Molecular dynamics simulation study of valyl-tRNA synthetase with its pre- and post-transfer editing substrates

Biophys Chem. 2009 Jul;143(1-2):34-43. doi: 10.1016/j.bpc.2009.03.009. Epub 2009 Mar 28.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / chemistry
  • Adenosine Monophosphate / metabolism*
  • Aspartic Acid / genetics
  • Computer Simulation
  • Lysine / genetics
  • Models, Molecular
  • Point Mutation
  • Protein Binding
  • Protein Conformation
  • RNA, Transfer / chemistry
  • RNA, Transfer / metabolism
  • Substrate Specificity
  • Thermus thermophilus / enzymology*
  • Threonine / chemistry
  • Threonine / metabolism*
  • Valine / chemistry
  • Valine / metabolism*
  • Valine-tRNA Ligase / chemistry*
  • Valine-tRNA Ligase / genetics
  • Valine-tRNA Ligase / metabolism*

Substances

  • Threonine
  • Aspartic Acid
  • Adenosine Monophosphate
  • RNA, Transfer
  • Valine-tRNA Ligase
  • Valine
  • Lysine