Hydrogen-bonded turns in proteins: The case for a recount

Nick Panasik, Patrick J. Fleming, George D. Rose

Research output: Contribution to journalArticle

Abstract

β-Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β-turns but lack the characteristic N - H(i) → O = C(i - 3) hydrogen bond of an authentic β-turn. Here, we identify potential hydrogen-bonded β-turns in the coil library, a Web-accessible database utility comprised of all residues not in repetitive secondary structure, neither α-helix nor β-sheet (http://www.roselab.jhu.edu/coil). In particular, candidate turns were identified as four-residue segments satisfying highly relaxed geometric criteria but lacking a strictly defined hydrogen bond. Such candidates were then subjected to a minimization protocol to determine whether slight changes in torsion angles are sufficient to shift the conformation into reference-quality geometry without deviating significantly from the original structure. This approach of applying constrained minimization to known structures reveals a substantial population of previously unidentified, stringently defined, hydrogen-bonded β-turns. In particular, 33% of coil library residues were classified as β-turns prior to minimization. After minimization, 45% of such residues could be classified as β-turns, with another 8% in 3 10 helixes (which closely resemble type III β-turns). Of the remaining coil library residues, 37% have backbone dihedral angles in left-handed polyproline II structure.

Original languageEnglish (US)
Pages (from-to)2910-2914
Number of pages5
JournalProtein Science
Volume14
Issue number11
DOIs
StatePublished - Nov 1 2005

Keywords

  • Computational analysis of protein structure
  • Hydrodynamics
  • Hydrogen bonds
  • Protein structure/folding
  • Structure
  • Thermodynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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