Methyl groups as probes of supra-molecular structure, dynamics and function

The development of new protein labeling strategies, along with optimized experiments that exploit the label, have significantly impacted on the types of biochemical problems that can now be addressed by solution NMR spectroscopy. Here we describe how methyl labeling of key residues in a highly deuterated protein background has facilitated studies of the structure, dynamics and interactions of supra-molecular particles. The methyl-labeling approach is briefly reviewed, followed by a summary of applications to three different molecular machines so as to illustrate the types of questions that can now be addressed. Areas where future innovations will lead to yet further improvements are highlighted as well.

[1]  G. Clore,et al.  Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. , 2009, Chemical reviews.

[2]  I. Bertini,et al.  NMR Spectroscopy of Paramagnetic Metalloproteins , 2005, Chembiochem : a European journal of chemical biology.

[3]  L. Kay,et al.  Probing supramolecular structure from measurement of methyl (1)H-(13)C residual dipolar couplings. , 2007, Journal of the American Chemical Society.

[4]  W. Wickner,et al.  SecA promotes preprotein translocation by undergoing ATP-driven cycles of membrane insertion and deinsertion , 1994, Cell.

[5]  Renaldo Mendoza,et al.  NMR-Based Screening of Proteins Containing 13C-Labeled Methyl Groups , 2000 .

[6]  I. Ayala,et al.  An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein , 2009, Journal of biomolecular NMR.

[7]  L. Kay,et al.  A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylase , 2007, Proceedings of the National Academy of Sciences.

[8]  J. Lippincott-Schwartz,et al.  Optimal isotope labelling for NMR protein structure determinations , 2006 .

[9]  F. Richards,et al.  NMR sequential assignment of Escherichia coli thioredoxin utilizing random fractional deuteriation. , 1988, Biochemistry.

[10]  L. Kay,et al.  Probing side-chain dynamics in the proteasome by relaxation violated coherence transfer NMR spectroscopy. , 2007, Journal of the American Chemical Society.

[11]  Paul Schanda,et al.  SOFAST-HMQC Experiments for Recording Two-dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds , 2005, Journal of biomolecular NMR.

[12]  L. Kay,et al.  TROSY-based NMR evidence for a novel class of 20S proteasome inhibitors. , 2008, Biochemistry.

[13]  L. Kay,et al.  Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. , 1997, Biochemistry.

[14]  G. Wagner,et al.  A sensitive and robust method for obtaining intermolecular NOEs between side chains in large protein complexes , 2003, Journal of biomolecular NMR.

[15]  Yifan Cheng,et al.  Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. , 2008, Molecular cell.

[16]  Ad Bax,et al.  Three-dimensional triple-resonance NMR Spectroscopy of isotopically enriched proteins. 1990. , 1990, Journal of magnetic resonance.

[17]  G. Webb NMR Spectroscopy , 1972, Nature.

[18]  Ad Bax,et al.  Multidimensional nuclear magnetic resonance methods for protein studies , 1994 .

[19]  L. Kay,et al.  Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins. , 2004, Annual review of biochemistry.

[20]  S. Karamanou,et al.  Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR , 2007, Cell.

[21]  L. Kay,et al.  A robust and cost-effective method for the production of Val, Leu, Ile (δ1) methyl-protonated 15N-, 13C-, 2H-labeled proteins , 1999, Journal of biomolecular NMR.

[22]  G. Bodenhausen,et al.  Principles of nuclear magnetic resonance in one and two dimensions , 1987 .

[23]  R. Konrat,et al.  Simplification of protein NOESY spectra using bioorganic precursor synthesis and NMR spectral editing. , 2004, Journal of the American Chemical Society.

[24]  A M Gronenborn,et al.  Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. , 1991, Science.

[25]  Gaetano T Montelione,et al.  Automated protein fold determination using a minimal NMR constraint strategy , 2003, Protein science : a publication of the Protein Society.

[26]  Walid A Houry,et al.  Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Daiwen Yang,et al.  A Sensitivity-Enhanced Method for Measuring Heteronuclear Long-Range Coupling Constants from the Displacement of Signals in Two 1D Subspectra , 1996 .

[28]  D. Kendall,et al.  Signal Peptide Determinants of SecA Binding and Stimulation of ATPase Activity* , 2000, The Journal of Biological Chemistry.

