Liang J, Edelsbrunner H, Fu P, Sudhakar P V, Subramaniam S
National Center for Supercomputing Applications, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana 61801, USA.
Proteins. 1998 Oct 1;33(1):18-29.
The structures of proteins are well-packed, yet they contain numerous cavities which play key roles in accommodating small molecules, or enabling conformational changes. From high-resolution structures it is possible to identify these cavities. We have developed a precise algorithm based on alpha shapes for measuring space-filling-based molecular models (such as van der Waals, solvent accessible, and molecular surface descriptions). We applied this method for accurate computation of the surface area and volume of cavities in several proteins. In addition, all of the atoms/residues lining the cavities are identified. We use this method to study the structure and the stability of proteins, as well as to locate cavities that could contain structural water molecules in the proton transport pathway in the membrane protein bacteriorhodopsin.
蛋白质的结构紧密排列，但其中包含许多腔，这些腔在容纳小分子或促成构象变化方面发挥着关键作用。从高分辨率结构中可以识别出这些腔。我们基于α形状开发了一种精确算法，用于测量基于空间填充的分子模型（如范德华模型、溶剂可及模型和分子表面描述）。我们将此方法应用于精确计算几种蛋白质中腔的表面积和体积。此外，还识别出了构成腔内壁的所有原子/残基。我们使用此方法研究蛋白质的结构和稳定性，以及在膜蛋白细菌视紫红质的质子传输途径中定位可能包含结构水分子的腔。
