Combination of resonance Raman spectroscopy and docking simulations to study the nonspecific binding of a free-base porphyrin to a globular protein.
Understanding the conformational changes induced by small ligands noncovalently bound to proteins is a central problem in biophysics. We focus on the binding location of the water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin, to a globular protein, β-lactoglobulin, which has been observed to partially unfold when irradiated by laser light. Identifying the binding location is necessary to determine the mechanism of action as well as the atoms and residues involved in the photoinduced partial unfolding. Such atomic details are typically investigated by nuclear magnetic resonance or X-ray crystallography. However, for biomolecules in solution at the low concentrations (μM) required to deliver uniform laser irradiation, these traditional techniques do not currently provide sufficient information, and one must rely upon less direct spectroscopic methods. We describe a method that uses resonance Raman spectroscopy and density functional theory (DFT) to select the most likely binding configuration among a set of solutions yielded by computational docking algorithms. This methodology may be generalized to use with other ligand-protein complexes where the ligand structure is amenable to DFT simulations.
General Dynamics Information Technology, San Antonio, Texas 78234, USA.
James E
JE
Parker
Robert J
RJ
Thomas
Dayla
D
Morisson
Lorenzo
L
Brancaleon
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D018360:Crystallography, X-Ray; D007782:Lactoglobulins / Q000737:chemistry / Q000378:metabolism*; D062105:Molecular Docking Simulation; D011166:Porphyrins / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D058767:Protein Unfolding; D013059:Spectrum Analysis, Raman
D007782:Lactoglobulins; D011166:Porphyrins; C541374:mesotetrakis(sulfonatophenyl)porphyrin