[29]  G. Montelione,et al.  Conformation-independent sequential NMR connections in isotope-enriched polypeptides by 1H13C15N triple-resonance experiments , 1990 .

[30]  R. Isaacson,et al.  Automated assignment in selectively methyl-labeled proteins. , 2009, Journal of the American Chemical Society.

[31]  Dmitry M Korzhnev,et al.  Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme. , 2004, Journal of the American Chemical Society.

[32]  P. Tauc,et al.  Coupling of homotropic and heterotropic interactions in Escherichia coli aspartate transcarbamylase. , 1982, Journal of molecular biology.

[33]  S. Grzesiek,et al.  Carbon-13 line narrowing by deuterium decoupling in deuterium/carbon-13/nitrogen-15 enriched proteins. Application to triple resonance 4D J connectivity of sequential amides , 1993 .

[34]  R. Riek,et al.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[35]  L. Kay,et al.  Overcoming the overlap problem in the assignment of 1H NMR spectra of larger proteins by use of three-dimensional heteronuclear 1H-15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1 beta. , 1989, Biochemistry.

[36]  T Pawson,et al.  Selective methyl group protonation of perdeuterated proteins. , 1996, Journal of molecular biology.

[37]  W. Lipscomb Aspartate transcarbamylase from Escherichia coli: activity and regulation. , 1994, Advances in enzymology and related areas of molecular biology.

[38]  F. Dahlquist,et al.  The contact interface of a 120 kD CheA-CheW complex by methyl TROSY interaction spectroscopy. , 2005, Journal of the American Chemical Society.

[39]  J. Changeux,et al.  ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.

[40]  J. Hendrick,et al.  Preprotein translocase of Escherichia coli: solubilization, purification, and reconstitution of the integral membrane subunits SecY/E. , 1991, Methods in cell biology.

[41]  L. Kay,et al.  Quantitative 13C and 2H NMR relaxation studies of the 723-residue enzyme malate synthase G reveal a dynamic binding interface. , 2005, Biochemistry.

[42]  N. Dixon,et al.  Sequence-specific and stereospecific assignment of methyl groups using paramagnetic lanthanides. , 2007, Journal of the American Chemical Society.

[43]  Weontae Lee,et al.  A Suite of Triple Resonance NMR Experiments for the Backbone Assignment of 15N, 13C, 2H Labeled Proteins with High Sensitivity , 1994 .

[44]  Yifan Cheng Toward an atomic model of the 26S proteasome. , 2009, Current opinion in structural biology.

[45]  Kurt Wüthrich,et al.  NMR analysis of a 900K GroEL–GroES complex , 2002, Nature.

[46]  I. Ayala,et al.  Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies. , 2009, Journal of the American Chemical Society.

[47]  Feng Ni,et al.  Recent developments in transferred NOE methods , 1994 .

[48]  A. Spirin,et al.  A continuous cell-free translation system capable of producing polypeptides in high yield. , 1988, Science.

[49]  H K Schachman,et al.  Can a simple model account for the allosteric transition of aspartate transcarbamoylase? , 1988, The Journal of biological chemistry.

[50]  H. Crespi,et al.  Proton Magnetic Resonance of Proteins Fully Deuterated except for 1H-Leucine Side Chains , 1968, Science.

[51]  E. Eisenstein,et al.  Heterotropic effectors promote a global conformational change in aspartate transcarbamoylase. , 1990, Biochemistry.

[52]  Beat Vögeli,et al.  Longitudinal (1)H relaxation optimization in TROSY NMR spectroscopy. , 2002, Journal of the American Chemical Society.

[53]  K. Ito,et al.  SecY and SecA interact to allow SecA insertion and protein translocation across the Escherichia coli plasma membrane , 1997, The EMBO journal.

[54]  Masasuke Yoshida,et al.  Dynamic inter-subunit interactions in thermophilic F1-ATPase subcomplexes studied by cross-correlated relaxation-enhanced polarization transfer NMR , 2008, Journal of biomolecular NMR.

[55]  Christian Griesinger,et al.  Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients , 1999 .

[56]  J. Adams The proteasome: a suitable antineoplastic target , 2004, Nature Reviews Cancer.

