title: Membrane protein structure determination in membrana.
abstract: The two principal components of biological membranes, the lipid bilayer and the proteins integrated within it, have coevolved for specific functions that mediate the interactions of cells with their environment. Molecular structures can provide very significant insights about protein function. In the case of membrane proteins, the physical and chemical properties of lipids and proteins are highly interdependent; therefore structure determination should include the membrane environment. Considering the membrane alongside the protein eliminates the possibility that crystal contacts or detergent molecules could distort protein structure, dynamics, and function and enables ligand binding studies to be performed in a natural setting. Solid-state NMR spectroscopy is compatible with three-dimensional structure determination of membrane proteins in phospholipid bilayer membranes under physiological conditions and has played an important role in elucidating the physical and chemical properties of biological membranes, providing key information about the structure and dynamics of the phospholipid components. Recently, developments in the recombinant expression of membrane proteins, sample preparation, pulse sequences for high-resolution spectroscopy, radio frequency probes, high-field magnets, and computational methods have enabled a number of membrane protein structures to be determined in lipid bilayer membranes. In this Account, we illustrate solid-state NMR methods with examples from two bacterial outer membrane proteins (OmpX and Ail) that form integral membrane β-barrels. The ability to measure orientation-dependent frequencies in the solid-state NMR spectra of membrane-embedded proteins provides the foundation for a powerful approach to structure determination based primarily on orientation restraints. Orientation restraints are particularly useful for NMR structural studies of membrane proteins because they provide information about both three-dimensional structure and the orientation of the protein within the membrane. When combined with dihedral angle restraints derived from analysis of isotropic chemical shifts, molecular fragment replacement, and de novo structure prediction, orientation restraints can yield high-quality three-dimensional structures with few or no distance restraints. Using complementary solid-state NMR methods based on oriented sample (OS) and magic angle spinning (MAS) approaches, one can resolve and assign multiple peaks through the use of (15)N/(13)C labeled samples and measure precise restraints to determine structures.
authors.affiliation: Sanford-Burnham Medical Research Institute , 10901 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
authors.forename: Yong
authors.initials: Y
authors.lastname: Yao
authors.forename: Francesca M
authors.initials: FM
authors.lastname: Marassi
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D009682:Magnetic Resonance Spectroscopy; D008565:Membrane Proteins / Q000737:chemistry*
chemical_list: D001425:Bacterial Outer Membrane Proteins; D008565:Membrane Proteins
references.citation: Biophys J. 2001 Feb;80(2):994-1003
references.pmid: 11159466
references.citation: Biochemistry. 2008 Jun 24;47(25):6531-8
references.pmid: 18512961
references.citation: J Magn Reson. 2012 Jan;214(1):42-50
references.pmid: 22036904
references.citation: Angew Chem Int Ed Engl. 2012 Aug 13;51(33):8383-6
references.pmid: 22807290
references.citation: J Am Chem Soc. 2012 Feb 1;134(4):2047-56
references.pmid: 22217388
references.citation: Annu Rev Phys Chem. 2012;63:1-24
references.pmid: 22136620
references.citation: Acc Chem Res. 2013 Sep 17;46(9):2172-81
references.pmid: 23470103
references.citation: Chem Rev. 2004 Aug;104(8):3587-606
references.pmid: 15303829
references.citation: Nature. 2012 Nov 29;491(7426):779-83
references.pmid: 23086146
references.citation: J Biomol NMR. 2012 Nov;54(3):237-43
references.pmid: 23007199
references.citation: J Mol Biol. 2002 Nov 22;324(2):319-30
references.pmid: 12441110
references.citation: Trends Biochem Sci. 2011 Feb;36(2):117-25
references.pmid: 20724162
references.citation: J Magn Reson. 2000 May;144(1):162-7
references.pmid: 10783287
references.citation: J Magn Reson. 2006 Dec;183(2):329-32
references.pmid: 16997587
references.citation: Biochemistry. 2009 Apr 14;48(14):3100-8
references.pmid: 19309106
references.citation: Science. 2010 Feb 19;327(5968):1014-8
references.pmid: 20133520
references.citation: J Am Chem Soc. 1976 Feb 4;98(3):851-3
references.pmid: 1267937
references.citation: Biochim Biophys Acta. 2007 Dec;1768(12):3216-24
references.pmid: 17916325
references.citation: Methods. 2011 Dec;55(4):363-9
references.pmid: 21964394
references.citation: Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8551-6
references.pmid: 9238014
references.citation: Biochemistry. 2011 May 3;50(17):3408-10
references.pmid: 21425834
references.citation: Annu Rev Phys Chem. 2011;62:279-99
references.pmid: 21219138
references.citation: J Magn Reson. 1998 Nov;135(1):227-31
references.pmid: 9799698
references.citation: Structure. 1999 Oct 15;7(10):1301-9
references.pmid: 10545325
references.citation: Biochim Biophys Acta. 2011 Jan;1808(1):482-9
references.pmid: 20883662
references.citation: Annu Rev Biochem. 2008;77:363-82
references.pmid: 18410248
references.citation: Methods Mol Biol. 2012;895:153-65
references.pmid: 22760319
references.citation: Trends Biochem Sci. 2009 Apr;34(4):206-15
references.pmid: 19303305
references.citation: Q Rev Biophys. 1977 Aug;10(3):353-418
references.pmid: 335428
references.citation: J Magn Reson. 2011 Dec;213(2):421-2
references.pmid: 21890391
references.citation: J Chem Phys. 2011 Oct 7;135(13):134509
references.pmid: 21992326
references.citation: Infect Immun. 2008 Feb;76(2):612-22
references.pmid: 18025094
references.citation: Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):16974-9
references.pmid: 21969532
references.citation: FEBS Lett. 1975 Sep 15;57(2):213-8
references.pmid: 1175790
references.citation: Protein Sci. 2003 Mar;12(3):403-11
references.pmid: 12592011
references.citation: Curr Opin Chem Biol. 2011 Oct;15(5):690-5
references.pmid: 21862384
references.citation: Prog Nucl Magn Reson Spectrosc. 2010 Aug;57(2):181-228
references.pmid: 20633363
references.citation: J Am Chem Soc. 2013 Feb 6;135(5):1919-25
references.pmid: 23294159
references.citation: Science. 2010 Oct 22;330(6003):509-12
references.pmid: 20966252
references.citation: Nature. 2011 Jul 24;476(7358):109-13
references.pmid: 21785437
references.citation: Nat Struct Biol. 1998 Jul;5 Suppl:508-12
references.pmid: 9665180
references.citation: J Magn Reson. 2000 May;144(1):150-5
references.pmid: 10783285
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13533-7
references.pmid: 12370417
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4863-8
references.pmid: 22331896
references.citation: Top Curr Chem. 2012;306:89-118
references.pmid: 21598096
references.citation: Biochemistry. 1985 Aug 13;24(17):4671-9
references.pmid: 4063350
references.citation: Structure. 2011 Nov 9;19(11):1672-82
references.pmid: 22078566
references.citation: Annu Rev Biophys. 2009;38:385-403
references.pmid: 19245337
references.citation: Eur J Cell Biol. 2012 Apr;91(4):340-8
references.pmid: 22019511
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90
references.pmid: 18326625
references.citation: Nat Chem. 2012 Mar 18;4(5):410-7
references.pmid: 22522262
references.citation: Methods Enzymol. 2013;522:365-89
references.pmid: 23374193
references.citation: J Magn Reson. 2012 Mar;216:1-12
references.pmid: 22280934