Improved mapping of protein binding sites

T. Körtvélyesi, Michael Silberstein, Sheldon Dennis, Sandor Vajda

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Computational mapping methods place molecular probes - small molecules or functional groups - on a protein surface in order to identify the most favorable binding positions by calculating an interaction potential. Mapping is an important step in a number of flexible docking and drug design algorithms. We have developed improved algorithms for mapping protein surfaces using small organic molecules as molecular probes. The calculations reproduce the binding of eight organic solvents to lysozyme as observed by NMR, as well as the binding of four solvents to thermolysin, in good agreement with x-ray data. Application to protein tyrosine phosphatase 1B shows that the information provided by the mapping can be very useful for drug design. We also studied why the organic solvents bind in the active site of proteins, in spite of the availability of alternative pockets that can very tightly accommodate some of the probes. A possible explanation is that the binding in the relatively large active site retains a number of rotational states, and hence leads to smaller entropy loss than the binding elsewhere else. Indeed, the mapping reveals that the clusters of the ligand molecules in the protein's active site contain different rotational-translational conformers, which represent different local minima of the free energy surface. In order to study the transitions between different conformers, reaction path and molecular dynamics calculations were performed. Results show that most of the rotational states are separated by low free energy barriers at the experimental temperature, and hence the entropy of binding in the active site is expected to be high.

Original languageEnglish
Pages (from-to)173-186
Number of pages14
JournalJournal of Computer-Aided Molecular Design
Volume17
Issue number2-4
DOIs
Publication statusPublished - Feb 2003

Fingerprint

Binding sites
Protein Binding
Catalytic Domain
Binding Sites
proteins
Proteins
Molecular Probes
Drug Design
Entropy
Membrane Proteins
Organic solvents
Non-Receptor Type 1 Protein Tyrosine Phosphatase
Free energy
Molecules
rotational states
Thermolysin
probes
drugs
Molecular Dynamics Simulation
Muramidase

Keywords

  • Consensus site
  • Drug design
  • Enzyme active site
  • Ligand binding
  • Ligand motion
  • Molecular dynamics
  • Reaction path
  • site mapping

ASJC Scopus subject areas

  • Molecular Medicine

Cite this

Improved mapping of protein binding sites. / Körtvélyesi, T.; Silberstein, Michael; Dennis, Sheldon; Vajda, Sandor.

In: Journal of Computer-Aided Molecular Design, Vol. 17, No. 2-4, 02.2003, p. 173-186.

Research output: Contribution to journalArticle

Körtvélyesi, T. ; Silberstein, Michael ; Dennis, Sheldon ; Vajda, Sandor. / Improved mapping of protein binding sites. In: Journal of Computer-Aided Molecular Design. 2003 ; Vol. 17, No. 2-4. pp. 173-186.
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