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• W2011168082 abstract "Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK·MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design." @default.
• W2011168082 created "2016-06-24" @default.
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• W2011168082 date "2005-07-01" @default.
• W2011168082 modified "2023-10-12" @default.
• W2011168082 title "Loop Conformation and Dynamics of the Escherichia coli HPPK Apo-Enzyme and Its Binary Complex with MgATP" @default.
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• W2011168082 doi "https://doi.org/10.1529/biophysj.105.061556" @default.
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