[57]  L. Kay,et al.  Assignment of 15N, 13Cα, 13Cβ, and HN Resonances in an 15N,13C,2H Labeled 64 kDa Trp Repressor−Operator Complex Using Triple-Resonance NMR Spectroscopy and 2H-Decoupling , 1996 .

[58]  M. Wittekind,et al.  Incorporation of 1H/13C/15N-{Ile, Leu, Val} into a Perdeuterated, 15N-Labeled Protein: Potential in Structure Determination of Large Proteins by NMR , 1996 .

[59]  A. Bax,et al.  Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. , 1998, Journal of magnetic resonance.

[60]  L. Kay,et al.  Clioquinol inhibits the proteasome and displays preclinical activity in leukemia and myeloma , 2009, Leukemia.

[61]  G. Hervé,et al.  The stimulation of Escherichia coli aspartate transcarbamylase activity by adenosine triphosphate. Relation with the other regulatory conformational changes; a model. , 1978, Journal of molecular biology.

[62]  L. Kay,et al.  Methyl Groups as Probes of Structure and Dynamics in NMR Studies of High‐Molecular‐Weight Proteins , 2005, Chembiochem : a European journal of chemical biology.

[63]  L. Kay,et al.  Application of methyl-TROSY NMR to test allosteric models describing effects of nucleotide binding to aspartate transcarbamoylase. , 2009, Journal of molecular biology.

[64]  L. Kay,et al.  New developments in isotope labeling strategies for protein solution NMR spectroscopy. , 2000, Current opinion in structural biology.

[65]  G. Kreil Transfer of proteins across membranes. , 1981, Annual review of biochemistry.

[66]  L. Kay,et al.  A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin , 1990 .

[67]  L. Kay,et al.  Dynamics of methyl groups in proteins as studied by proton-detected 13C NMR spectroscopy. Application to the leucine residues of staphylococcal nuclease. , 1992, Biochemistry.

[68]  R. Huber,et al.  Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. , 1995, Science.

[69]  L. Kay,et al.  Cross-correlated relaxation enhanced 1H[bond]13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. , 2003, Journal of the American Chemical Society.

[70]  L. Kay,et al.  A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. , 1990, Biochemistry.

[71]  L. Kay,et al.  Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. , 2003, Journal of the American Chemical Society.

[72]  G. Wagner,et al.  Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. , 2000, Biochemistry.

[73]  L. Kay,et al.  Side chain assignments of Ile delta 1 methyl groups in high molecular weight proteins: an application to a 46 ns tumbling molecule. , 2003, Journal of the American Chemical Society.

[74]  L. Kay,et al.  An Isotope Labeling Strategy for Methyl TROSY Spectroscopy , 2004, Journal of biomolecular NMR.

[75]  O. Jardetzky,et al.  High-Resolution Nuclear Magnetic Resonance Spectra of Selectively Deuterated Staphylococcal Nuclease , 1968, Science.

[76]  R. Konrat,et al.  Synthesis of a 13C‐Methyl‐Group‐Labeled Methionine Precursor as a Useful Tool for Simplifying Protein Structural Analysis by NMR Spectroscopy , 2007, Chembiochem : a European journal of chemical biology.

[77]  Lewis E. Kay,et al.  Quantitative dynamics and binding studies of the 20S proteasome by NMR , 2007, Nature.

[78]  C. Hill,et al.  The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions. , 2005, Molecules and Cells.

[79]  Robert E. Cohen,et al.  Proteasomes and their kin: proteases in the machine age , 2004, Nature Reviews Molecular Cell Biology.

[80]  R. Isaacson,et al.  A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues. , 2007, Journal of the American Chemical Society.

[81]  Rong Li,et al.  NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein. , 2005, Biochemistry.

[82]  G von Heijne,et al.  Signal sequences. The limits of variation. , 1985, Journal of molecular biology.

[83]  C Chothia,et al.  Surface, subunit interfaces and interior of oligomeric proteins. , 1988, Journal of molecular biology.

[84]  David S. Latchman,et al.  Biochemistry (4th edn) , 1995 .

[85]  Lewis E. Kay,et al.  Production and Incorporation of 15N, 13C, 2H (1H-δ1 Methyl) Isoleucine into Proteins for Multidimensional NMR Studies , 1997 .