Abstract

Photosynthesis is the process responsible for nearly all life on Earth. Pigment-protein complexes, fundamental components of photosynthesis, are the subject of many studies to better understand this process and develop novel approaches to harvesting light energy. Observations of line shifts in the single-molecule optical spectra of such complexes through optical spectroscopy indicate structural changes in the chlorophyll environment. Nonetheless, the specific molecular elements responsible for the observed spectral dynamics remain largely unknown. In this project, we have studied the Water-Soluble Chlorophyll-binding Protein to elucidate some of these molecular-level mechanisms. Molecular Dynamics simulations of the complex were conducted at T1 = 300 K and T2= 165 K for 1 μs. The vicinity of the chlorophylls was determined by computing the pigments contact map. At 300 K, small conformational changes were discovered, involving side chain rotations of certain residues, primarily the non-polar Leucine and Valine. From those observations, the protein free energy landscape associated with this generalized coordinate was mapped, and the heights of the energy barriers were determined at around 1000-1500 cm−1. This range of values agrees with experimental results. To gain a deeper understanding of these residues dynamics, we performed Dynamical Network Analysis. It revealed high motion correlations between residues located in close proximity, suggesting a similar rate of conformational change among these residues. Through network connectivity analysis, we found a similar side chain rotation in the same residue in each monomer located farther from the pigments. The energy barrier height associated with this residue is also consistent with experimental results.