Identification of residues potentially involved in optical shifts in the water-soluble chlorophyll-a binding protein through molecular dynamics simulations

Abstract

Reversible light- and thermally-induced spectral shifts are universally observed in a wide variety of pigment-protein complexes, at temperatures ranging from cryogenic to ambient. They can be observed either directly, in single-molecule spectroscopy experiments, or via non-photochemical spectral hole burning. These shifts are important to understand, for example, to gain a clearer picture of the primary processes of photosynthesis, or of general features of the protein energy landscapes. In this article, we have employed large-scale molecular dynamics simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. The common requirement for all these mechanisms is the presence of doublewell (or multiple-well) features of the protein energy landscapes. In this work, from large-scale molecular dynamics simulations of the Water-Soluble Chlorophyll-binding Protein complex, we identified side chain rotations of certain amino acid residues as likely candidates for relevant multi-well landscape features. The protein free energy landscapes associated with side chain rotations feature energy barriers of around 1100- 1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric landscape and moment of inertia of a relevant magnitude.