In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations

Abstract

Most of the currently known light-harvesting complexes 2 (LH2) rings are formed by 8 or 9 subunits. As of now, questions like "what factors govern the LH2 ring size?" and "are there other ring sizes possible?" remain largely unanswered. Here, we investigate by means of molecular dynamics (MD) simulations and stochastic modeling the possibility of predicting the size of an LH2 ring from the sole knowledge of the high resolution crystal structure of a single subunit. Starting with single subunits of two LH2 rings with known size, that is, an 8-ring from Rs. moliscianum (MOLI) and a 9-ring from Rps. acidophila (ACI), and one with unknown size (referred to as X), we build atomic models of subunit dimers corresponding to assumed 8-, 9-, and 10-ring geometries. After inserting each of the dimers into a lipid-water environment, we determine the preferred angle between the corresponding subunits by three methods: (1) energy minimization, (2) free MD simulations, and (3) potential of mean force calculations. We find that the results from all three methods are consistent with each other, and when taken together, it allows one to predict with reasonable level of confidence the sizes of the corresponding ring structures. One finds that X and ACI very likely form a 9-ring, while MOLI is more likely to form an 8-ring than a 9-ring. Finally, we discuss both the merits and limitations of all three prediction methods.

Near-Infrared Spectroscopy for Predicting Structural Stability of Light-Harvesting Complex 2 from the Purple Bacteria

“…The light-absorbing pigments, BChl a and carotenoid, are noncovalently bound to two low-molecular weight apoproteins, a and b. [5] Within the complex, BChls are fixed on proteins with well-ordered orientations and are labeled according to their NIR absorption as B800 and B850. The absorption spectra of LH2 from different species of purple bacteria are similar but not identical, though they have identical BChl a molecules and structural principles.…”