Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides

Jan K. Rainey, Larry Fliegel, Brian D. Sykes

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)

Abstract

Peptides corresponding to transmembrane (TM) segments from membrane proteins provide a potential route for the determination of membrane protein structure. We have determined that 2 functionally critical TM segments from the mammalian Na+/H+ exchanger display well converged structure in regions separated by break points. The flexibility of these break points results in conformational sampling in solution. A brief review of available NMR structures of helical membrane proteins demonstrates that there are a number of published structures showing similar properties. Such flexibility is likely indicative of kinks in the full-length protein. This minireview focuses on methods and protocols for NMR structure calculation and analysis of peptide structures under conditions of conformational sampling. The methods outlined allow the identification and analysis of structured peptides containing break points owing to conformational sampling and the differentiation between oligomerization and ensemble-averaged observation of multiple peptide conformations.

Original languageEnglish
Pages (from-to)918-929
Number of pages12
JournalBiochemistry and Cell Biology
Volume84
Issue number6
DOIs
Publication statusPublished - Dec 2006

ASJC Scopus Subject Areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Review

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