Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Brünger AT, Clore GM, Gronenborn AM, Karplus M (1986): Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin. Proc Natl Acad Sci USA 83:3801–3805
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 8:84–94
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983): CHARMM: A program for macromolecular energy minimization and dynamics calculations. J Comput Chem 4:187–217
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 Ltd
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 186:435–55
Cross TA, Opella SJ (1983): Protein structure by solid state NMR. J Am Chem Soc 105:306–308
Engh RA, Huber R (1991): Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst A47:392–400
Fields CG, Fields GB, Petefish J, Van Wart HE, Cross TA (1988): Solid phase peptide synthesis and solid state NMR spectroscopy of [Ala3–15N][Vall] gramicidin A Proc Nat Acad Sci USA 85:1384–1388
Havel TF, Wüthrich K (1985): An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J Mol Biol 182:281–294
Hu W, Lee K-C, Cross TA (1993): Tryptophans in membrane proteins: indole ring orientations and functional implications in the gramicidin channel. Biochemistry 32:7035–7047
Jeffrey GA, Saenger W (1994): Hydrogen Bonding in Biological Structures. Berlin, Germany: Springer-Verlag
Ketchem RR, Hu W, Cross TA (1993): High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science 261:1457–1460
Kirkpatrick S, Gelatt Jr CD, Vecchi MP (1983): Optimization by simulated annealing. Science 220:671–680
Langs DA (1988): Three-dimensional structure at 0.86 Å of the uncomplexed form of the transmembrane ion channel peptide gramicidin A. Science 241:188–191
Lazo ND, Hu W, Cross TA (1995): Low-temperature solid-state 15N NMR characterization of polypeptide backbone librations. J Mag Res Ser B 106:43–50
Lazo ND, Hu W, Lee K-C, Cross TA (1993): Rapidly-frozen polypeptide samples for characterization of high definition dynamics by solid-state NMR spectroscopy. Biochem Biophys Res Commun 197:904–909
Lee K-C, Cross TA (1994): Side-chain structure and dynamics at the lipid-protein interface: Val1 of the gramicidin A channel. Biophys J 66:1380–1387
Lee K-C, Huo S, Cross TA (1995): Lipid-peptide interface: Valine conformation and dynamics in the gramicidin channel. Biochemistry 34:857–867
Logan TM, Zhou M-M, Nettesheim DG, Meadows RP, Van Etten RL, Fesik SW (1994): Solution structure of a low molecular weight protein tyrosine phosphatase. Biochemistry 33:11087–11096
Lomize AL, Orechov VY, Arseniev AS (1992): Refinement of the spatial structure of the gramicidin A transmembrane ion-channel. Bioorg Khim 18:182–200
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: A143
Mai W, Hu W, Wang C, Cross TA (1993): Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: The polypeptide backbone of gramicidin A in a lipid bilayer. Protein Sci 2:532–542
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953): Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092
Nicholson LK, Cross TA (1989): Gramicidin cation channel: An experimental determination of the right-handed helix sense and verification of the β-type hydrogen bonding. Biochemistry 28:9379–9385
Nicholson LK, Teng Q, Cross TA (1991): Solid-state nuclear magnetic resonance derived model for dynamics in the polypeptide backbone of the gramicidin A channel. J Mol Biol 218:621–637
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 University
North CL, Cross TA (1993): Analysis of polypeptide backbone T1 relaxation data using an experimentally derived model. J Mag Res Ser B 101:35–43
Opella SJ, Stewart PL, Valentine KG (1987): Protein structure by solid state NMR spectroscopy. Q Rev Biophys 19:7–49
Pascal SM, Cross TA (1992) Structure of an isolated gramicidin A double helical species by high-resolution nuclear magnetic resonance. J Mol Biol 226:1101–1109
Teng Q, Nicholson LK, Cross TA (1989): Experimental determination of torsion angles in the polypeptide backbone of the gramicidin A channel by solid state nuclear magnetic resonance. J Mol Biol 218:607–619
Urry DW (1971): The gramicidin A transmembrane channel: A proposed n(L,D) helix. Proc Natl Acad Sci USA 68:672–676
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1996 Birkhäuser Boston
About this chapter
Cite this chapter
Ketchem, R.R., Roux, B., Cross, T.A. (1996). Computational Refinement Through Solid State NMR and Energy Constraints of a Membrane Bound Polypeptide. In: Merz, K.M., Roux, B. (eds) Biological Membranes. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-8580-6_10
Download citation
DOI: https://doi.org/10.1007/978-1-4684-8580-6_10
Publisher Name: Birkhäuser Boston
Print ISBN: 978-1-4684-8582-0
Online ISBN: 978-1-4684-8580-6
eBook Packages: Springer Book Archive