Measurement of protein surface shape by solid angles |
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| Affiliation: | 1. Laboratório Associado de Plasma (LAP), Instituto Nacional de Pesquisas Espaciais (INPE)/MCT, CP 515, São José dos Campos, São Paulo CEP 1224 7-9 70, Brazil;2. Universidade de Santa Catarina, Departamento de Engenharia Mecanica, 88040-900 Florianopolis, Santa Catarina, Brazil;3. Università di Perugia, Dipartimento di Chimica, Biologia e Biotecnologie, 06123 Perugia, Italy;4. Universidade de Brasìlia, Instituto de Fìsica – Campus Universitàrio Darcy Ribeiro, Brasìlia, Brazil;5. Consiglio Nazionale delle Ricerche, Istituto di Struttura della Materia, 00016 Roma, Italy;6. Instituto de Física, Universidade Federal da Bahia, 40210 Salvador, Brazil;1. State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China;2. Beijing Institute of Astronautical Systems Engineering, Beijing 100076, China;1. Ural Federal University, Lenin Av. 51, Ekaterinburg, Russia;2. University of Vienna, Sensengasse 8, Vienna, Austria;1. Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico;2. Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA |
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| Abstract: | A method for measuring the gross shape of local regions of protein surface is presented and applied to an examination of three proteins. Any point on the protein surface can be assigned a number that measures the degree of convexity or concavity of the surface in the vicinity of the point. This number is computed by centring a sphere at that point and measuring how much of the sphere lies inside the protein. The sphere radius is a parameter chosen according to the scale of the features that are being analysed. The amount of sphere intersecting the protein is interpreted as a solid angle, denoted omega. Three proteins are analysed by this method: lysozyme, Superoxide dismutase and chymotrypsin. The resulting omega values are used to colour code the protein surfaces displayed on a colour raster graphics terminal. The method can be seen to reliably identify protrusions and depressions. The difficulty of developing a generally useful method for measuring protein surface shape is discussed. Possible applications of the solid-angle method include the analysis of shape complementarity at protein interfaces, the development of computer algorithms for predicting complexes between proteins, or between proteins and ligands, the identification of homologous epitopes on different proteins that might be immunologically crossreactive, and the determination of correlations between surface geometry and chemical properties. |
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