Impact of non-proteinogenic amino acid norvaline and proteinogenic valine misincorporation on a secondary structure of a model peptide

Norvaline (Nva) is a natural, non-proteinogenic, unbranched amino acid, not encoded by the genetic code. Nva is isomeric with proteinogenic amino acid valine (Val) and can compete with Val for misrecognition by isoleucyl-tRNA synthetase (IleRS). IleRS proofreading mechanisms prevent misincorporation of both amino acids into proteins at Ile positions. Although IleRS uses both pre-transfer editing of Val-AMP within the synthetic site [1] and deacylation of misacylated Val-tRNAIle [2,3] and Nva-tRNAIle [4] within the post-transfer editing domain to maintain the accuracy of protein synthesis, it has been shown that in circumstances of impaired editing both Val and Nva are toxic for cell [4,5]. Our previous experimental study compared the effect of Nva and Val mistranslation into E. coli proteome at Ile positions and showed that proteome-wide substitution of Ile with Nva resulted in a higher toxicity in comparison to the proteome-wide substitution of Ile with Val [4]. These three amino acids differ in their propensities towards secondary structure elements [6,7]. Namely Ile and Val exhibit high β-sheet propensities, whereas Nva belongs to a good helix-forming residue, therefore exhibiting different effects on proteome stability upon misincorporation. Previous experimental study [8], where authors used combinatorial mutagenesis to examine the effects of introducing alanine, a good α-helix-forming residue and valine, a poor helix-forming residue at 12 positions in a native α-helix 1 of the N-terminal domain of λ repressor [8], clearly demonstrated that Ala and Val are equally well tolerated at the majority of examined sites, although showing opposite helix-forming propensities. Surprisingly, the authors also discovered that α-helix 1 of λ repressor can accommodate up to four valines, a poor helix-forming residue, with retention of biological activity and α-helix structure. On the other hand, a tolerance of a β-sheet to multiple mutations, especially in light of Val/Nva misincorporation at Ile sites, has not yet been studied. To investigate why Nva misincorporation into proteins is more deleterious compared to Val [4] we opted for in silico approach. We chose the envelope HIV-1 IIIB V3 peptide [9], a natural β-hairpin with three isoleucines and we misincorporated Nva and Val at all three Ile positions. By applying classical molecular dynamics simulations at different temperatures, we could elegantly study how the β-hairpin structure stability is affected by misincorporation at isoleucine positions. Obtained results suggest a possible mechanism for the observed higher toxicity of norvaline compared to valine.

留言 (0)

沒有登入
gif