Energy flow and intersubunit signalling in GSAM: A non-equilibrium molecular dynamics study

Abstract

Non-equilibrium molecular dynamics simulations of vibrational energy flow induced by the imposition of a thermal gradient have been performed on the μ2-dimeric enzyme glutamate-1-semialdehyde aminomutase (GSAM), the key enzyme in the biosynthesis of chlorophyll, in order to identify energy transport pathways and to elucidate their role as potential allosteric communication networks for coordinating functional dynamics, specifically the negative cooperativity observed in the motion of the two active site gating loops. Fully atomistic MD simulations of thermal diffusion were executed with a GROMACS simulation package on a fully solvated GSAM enzyme by heating various active site target ligands (initially, catalytic intermediates and cofactors) to 300K while holding the remainder of the protein and the solvent bath at 10K and monitoring the temperature T(t) of all the enzyme residues as a function of time over a 1ns observation window. Energy is observed to be deposited in a relatively small number of discrete chains of residues most of which contribute to specific structural or biochemical functionality. Thermal linkages between all thermally active chains were established by isolating a specific pair of chains and performing a thermal diffusion simulation on the pair, one held at 300K and the other at 10K, with the rest of the protein frozen in its initial atomic configuration and thus thermally unresponsive. Proceeding in this way, it was possible to map out multiple pathways of vibrational energy flow leading from one of the active sites through a network of contiguous residues, many of which were evolutionarily conserved and linked by hydrogen bonds, into the other active site and ultimately to the other gating loop.