Computational Analysis of Ammonia Transfer Along Two Intramolecular Tunnels in Staphylococcus aureus Glutamine-Dependent Amidotransferase (GatCAB)
| Autor: | G. Andrés Cisneros, Sajeewa W. Dewage |
|---|---|
| Rok vydání: | 2015 |
| Předmět: |
chemistry.chemical_classification
Staphylococcus aureus biology Stereochemistry Chemistry Glutamine Nitrogenous Group Transferases Mutant Molecular Dynamics Simulation biology.organism_classification Article Surfaces Coatings and Films Enzyme Ammonia Catalytic Domain Intramolecular force Mutation Materials Chemistry Protein biosynthesis Thermodynamics Physical and Theoretical Chemistry Bacteria Archaea Glutamine amidotransferase |
| Zdroj: | The Journal of Physical Chemistry B. 119:3669-3677 |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/jp5123568 |
| Popis: | Most bacteria and all archaea misacylate the tRNAs corresponding to Asn and Gln with Asp and Glu (Asp-tRNA(Asn) and Glu-tRNA(Gln)).The GatCAB enzyme of most bacteria converts misacylated Glu-tRNA(Gln) to Gln-tRNA(Gln) 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. |
| Databáze: | OpenAIRE |
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