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.

Keywords:

• Raman spectroscopy
• density functional theory
• docking
• porphyrin
• tubulin

Acknowledgments

The authors would also like to thank Gary Noojin for crucial technical support and expertise.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

Funding was provided by the Air Force Research Laboratory, Human Effectiveness Directorate and [grant number 12RH09COR] from the Air Force Office of Scientific Research. This work was supported in part by a grant of computer time from the DoD High-Performance Computing Modernization Program at the Army Research Laboratory; DoD Supercomputing Resource Center. B.M. is supported by the Consortium Research Fellows Program [grant number FA8650-13-2-6366].