Insights into the mobility of methyl-bearing side chains in proteins from 3JCC and 3JCN couplings

James J. Chou, David A. Case, Ad Bax

Research output: Contribution to journalArticlepeer-review

123 Scopus citations

Abstract

Side-chain dynamics in proteins can be characterized by the NMR measurement of 13C and 2H relaxation rates. Evaluation of the corresponding spectral densities limits the slowest motions that can be studied quantitatively to the time scale on which the overall molecular tumbling takes place. A different measure for the degree of side-chain order about the Cα-Cβ bond (χ1 angle) can be derived from 3JC′-Cγ and 3JN-Cγ couplings. These couplings can be measured at high accuracy, in particular for Thr, Ile, and Val residues. In conjunction with the known backbone structures of ubiquitin and the third IgG-binding domain of protein G, and an extensive set of 13C-1H side-chain dipolar coupling measurements in oriented media, these 3J couplings were used to parametrize empirical Karplus relationships for 3JC′-Cγ and 3JN-Cγ. These Karplus curves agree well with results from DFT calculations, including an unusual phase shift, which causes the maximum 3JCC and 3JCN couplings to occur for dihedral angles slightly smaller than 180°, particularly noticeable in Thr residues. The new Karplus curves permit determination of rotamer populations for the χ1 torsion angles. Similar rotamer populations can be derived from side-chain dipolar couplings. Conversion of these rotamer populations into generalized order parameters, SJ2 and SD2, provides a view of side-chain dynamics that is complementary to that obtained from 13C and 2H relaxation. On average, results agree well with literature values for 2H-relaxation-derived Srel2 values in ubiquitin and HIV protease, but also identify a fraction of residues for which SJ,D2 < Srel2. This indicates that some of the rotameric averaging occurs on a time scale too slow to be observable in traditional relaxation measurements.

Original languageEnglish (US)
Pages (from-to)8959-8966
Number of pages8
JournalJournal of the American Chemical Society
Volume125
Issue number29
DOIs
StatePublished - Jul 23 2003
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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