Constrained modeling of spin-labeled major coat protein mutants from M13 bacteriophage in a phospholipid bilayer
| Autor: | Tibor Páli, Derek Marsh, Marcus A. Hemminga, Denys Bashtovyy |
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| Rok vydání: | 2001 |
| Předmět: |
Models
Molecular M13 bacteriophage Molecular model Lipid Bilayers Biophysics Phospholipid Molecular modeling Biochemistry Article Maleimides Molecular dynamics chemistry.chemical_compound Capsid Cysteine Protein Structure Quaternary Spin label Lipid bilayer Nuclear Magnetic Resonance Biomolecular Molecular Biology Phospholipids Viral coat protein biology Chemistry Electron Spin Resonance Spectroscopy Membrane Proteins Site-directed spin-labeling Site-directed spin labeling biology.organism_classification Protein Structure Tertiary Crystallography Biofysica Solvation shell Amino Acid Substitution Membrane protein Mutation Capsid Proteins Spin Labels EPS Electron paramagnetic resonance Lipid-protein interaction Bacteriophage M13 |
| Zdroj: | Protein Science, 10, 979-987 Protein Science Protein Science 10 (2001) |
| ISSN: | 1469-896X 0961-8368 |
| DOI: | 10.1110/ps.43801 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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