π-π stacking interactions in tryptophan-lumiflavin-tyrosine: a structural model for riboflavin insertion into riboflavin-binding protein

Abstract

Context

Riboflavin (RF), also known as B2 vitamin, is the precursor to flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), two co-enzymes involved in many electron transport processes. Interactions of the isoalloxazine ring, common to all three compounds, are of great interest due to their biological function in flavoproteins and relevance in the transport by the carrier protein leading to development of drug delivery strategies and non-invasive diagnostics techniques. Based on protein crystallographic data, a computational investigation of the interactions in the complexes between lumiflavin, a model compound, and aromatic amino acids, tyrosine and tryptophan, was pursued with the goal of characterizing noncovalent interactions. Density functional theory (DFT) served as the computation framework for all calculations, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6–311+ +g** basis set. The solvation effects were incorporated through the implementation of the polarizable continuum model (PCM) simulating an aqueous solvent environment. The geometries of the five most stable complexes show exclusively p-p interactions among the aromatic moieties in a displaced parallel plane stacking arrangement with interplanar heights and displacements in the range of 3.22–3.62 Å and 0.50–0.63 Å, respectively, at ωB97XD level. The calculated total energies and binding energies indicate two stabilizing p-p interactions: lumiflavin-tyrosine and lumiflavin-tryptophan, with the later stronger for the more stable complexes by 2 kcal mol⁻¹. The complexes are less entropically favored than the independent molecules as verified by the positive association free Gibbs energies with LC-ωPBE and nearly zero with ωB97XD. Orbital analysis indicates a smaller HOMO–LUMO gap for complexes compared to the individual compounds suggesting a charge transfer component to the interaction. Moreover, the HOMO is localized on tryptophan and HOMO-1 on tyrosine, consistent with the strength of the respective interactions with lumiflavin.

Methods

The initial geometry was based on the atom coordinates of the bonding tryptophan-riboflavin-tyrosine region in the protein crystallographic data with the ribityl tail being discarded, leading to a model complex: tryptophan-lumiflavin-tyrosine. The initial conformational search using the Amber force field within the Gabedit led to 30 unique conformations. The subsequent calculations, energy optimization and orbital analysis, were performed in Guassian16 at density functional theory (DFT) level, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6–311+ +g** basis set. The solvent, water, was accounted for using the polarized continuum model (PCM).