Computational Refinement Through Solid State NMR and Energy Constraints of a Membrane Bound Polypeptide
The determination of macromolecular structures in anisotropic environments such as membranes is vital to the field of structural biology. While solid state nuclear magnetic resonance spectroscopy (SSNMR) methods have been demonstrated for obtaining three dimensional structures of membrane bound polypeptides (Cross and Opella, 1983; Ketchem et al, 1993; Opella et al, 1987), computational refinement methods are needed for optimally utilizing these constraints in such a molecular environment. Methods for structural determination and refinement of macromolecules in solution have fully evolved (Briinger et al, 1986; Clore et al, 1985; Havel and Wüthrich, 1985), but the nature of the constraints obtained for membrane proteins are such that a new refinement procedure must be developed. Described here is such a technique that has the ability to optimize the structure of a membrane protein in order to best represent the experimental data and determine its high-resolution structure.
KeywordsTorsion Angle Penalty Function Initial Structure Quadrupolar Splitting Internuclear Distance
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- Bystrov VF, Arseniev AS, Barsukov IL, Lomize AL (1987): 2D NMR of single and double stranded helices of gramicidin A in micelles and solutions. Bull Magn Reson 8:84–94Google Scholar
- Case DA, Wright PE (1993): Determination of high-resolution NMR structures of proteins. In: NMR of Proteins Clore GM, Gronenborn AM, eds. London: The Macmillan Press LtdGoogle Scholar
- Clore GM, Gronenborn AM, Brünger AT, Karplus M (1985): Solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli. Combined use of 1H nuclear magnetic resonance and restrained molecular dynamics. J Mol Biol 186:435–55PubMedCrossRefGoogle Scholar
- Engh RA, Huber R (1991): Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst A47:392–400Google Scholar
- Jeffrey GA, Saenger W (1994): Hydrogen Bonding in Biological Structures. Berlin, Germany: Springer-VerlagGoogle Scholar
- Mackerell AD Jr, Bashford D, Bellot M, Dunbrack RL, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Nguyen DT, Ngo T, Prodhom B, Roux B, Schlenkrich B, Smith J, Stote R, Straub J, Wiorkiewicz-Kuczera J, Karplus M (1992); Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations. Biophys J 61: A143Google Scholar
- North CL (1993): Peptide backbone librations of the gramicidin A transmembrane channel as measured by solid state nuclear magnetic resonance. Implications for proposed mechanisms of ion transport (dissertation). Tallahasee, FL: Florida State UniversityGoogle Scholar