Computational Analysis of Ammonia Transfer Along Two Intramolecular Tunnels in Staphylococcus aureus Glutamine-Dependent Amidotransferase (GatCAB)

Abstract

Most bacteria and all archaea misacylate the tRNAs corresponding to Asn and Gln with Asp and Glu (Asp-tRNAAsn and Glu-tRNAGln). The GatCAB enzyme of most bacteria converts misacylated Glu-tRNAGln to Gln-tRNAGln in order to enable the incorporation of glutamine during protein synthesis. The conversion process involves the intramolecular transfer of ammonia between two spatially separated active sites. This study presents a computational analysis of the two putative intramolecular tunnels that have been suggested to describe the ammonia transfer between the two active sites. Molecular dynamics simulations have been performed for wild-type GatCAB of S. aureus and its mutants: T175(A)V, K88(B)R, E125(B)D, and E125(B)Q. The two tunnels have been analyzed in terms of free energy of ammonia transfer along them. The probability of occurrence of each type of tunnel and the variation of the probability for wild-type GatCAB and its mutants is also discussed.

Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl‐tRNA amidotransferase

“…D185 forms an edge of Tunnel I, right at the branching point of the two tunnels. The clear importance of this residue for GatCAB activity along with the minimal effects of mutations on structure and interdomain communication provide further support to our computational analyses [30] that revealed that the free energy of migration through Tunnel I is lower than that of Tunnel II. Furthermore, Tunnel I is similar to ammonia exit channels from amidases like that found in fatty acid amide hydrolase [27].…”

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

“…All EDA calculations were carried out with an in-house FORTRAN90 program to determine the nonbonded interactions (Coulomb and VdW interactions) for all the residues 48–50 . The average non-bonded interaction between a particular cytosine derivative and every other residue, ΔE int , is approximated by ΔE int =<ΔE i >, where i represents an individual residue, ΔE i represents the nonbonded interaction (Coulomb or VdW) between residue i and the particular cytosine derivative, and the broken brackets represent averages over the complete production ensemble obtained from the MD simulations.…”

Computational Investigation of O2Diffusion Through an Intra–molecular Tunnel in AlkB; Influence of Polarization on O2Transport

“…19,22 A second approach involves the determination of the potential of mean force (PMF). 22,30 Extensive sampling is essential to obtain accurate PMFs since incomplete sampling can result in large errors in the 2 All rights reserved. No reuse allowed without permission.…”

“…This analysis has been previously employed for QM/MM and MD simulations to study a number of protein systems. 5,6,30,[78][79][80] …”