Algorithms for computational solvent mapping of proteins.
Computational mapping methods place molecular probes (small molecules or functional groups) on a protein surface to identify the most favorable binding positions by calculating an interaction potential. We have developed a novel computational mapping program called CS-Map (computational solvent mapping of proteins), which differs from earlier mapping methods in three respects: (i) it initially moves the ligands on the protein surface toward regions with favorable electrostatics and desolvation, (ii) the final scoring potential accounts for desolvation, and (iii) the docked ligand positions are clustered, and the clusters are ranked on the basis of their average free energies. To understand the relative importance of these factors, we developed alternative algorithms that use the DOCK and GRAMM programs for the initial search. Because of the availability of experimental solvent mapping data, lysozyme and thermolysin are considered as test proteins. Both DOCK and GRAMM speed up the initial search, and the combined algorithms yield acceptable mapping results. However, the DOCK-based approaches place the consensus site farther from its experimentally determined position than CS-Map, primarily because of the lack of a solvation term in the initial search. The GRAMM-based program also finds the correct consensus site for thermolysin. We conclude that good sampling is the most important requirement for successful mapping, but accounting for desolvation and clustering of ligand positions also help to reduce the number of false positives.
Kortvelyesi
Tamas
T
Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA.
Dennis
Sheldon
S
Silberstein
Michael
M
Brown
Lawrence
L
Vajda
Sandor
S
D019840:2-Propanol / Q000737:chemistry / Q000378:metabolism; D000096:Acetone / Q000737:chemistry / Q000378:metabolism; D000097:Acetonitriles / Q000737:chemistry / Q000378:metabolism; D000465:Algorithms; D001665:Binding Sites; D001667:Binding, Competitive; D003198:Computer Simulation; D004527:Egg Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D019800:Phenol / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012997:Solvents / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D013820:Thermolysin / Q000737:chemistry / Q000378:metabolism
D000097:Acetonitriles; D004527:Egg Proteins; D011506:Proteins; D012997:Solvents; D000096:Acetone; D019800:Phenol; D009113:Muramidase; D013820:Thermolysin; D019840:2-Propanol; C032159:acetonitrile