These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Search MEDLINE/PubMed

  • Title: Conformational analysis of a nitroxide side chain in an α-helix with density functional theory.
    Author: Warshaviak DT, Serbulea L, Houk KN, Hubbell WL.
    Journal: J Phys Chem B; 2011 Jan 20; 115(2):397-405. PubMed ID: 21162593.
    Abstract:
    In site directed spin labeling, a nitroxide side chain is introduced at a selected site in a protein; the most commonly used is a disulfide-linked side chain designated R1. The electron paramagnetic resonance (EPR) spectra of R1, and the interspin distance between pairs of R1 residues as determined by dipolar EPR spectroscopy, encode a wealth of information on the protein structure and dynamics. However, extracting this information requires structural and dynamical models of the R1 side chain, that is, the favored rotamers, the intraresidue interactions that stabilize them, and the internal modes of motion. X-ray crystal structures of R1 in proteins have revealed a set of preferred rotamers in the crystal lattice. To identify the intraresidue interactions that stabilize particular rotamers of R1 in the absence of interactions with nearby side chains in a helix, and to evaluate models for the internal motion of the side chain, quantum mechanical calculations were performed on a relevant fragment of R1 in a 10-residue α-helix. Relative rotamer energies were determined in the gas phase, and solvation energies were estimated from a continuum solvent model that includes both electrostatic and hydrophobic contributions. The results identified preferred rotamers that are in agreement with the X-ray crystallographic studies. The rotamers are apparently stabilized by intraresidue sulfur-backbone interactions, suggesting that the preferred rotamers may be the same at all solvent-exposed helix sites.
    [Abstract] [Full Text] [Related] [New Search]