A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase.

ABSTRACT: The transfer of ammonia in carbamoyl phosphate synthetase (CPS) was investigated by molecular dynamics simulations and experimental characterization of mutations within the ammonia tunnel. In CPS, ammonia is derived from the hydrolysis of glutamine and this intermediate must travel approximately 45 A from the site of formation in the small subunit to the site of utilization in the large subunit. In this investigation, the migration of ammonia was analyzed from the exit of the small subunit through the large subunit where it ultimately reacts with the carboxy phosphate intermediate. Potential of mean force calculations along the transfer pathway for ammonia indicate a relatively low free-energy barrier for the translocation of ammonia. The highest barrier of 7.2 kcal/mol is found at a narro

SUBMITTER: Fan Y 

PROVIDER: S-EPMC2748306 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature