Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.

Journal Article (Journal Article)

Optimization of reaction paths for enzymatic systems is a challenging problem because such systems have a very large number of degrees of freedom and many of these degrees are flexible. To meet this challenge, an efficient, robust and general approach is presented based on the well-known nudged elastic band reaction path optimization method with the following extensions: (1) soft spectator degrees of freedom are excluded from path definitions by using only inter-atomic distances corresponding to forming/breaking bonds in a reaction; (2) a general transformation of the distances is defined to treat multistep reactions without knowing the partitioning of steps in advance; (3) a multistage strategy, in which path optimizations are carried out for reference systems with gradually decreasing rigidity, is developed to maximize the opportunity of obtaining continuously changing environments along the path. We demonstrate the applicability of the approach using the acylation reaction of type A beta-lactamase as an example. The reaction mechanism investigated involves four elementary reaction steps, eight forming/breaking bonds. We obtained a continuous minimum energy path without any assumption on reaction coordinates, or on the possible sequence or the concertedness of chemical events. We expect our approach to have general applicability in the modeling of enzymatic reactions with quantum mechanical/molecular mechanical models.

Full Text

Duke Authors

Cited Authors

  • Xie, L; Liu, H; Yang, W

Published Date

  • May 2004

Published In

Volume / Issue

  • 120 / 17

Start / End Page

  • 8039 - 8052

PubMed ID

  • 15267723

Electronic International Standard Serial Number (EISSN)

  • 1089-7690

International Standard Serial Number (ISSN)

  • 0021-9606

Digital Object Identifier (DOI)

  • 10.1063/1.1691404


  • eng