Angular variances for internal bond rotations of side chains in GXG-based tripeptides derived from13C-NMR relaxation measurements: Implications to protein folding

Abstract

The study of backbone and side‐chain internal motions in proteins and peptides is crucial to having a better understanding of protein/peptide “structure” and to characterizing unfolded and partially folded states of proteins and peptides. To achieve this, however, requires establishing a baseline for internal motions and motional restrictions for all residues in the fully, solvent‐exposed “unfolded state.” GXG‐based tripeptides are the simpliest peptides where residue X is fully solvent exposed in the context of an actual peptide. In this study, a series of GXG‐based tripeptides has been synthesized with X being varied to include all twenty common amino acid residues. Proton‐coupled and ‐decoupled 13C‐nmr relaxation measurements have been performed on these twenty tripeptides and various motional models (Lipari–Szabo model free approach, rotational anisotropic diffusion, rotational fluctuations within a potential well, rotational jump model) have been used to analyze relaxation data for derivation of angular variances and motional correlation times for backbone and side‐chain χ1 and χ2 bonds and methyl group rotations. At 298 K, backbone motional correlation times range from about 50 to 85 ps, whereas side‐chain motional correlation times show a much broader spread from about 18 to 80 ps. Angular variances for backbone ϕ,ψ bond rotations range from 11° to 23° and those for side chains vary from 5° to 24° for χ1 bond rotations and from 5° to 27° for χ2 bond rotations. Even in these peptide models of the “unfolded state,” side‐chain angular variances can be as restricted as those for backbone and β‐branched (valine, threonine, and isoleucine) and aromatic side chains display the most restricted motions probably due to steric hinderence with backbone atoms. Comparison with motional data on residues in partially folded, β‐sheet‐forming peptides indicates that side‐chain motions of at least hydrophobic residues are less restricted in the partially folded state, suggesting that an increase in side‐chain conformational entropy may help drive early‐stage protein folding. © 1999 John Wiley & Sons, Inc. Biopoly 49: 373–383, 1999

Comparison of 13CαH and 15NH backbone dynamics in protein GB1

“…This hierarchy ranges from picoseconds to nanoseconds to microseconds to milliseconds and slower. NMR relaxation studies, which are most sensitive to motions occurring on the nanosecond to picosecond time scales, on small GXG tripeptides devoid of folded structure revealed that internal motions for backbone C α H and NH groups fall in the 70‐ to 100‐psec range (Mikhailov et al 1999), whereas in protein GB1, internal motions for backbone groups fall in the subnanosecond to 5‐nsec range, as well as in the picosecond range. Internal motions on the picosecond time scale were mostly omitted from this discussion primarily because these faster time scale motions are least accurately determined as mentioned above.…”

A Conformational Flexibility Scale for Amino Acids in Peptides

“…These peptides adopt random‐coil conformations according to CD measurements 22. Since the conformational changes required for end‐to‐end contact derive from fast rotations about the NC α and C α C bonds,23 and since different α substituents are expected to hinder these bond rotations to a different degree, we expected different collision frequencies when the probe and the quencher are separated by different amino acids. This arrangement should allow us to correlate the collision frequency with the type of amino acid and thereby build up a flexibility scale (Table 1).…”

Deuterium Spin Probes of Side-Chain Dynamics in Proteins. 2. Spectral Density Mapping and Identification of Nanosecond Time-Scale Side-Chain Motions

“…The meaning of the best-fit order parameters S f 2 extracted from fits using the LS-2 and -3 models in cases where slow side-chain dynamics is present is discussed below. Theoretical treatments which draw the connection between the model-free parameters and more fundamental quantities describing side-chain torsional dynamics have been presented in a number of recent papers. − …”