The DEAD box helicase YxiN maintains a closed conformation during ATP hydrolysis

DEAD box helicases unwind RNA duplexes at the expense of ATP hydrolysis. Recently, unwinding has been demonstrated in the absence of ATP hydrolysis. Herein, we show that ADP.BeF(x) supports RNA unwinding by YxiN, a DEAD box helicase that specifically recognizes a hairpin in 23S rRNA. ADP.AlF(x) and ADP.MgF(x) do not promote RNA unwinding, but all ATP analogues induce a closed conformation of the helicase core as required for RNA unwinding. Our results show that the interdomain cleft in the helicase core closes upon ATP binding at the beginning of the cycle. Reopening occurs after ATP hydrolysis, most likely coupled to phosphate release.

Residual Dipolar Couplings in Short Peptides Reveal Systematic Conformational Preferences of Individual Amino Acids

Residual dipolar couplings (RDCs) observed by NMR in solution under weak alignment conditions can monitor average net orientations and order parameters of individual bonds. By their simple geometrical dependence, RDCs bear particular promise for the quantitative characterization of conformations in partially folded or unfolded proteins. We have systematically investigated the influence of amino acid substitutions X on the conformation of unfolded model peptides EGAAXAASS as monitored by their (1)H(Nu)-(15)N and (1)H(alpha)-(13)C(alpha) RDCs detected at natural abundance of (15)N and (13)C in strained polyacrylamide gels. In total, 14 single amino acid substitutions were investigated. The RDCs show a specific dependence on the substitution X that correlates to steric or hydrophobic interactions with adjacent amino acids. In particular, the RDCs for the glycine and proline substitutions indicate less or more order, respectively, than the other amino acids. The RDCs for aromatic substitutions tryptophane and tyrosine give evidence of a kink in the peptide backbone. This effect is also observable for orientation by Pf1 phages and corroborated by variations in (13)C(alpha) secondary shifts and (3)J(HNH)(alpha) scalar couplings in isotropic samples. RDCs for a substitution with the beta-turn sequence KNGE differ from single amino acid substitutions. Terminal effects and next neighbor effects could be demonstrated by further specific substitutions. The results were compared to statistical models of unfolded peptide conformations derived from PDB coil subsets, which reproduce overall trends for (1)H(Nu)-(15)N RDCs for most substitutions, but deviate more strongly for (1)H(alpha)-(13)C(alpha) RDCs. The outlined approach opens the possibility to obtain a systematic experimental characterization of the influence of individual amino acid/amino acid interactions on orientational preferences in polypeptides.