BIOPHYSICAL THEORY AND MODELING |
Loop Conformation and Dynamics of the E. coli HPPK Apo-
enzyme and Its Binary Complex with MgATP
Rong Yang 1, Matthew C. Lee 1, Honggao Yan 2 and Yong Duan 3*
1 University of Delaware
2 Michigan State University
3 University of California at Davis
* To whom correspondence should be addressed. E-mail: duan{at}ucdavis.edu.
Submitted on February 17, 2005
Revised on March 28, 2005
Accepted on 5 April 2005
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Abstract |
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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 HPPKMgATP 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.
Key Words:
AMBER ff03, antibacterial drug design, induced fit, locally enhanced sampling, molecular dynamics, pyrophosphokinase
