Molecular Dynamics Simulations of the <i>Escherichia
coli</i> HPPK Apo-enzyme Reveal a Network of Conformational Transitions
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Abstract
6-Hydroxymethyl-7,8-dihydropterin
pyrophosphokinase (HPPK) catalyzes
the first reaction in the folate biosynthetic pathway. Comparison
of its X-ray and nuclear magnetic resonance structures suggests that
the enzyme undergoes significant conformational change upon binding
to its substrates, especially in three catalytic loops. Experimental
research has shown that even when confined by crystal contacts, loops
2 and 3 remain rather flexible when the enzyme is in its apo form,
raising questions about the putative large-scale induced-fit conformational
change of HPPK. To investigate the loop dynamics in a crystal-free
environment, we performed conventional molecular dynamics simulations
of the apo-enzyme at two different temperatures (300 and 350 K). Our
simulations show that the crystallographic <i>B</i>-factors
considerably underestimate the loop dynamics; multiple conformations
of loops 2 and 3, including the open, semi-open, and closed conformations
that an enzyme must adopt throughout its catalytic cycle, are all
accessible to the apo-enzyme. These results revise our previous view
of the functional mechanism of conformational change upon MgATP binding
and offer valuable structural insights into the workings of HPPK.
In this paper, conformational network analysis and principal component
analysis related to the loops are discussed to support the presented
conclusions