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

¹ Institute of Biophysics, Biological Research Centre, 6701 Szeged, Hungary
² Abteilung Spektroskopie, Max-Planck-Institut für Biophysikalische Chemie, 37070 Göttingen, Germany
³ Department of Biomolecular Sciences, Wageningen University and Research Centre, 6700 ET Wageningen, The Netherlands

Reprint requests to: Tibor Páli, Institute of Biophysics, Biological Research Centre, P.O. Box 521, 6701 Szeged, Hungary; e-mail: tpali{at}szbk.u-szeged.hu; fax: 36 62 433133.

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 satisfies these criteria simultaneously. The model presented here is useful for the interpretation of future experimental data on membranous M13 coat protein systems. It is also a good starting point for full-scale molecular dynamics simulations and for the design of further site-specific spectroscopic experiments.

Keywords: Viral coat protein; M13 bacteriophage; site-directed spin-labeling; molecular modeling; electron paramagnetic resonance; membrane protein; lipid-protein interaction

Abbreviations: DOPC, dioleoylphosphatidylcholine • EPR, electron paramagnetic resonance • NMR, nuclear magnetic resonance • DodPC, dodecylphosphocholine • SDS, sodium dodecyl sulphate • 5-MSL, 5-maleimidoproxyl

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