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

Computational and Structural Biotechnology Journal
C Harder-ViddalJ Stetefeld

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 300 K while holding the remainder of the protein and the solvent bath at 10 K and monitoring the temperature T ( t ) of all the enzyme residues as a function of time over a 1 n s 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 ch...Continue Reading

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Citations

Oct 28, 2020·The Journal of Physical Chemistry. B·Humanath PoudelDavid M Leitner

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Methods Mentioned

BETA
X-ray

Software Mentioned

GROMACS
PyMOL
ClustalW
PRODRG2
BLAST
DAVA
PSI

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