title: Resonance Raman and vibrational mode analysis used to predict ligand geometry for docking simulations of a water soluble porphyrin and tubulin.
abstract: The ability to modify the conformation of a protein by controlled partial unfolding may have practical applications such as inhibiting its function or providing non-native photosensitive properties. A water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP), non-covalently bound to tubulin can be used as a photosensitizer, which upon irradiation can lead to conformational changes of the protein. To fully understand the mechanism responsible for this partial unfolding and determine the amino acid residues and atoms involved, it is essential to find the most likely binding location and the configuration of the ligand and protein. Techniques typically used to analyze atomic position details, such as nuclear magnetic resonance and X-ray crystallography, require large concentrations, which are incompatible with the dilute conditions required in experiments for photoinduced mechanisms. Instead, we develop an atomistic description of the TSPP-tubulin complex using vibrational mode analysis from density functional theory calculations correlated to resonance Raman spectra of the porphyrin paired with docking simulations. Changes in the Raman peaks of the porphyrin molecule correlate with changes in its structural vibrational modes when bound to tubulin. The data allow us to construct the relative geometry of the porphyrin when bound to protein, which are then used with docking simulations to find the most likely configuration of the TSPP-tubulin complex.
authors.affiliation: a Department of Physics and Astronomy , The University of Texas at San Antonio , San Antonio , TX 78249 , USA.|c Optical Radiation Bioeffects Branch, Bioeffects Division, Human Effectiveness Directorate, 711th Human Performance Wing , Air Force Research Laboratory , JBSA Fort Sam Houston, TX 78234 , USA.
authors.forename: Brady
authors.initials: B
authors.lastname: McMicken
authors.affiliation: a Department of Physics and Astronomy , The University of Texas at San Antonio , San Antonio , TX 78249 , USA.|b General Dynamics Information Technology , JBSA Fort Sam Houston, TX 78234 , USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Parker
authors.affiliation: c Optical Radiation Bioeffects Branch, Bioeffects Division, Human Effectiveness Directorate, 711th Human Performance Wing , Air Force Research Laboratory , JBSA Fort Sam Houston, TX 78234 , USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Thomas
authors.affiliation: a Department of Physics and Astronomy , The University of Texas at San Antonio , San Antonio , TX 78249 , USA.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Brancaleon
mesh_terms: D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D011166:Porphyrins / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D014404:Tubulin / Q000737:chemistry*
chemical_list: D008024:Ligands; D011166:Porphyrins; D014404:Tubulin
keywords: Raman spectroscopy; density functional theory; docking; porphyrin; tubulin