19 February 2011 Correlating computational docking predictions with Raman spectroscopy for β-lactoglobulin-porphyrin complexes
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Proceedings Volume 7897, Optical Interactions with Tissue and Cells XXII; 789717 (2011); doi: 10.1117/12.881729
Event: SPIE BiOS, 2011, San Francisco, California, United States
Abstract
Computational molecular docking simulations (Dock and AutoDock) may provide a wealth of structural information related to the bound configuration of protein-ligand complexes, but they require verification to ensure their results correctly predict the bound complex. Resonance Raman spectroscopy data has been collected to correlate normal mode vibrations observed in the bound configurations to computationally generated structures in order to determine the best match between the in silico model and experiment. This methodology was used to determine the bound structures at an atomistic level of β-lactoglobulin (BLG) and meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP) in aqueous solutions at pH 7 and 9. Comparisons of Raman spectra of TSPP before and after binding to BLG yield line shifts that are generated by the noncovalent binding of the ligand to the protein. Previous studies have shown that the Tanford transition in BLG, which occurs above pH 7.9, destabilizes the protein, allowing it to undergo a laser-induced structural change when bound to TSPP and illuminated by at least 0.3 J of laser energy. By examining the structures at pHs above and below the transition, we hope to reveal the mechanism of action that initiates the laser-induced changes in the protein. Future studies will use the computed bound configuration as an initial condition for molecular dynamics simulations of the laser-protein-complex interaction to predict the final state of the protein after irradiation.
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James Parker, Lorenzo Brancaleon, "Correlating computational docking predictions with Raman spectroscopy for β-lactoglobulin-porphyrin complexes", Proc. SPIE 7897, Optical Interactions with Tissue and Cells XXII, 789717 (19 February 2011); doi: 10.1117/12.881729; https://doi.org/10.1117/12.881729
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KEYWORDS
Raman spectroscopy

Proteins

Computer simulations

Data modeling

Chemical species

Molecular lasers

Molecules

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