependent on cavity surface area.
蛋白质表面腔的几何形状促进了各种生化功能。为了更好地理解蛋白质腔的生化性质，人们对蛋白质结构中的功能和非功能表面腔的形状、大小、化学性质和进化性质进行了详尽的调查。然而，由于表面腔的刚性不是结构数据的特征，因此更难以检查。本文使用刚性分析来评估和分析分子刚性，首次调查了腔特性（如大小和残基含量）与腔刚性之间的关系。我们的调查对来自 12785 条连续非冗余蛋白质链的 120323 个腔进行了各种刚性度量的测量。我们使用了基于体积的分析腔几何 VASP-E 算法。我们的结果表明，蛋白质腔的刚性特性取决于腔表面积。
