Combination of Resonance
Raman Spectroscopy and Docking
Simulations to Study the Nonspecific Binding of a Free-Base Porphyrin
to a Globular Protein
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Abstract
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
(<i>p</i>-sulfonatophenyl) porphyrin, to a globular protein, <i>β-</i>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