Constrained modeling of spin-labeled major coat protein mutants from M13 bacteriophage in a phospholipid bilayer

Protein Science : a Publication of the Protein Society
D BashtovyyT Páli

Abstract

The family of three-dimensional molecular structures of the major coat protein from the M13 bacteriophage, which was determined in detergent micelles by NMR methods, has been analyzed by constrained geometry optimization in a phospholipid environment. A single-layer solvation shell of dioleoyl phosphatidylcholine lipids was built around the protein, after replacing single residues by cysteines with a covalently attached maleimide spin label. Both the residues substituted and the phospholipid were chosen for comparison with site-directed spin labeling EPR measurements of distance and local mobility made previously on membranous assemblies of the M13 coat protein purified from viable mutants. The main criteria for identifying promising candidate structures, out of the 300 single-residue mutant models generated for the membranous state, were 1) lack of steric conflicts with the phospholipid bilayer, 2) good match of the positions of spin-labeled residues along the membrane normal with EPR measurements, and 3) a good match between the sequence profiles of local rotational freedom and a structural restriction parameter for the spin-labeled residues obtained from the model. A single subclass of structure has been identified that best...Continue Reading

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Citations

Aug 15, 2009·European Biophysics Journal : EBJ·Marcus A HemmingaDavid Stopar
Aug 29, 2012·PLoS Computational Biology·Victor SeguritanAnca M Segall
Mar 28, 2003·Biochimica Et Biophysica Acta·David StoparMarcus A Hemminga
Aug 15, 2006·Biophysical Journal·David StoparMarcus A Hemminga
Apr 28, 2006·Protein Science : a Publication of the Protein Society·Tibor PáliDerek Marsh
Aug 20, 2009·The Journal of Physical Chemistry. B·Francesco ScarpelliMartina Huber
Nov 3, 2004·Biochimica Et Biophysica Acta·Derek Marsh, Tibor Páli

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