The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study.
We report on an atomistic molecular dynamics simulation of the complete conformational transition of Escherichia coli adenylate kinase (ADK) using the recently developed TEE-REX algorithm. Two phases characterize the transition pathway of ADK, which folds into the domains CORE and LID and the AMP binding domain AMPbd. Starting from the closed conformation, half-opening of the AMPbd precedes a partially correlated opening of the LID and AMPbd, defining the second phase. A highly stable salt bridge D118-K136 at the LID-CORE interface, contributing substantially to the total nonbonded LID-CORE interactions, was identified as a major factor that stabilizes the open conformation. Alternative transition pathways, such as AMPbd opening following LID opening, seem unlikely, as full transition events were not observed along this pathway. The simulation data indicate a high enthalpic penalty, possibly obstructing transitions along this route.
Kubitzki
Marcus B
MB
Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
de Groot
Bert L
BL
D000263:Adenylate Kinase / Q000737:chemistry*; D000465:Algorithms; D003198:Computer Simulation; D004926:Escherichia coli / Q000201:enzymology; D008968:Molecular Conformation; D011487:Protein Conformation; D012984:Software; D013816:Thermodynamics
D000263:Adenylate Kinase