Mapping the conformational landscape of urea-denatured ubiquitin using residual dipolar couplings

Sebastian Meier, Stephan Grzesiek, Martin Blackledge

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Characterization of the unfolded state is a fundamental prerequisite for understanding protein stability and folding. We have investigated local conformational sampling in urea-denatured ubiquitin at pH 2.5 by measuring an extensive set of residual dipolar couplings (RDCs) under conditions of partial molecular alignment. Seven experimental RDCs per peptide unit, including complementary fixed-geometry and interproton (H-1(N)-H-1(N) and H-1(N)-H-1(alpha)) couplings, were used to investigate the structural properties of the peptide chain. Amino-acid-specific potentials that simultaneously reproduce all RDCs in the molecule are found to sample more extended conformations than the standard statistical coil description. Analysis of (3)J(HNH alpha) scalar couplings measured under the same conditions suggests that neither polyproline II nor extended beta-regions dominate this additional sampling of extended conformations. Using this approach we propose a model of the conformational landscape throughout the peptide chain of urea-denatured ubiquitin, providing an essential description for understanding the unfolded state.
Original languageEnglish
JournalJournal of the American Chemical Society
Volume129
Issue number31
Pages (from-to)9799-9807
Number of pages9
ISSN0002-7863
DOIs
Publication statusPublished - 2007
Externally publishedYes

Keywords

  • Protein Conformation
  • Protein Denaturation
  • Protein Folding
  • Protons
  • Ubiquitin
  • Urea
  • 8W8T17847W Urea
  • Mapping
  • Mathematical models
  • Molecular orientation
  • pH effects
  • Proteins
  • amino acid
  • peptide
  • proline
  • ubiquitin
  • urea
  • article
  • beta sheet
  • dipole
  • measurement
  • molecular model
  • pH
  • protein conformation
  • protein denaturation
  • protein folding
  • protein stability
  • reproducibility
  • Dipolar couplings
  • Statistical coil description
  • UBIQUITIN
  • L
  • X
  • CHEMISTRY,
  • INTRINSICALLY UNSTRUCTURED PROTEINS
  • LIQUID-CRYSTALLINE PHASE
  • X-RAY-SCATTERING
  • UNFOLDED PROTEINS
  • STRUCTURAL-CHARACTERIZATION
  • ANGULAR-DEPENDENCE
  • LONG-RANGE
  • NMR
  • CONSTANTS
  • STATE
  • ubiquitin 60267-61-0 denatured
  • urea 57-13-6
  • 10060, Biochemistry studies - General
  • 10064, Biochemistry studies - Proteins, peptides and amino acids
  • protein modeling mathematical and computer techniques
  • residual dipolar coupling laboratory techniques
  • Biochemistry and Molecular Biophysics
  • Methods and Techniques

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