Identification of substrate binding sites in enzymes by computational solvent mapping

Michael Silberstein, Sheldon Dennis, Lawrence Brown, T. Körtvélyesi, Karl Clodfelter, Sandor Vajda

Research output: Contribution to journalArticle

64 Citations (Scopus)

Abstract

Enzyme structures determined in organic solvents show that most organic molecules cluster in the active site, delineating the binding pocket. We have developed algorithms to perform solvent mapping computationally, rather than experimentally, by placing molecular probes (small molecules or functional groups) on a protein surface, and finding the regions with the most favorable binding free energy. The method then finds the consensus site that binds the highest number of different probes. The probe-protein interactions at this site are compared to the intermolecular interactions seen in the known complexes of the enzyme with various ligands (substrate analogs, products, and inhibitors). We have mapped thermolysin, for which experimental mapping results are also available, and six further enzymes that have no experimental mapping data, but whose binding sites are well characterized. With the exception of haloalkane dehalogenase, which binds very small substrates in a narrow channel, the consensus site found by the mapping is always a major subsite of the substrate-binding site. Furthermore, the probes at this location form hydrogen bonds and non-bonded interactions with the same residues that interact with the specific ligands of the enzyme. Thus, once the structure of an enzyme is known, computational solvent mapping can provide detailed and reliable information on its substrate-binding site. Calculations on ligand-bound and apo structures of enzymes show that the mapping results are not very sensitive to moderate variations in the protein coordinates.

Original languageEnglish
Pages (from-to)1095-1113
Number of pages19
JournalJournal of Molecular Biology
Volume332
Issue number5
DOIs
Publication statusPublished - Oct 3 2003

Fingerprint

Binding Sites
Enzymes
haloalkane dehalogenase
Ligands
Thermolysin
Molecular Probes
Hydrogen
Catalytic Domain
Membrane Proteins
Proteins

Keywords

  • Ligand binding
  • Organic solvent
  • Protein solvation
  • Structural genomics
  • X-ray structure

ASJC Scopus subject areas

  • Virology

Cite this

Identification of substrate binding sites in enzymes by computational solvent mapping. / Silberstein, Michael; Dennis, Sheldon; Brown, Lawrence; Körtvélyesi, T.; Clodfelter, Karl; Vajda, Sandor.

In: Journal of Molecular Biology, Vol. 332, No. 5, 03.10.2003, p. 1095-1113.

Research output: Contribution to journalArticle

Silberstein, Michael ; Dennis, Sheldon ; Brown, Lawrence ; Körtvélyesi, T. ; Clodfelter, Karl ; Vajda, Sandor. / Identification of substrate binding sites in enzymes by computational solvent mapping. In: Journal of Molecular Biology. 2003 ; Vol. 332, No. 5. pp. 1095-1113.
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