An implementation of the nudged elastic band algorithm and application to the reaction mechanism of HGXPRTase from Plasmodium falciparum.
The understanding of transition processes, such as chemical reactions, is a central topic in theoretical molecular science. A common approach for investigating such processes is to calculate paths between reactant and product structures that are representative of the transition. Many approaches have been proposed to determine such paths but, in this paper, we examine the nudged elastic band algorithm which was recently introduced by Jónsson and co-workers and has been used to study a wide range of transition problems. We describe our implementation of the method in the simulation program Dynamo and some modifications to the original algorithm that we found improve its efficiency. The use of the method is illustrated by an application to the reaction mechanism of the enzyme hypoxanthine-guanine-xanthine phosphoribosyltransferase from Plasmodium falciparum.
Crehuet
Ramon
R
Institut d'Investigacions Químiques i Ambientals de Barcelona (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain. rcsqtc@iiqab.csic.es
Thomas
Aline
A
Field
Martin J
MJ
D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D004548:Elasticity; D008958:Models, Molecular; D010430:Pentosyltransferases / Q000737:chemistry* / Q000378:metabolism; D010963:Plasmodium falciparum / Q000201:enzymology*; D015800:Protozoan Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
D004151:Dipeptides; D015800:Protozoan Proteins; D010430:Pentosyltransferases; C083867:hypoxanthine-guanine-xanthine phosphoribosyltransferase; D000409:Alanine