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Research Article

Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins

  1. Jie Liang1,2,†,
  2. Herbert Edelsbrunner2,
  3. Ping Fu1,
  4. Pamidighantam V. Sudhakar1,
  5. Shankar Subramaniam1,3,*

Article first published online: 7 DEC 1998

DOI: 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 33, Issue 1, pages 18–29, 1 October 1998

Additional Information

How to Cite

Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P. V. and Subramaniam, S. (1998), Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins, 33: 18–29. doi: 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H

Author Information

  1. 1

    National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois

  2. 2

    Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois

  3. 3

    Beckman Institute for Advanced Science and Technology, Departments of Biochemistry, Molecular & Integrative Physiology, and Chemical Engineering, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois

  1. †

    Department of Cheminformatics, SmithKline Beecham Pharmaceuticals, PO Box 1539, UW2940, 709 Swedeland Road, King of Prussia, PA 19406

*Beckman Institute for Advanced Science and Technology, Departments of Biochemistry, Molecular & Integrative Physiology, and Chemical Engineering, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801

Publication History

  1. Issue published online: 7 DEC 1998
  2. Article first published online: 7 DEC 1998
  3. Manuscript Accepted: 7 APR 1998
  4. Manuscript Received: 3 SEP 1996

Funded by

  • NSF. Grant Numbers: ASC 94-04900, ASC 92-00301, CCR 91-18874, ASC 89-02829, MCB 92-19619, DBI 94-04223
  • ONR. Grant Number: N00014-95-1-0692

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Keywords:

  • molecular cavities;
  • packing defects;
  • Delaunay complex;
  • alpha shape;
  • structural solvent in proteins

Abstract

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. Proteins 33:18–29, 1998. © 1998 Wiley-Liss, Inc.

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