1. Molecular dynamics simulation study of valyl-tRNA synthetase with its pre- and post-transfer editing substrates.
- Author
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Bharatham N, Bharatham K, Lee Y, and Woo Lee K
- Subjects
- Adenosine Monophosphate chemistry, Aspartic Acid genetics, Computer Simulation, Lysine genetics, Models, Molecular, Point Mutation, Protein Binding, Protein Conformation, RNA, Transfer chemistry, RNA, Transfer metabolism, Substrate Specificity, Threonine chemistry, Valine chemistry, Valine-tRNA Ligase genetics, Adenosine Monophosphate metabolism, Thermus thermophilus enzymology, Threonine metabolism, Valine metabolism, Valine-tRNA Ligase chemistry, Valine-tRNA Ligase metabolism
- Abstract
The main role of aminoacyl-tRNA synthetases (aaRSs) is to transfer the cognate amino acids to the 3'-end of their tRNA by strictly discriminating from non-cognate amino acids. Some aaRSs accomplish this via proofreading and editing mechanisms, among which valyl-tRNA synthetase (ValRS) hydrolyses the non-cognate amino acid, threonine. In ValRS, existence of pre-transfer editing process is still unclear, although crystal structure of editing site with pre-transfer substrate analog (Thr-AMS) was released. In the case of isoleucyl-tRNA synthetase (IleRS), editing mechanism is well studied and mutational analyses revealed the existence of post- and pre-transfer editing mechanisms. Our aim is to investigate the possibility of pre-transfer editing process by performing molecular dynamics (MD) simulation studies. Simulations were carried out for ValRS with pre-transfer substrates (Thr-AMP/Val-AMP) and post-transfer substrates (Thr-A76/Val-A76) to understand their binding pattern. Two important point mutation studies were performed to observe their effect on editing process. This study also intends to compare and contrast the pre-transfer editing with post-transfer editing of ValRS. Interestingly, the MD simulation results revealed that non-cognate substrates (Thr-AMP/Thr-A76) bind more strongly than the cognate substrates (Val-AMP/Val-A76) in both pre- and post-transfer editing respectively. The editing site mutations (Lys270Ala and Asp279Ala) severely affected the binding ability of pre-transfer substrate (Thr-AMP) by different ways. Even though pre- and post-transfer substrates bind to the same site, specific differences were observed which has led us to believe the existence of the pre-transfer editing process in ValRS.
- Published
- 2009
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