The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method
 

The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method


Abstract Protein internal motions influence observables of NMR experiments. The effect of internal motions occurring at the sub-nanosecond timescale can be described by NMR order parameters. Here, we report that the use of order parameters derived from Molecular Dynamics (MD) simulations of two holo-structures of Protein Kinase A increase the discrimination power of INPHARMA, an NMR based methodology that selects docked ligand orientations by maximizing the correlation of back-calculated to experimental data. By including internal motion in the back-calculation of the INPHARMA transfer, we obtain a more realistic description of the system, which better represents the experimental data. Furthermore, we propose a set of generic order parameters, derived from MD simulations of globular proteins, which can be used in the back-calculation of INPHARMA NOEs for any proteinâ??ligand complex, thus by-passing the need of obtaining system-specific order parameters for new proteinâ??ligand complexes.

• Content Type Journal Article
• Category Article
• Pages 1-12
• DOI 10.1007/s10858-012-9662-1
• Authors
  • Benjamin Stauch, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
  • Julien Orts, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
  • Teresa Carlomagno, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738

Source: Journal of Biomolecular NMR