Sequence-Dependent Correction of Random Coil NMR Chemical Shifts

Abstract

Random coil chemical shifts are commonly used to detect secondary structure elements in proteins in chemical shift index calculations. While this technique is very reliable for folded proteins, application to unfolded proteins reveals significant deviations from measured random coil shifts for certain nuclei. While some of these deviations can be ascribed to residual structure in the unfolded protein, others are clearly caused by local sequence effects. In particular, the amide nitrogen, amide proton, and carbonyl carbon chemical shifts are highly sensitive to the local amino acid sequence. We present a detailed, quantitative analysis of the effect of the 20 naturally occurring amino acids on the random coil shifts of (15)N(H), (1)H(N), and (13)CO resonances of neighboring residues, utilizing complete resonance assignments for a set of five-residue peptides Ac-G-G-X-G-G-NH(2). The work includes a validation of the concepts used to derive sequence-dependent correction factors for random coil chemical shifts, and a comprehensive tabulation of sequence-dependent correction factors that can be applied for amino acids up to two residues from a given position. This new set of correction factors will have important applications to folded proteins as well as to short, unstructured peptides and unfolded proteins.

NMR studies of the solution conformation of the sex peptide from Drosophila melanogaster

“…2) expected for a-helices [19]. The CSDs in the N-terminal Trp-rich region should be interpreted with caution, since they may be influenced by aromatic ring current as well as conformational effects [20], although analyses of NOEs provide evidence for a b-turn at the Trp 3 Pro 4 Trp 5 Asn 6 motif (see below). In the central Hyp-rich region (the CSDs of Hyp have not been documented), the Dd Ha and Dd Ca values for non-Hyp residues clearly suggest that b-structure is favored (Fig.…”

Temperature‐dependent structural changes in intrinsically disordered proteins: Formation of α‒helices or loss of polyproline II?

“…45 Several sets of random coil chemical shifts have been determined based on studies of small peptides under denaturing conditions, 46,39 including attempts to quantify the effects of the nearest neighbors. 47 Chemical shift perturbations from more distant neighbors, however, contribute to the noise in the secondary chemical shifts. By using the unfolded state of the protein as the reference, the intrinsic structural preferences of the peptide chain beyond the effects of the nearest neighbors are taken into account.…”

Accurate Random Coil Chemical Shifts from an Analysis of Loop Regions in Native States of Proteins

“…To better account for sequence-dependent effects on chemical shifts, in principle, we could use amino acid triplets (or quintuples and so on); however, larger databases would be required to derive the corresponding parameters in these cases. Here, in order to at least partially take into account next-nearestneighbor effects, 2 we considered two additional pairwise terms (eq S1 in the SI).…”