DFT-Based Simulations of Amide I′ IR Spectra of a Small Protein in Solution Using Empirical Electrostatic Map with a Continuum Solvent Model

• Published in: The journal of physical chemistry. B 2012-09, Vol.116 (35), p.10739-10747
• Main Authors: Welch, William R. W, Kubelka, Jan
• Format: Article
• Language: English
• Subjects: Amides; Amides - chemistry; Computer simulation; Continuums; Electrostatics; Holes; Molecular Dynamics Simulation; Protein Structure, Tertiary; Proteins; Solutions - chemistry; Solvents; Solvents - chemistry; Spectra; Spectrophotometry, Infrared; Static Electricity; Viral Core Proteins - chemistry; Viral Core Proteins - metabolism
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp305387x

A continuum solvent model was tested for simulations of amide I′ IR spectra for a 40-residue subdomain of P22 viral coat protein in aqueous solution. Spectra obtained using DFT (BPW91/6-31G**) parameters for a reduced all-Ala representation of the protein were corrected by an electrostatic potential map obtained from the solvent cavity surface and AMBER99 side-chain atom partial charges. Various cavity sizes derived from van der Waals atomic radii with an added effective solvent radius up to 2.0 Å were tested. The interplay of the side-chain and solvent electrostatic effects was investigated by considering the side chains and solvent separately as well as together. The sensitivity to side-chain conformational fluctuations and to the parametrization of Cβ group partial charges was also tested. Simulation results were compared to the experimental amide I′ spectra of P22 subdomain, including two 13C isotopically edited variants, as well as to the previous simulations based on the molecular dynamics trajectory in explicit solvent. For small cavity sizes, between van der Waals and that with added solvent radius of 0.5 Å, better qualitative agreement with experiment was obtained than with the explicit solvent representation, in particular for the 13C-labeled spectra. Larger protein cavities led to progressively worse predictions due to increasingly stronger electrostatic effects of side chains, which could no longer be well compensated for by the solvent potential. Balance between side-chain and solvent electrostatic effects is important in determining the width and shape of the simulated amide I′, which is also virtually unaffected by side-chain-geometry fluctuations. The continuum solvent model combined with the electrostatic map is a computationally efficient and potentially robust approach for the simulations of IR spectra of proteins in solution.