NMR Studies of Large Proteins.

Recent breakthroughs in isotope-labeling and pulse sequence techniques have enabled the NMR characterization of large protein systems with molecular masses of hundreds of kilodaltons. NMR studies of a great variety of large proteins have provided unique insights into the binding, dynamic, and allosteric mechanisms. Here we present a brief summary of these developments by highlighting few cases that exemplify the uniqueness of NMR in providing atomic resolution information into key dynamic processes and structures of protein complexes with high degree of flexibility.

[1]  W. Dalton,et al.  The proteasome. , 2004, Seminars in oncology.

[2]  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.

[3]  Jonathan Weissman,et al.  Molecular Chaperones and Protein Quality Control , 2006, Cell.

[4]  Albert C. Pan,et al.  The Dynamic Process of β2-Adrenergic Receptor Activation , 2013, Cell.

[5]  G. Wider.  Technical aspects of NMR Spectroscopy with biological macromolecules and studies of hydration in solution , 1998 .

[6]  C. Kalodimos.  NMR reveals novel mechanisms of protein activity regulation , 2011, Protein science : a publication of the Protein Society.

[7]  T. Rapoport.  Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes , 2007, Nature.

[8]  L. Kay,et al.  Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy , 2006, Nature Protocols.

[9]  A. Matouschek,et al.  Regulated protein turnover: snapshots of the proteasome in action , 2014, Nature Reviews Molecular Cell Biology.

[10]  Y. Kashi,et al.  Residues in chaperonin GroEL required for polypeptide binding and release , 1994, Nature.

[11]  L. Kay,et al.  The proteasome antechamber maintains substrates in an unfolded state , 2010, Nature.

[12]  S. Rasmussen,et al.  The structure and function of G-protein-coupled receptors , 2009, Nature.

[13]  Rémy Sounier,et al.  Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins. , 2015, Current opinion in structural biology.

[14]  L. Kay,et al.  Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer , 2017, Journal of Biomolecular NMR.

[15]  James Lowe,et al.  Ubiquitin-like protein conjugation and the ubiquitin–proteasome system as drug targets , 2010, Nature Reviews Drug Discovery.

[16]  L. Kay,et al.  Intrinsic dynamics of an enzyme underlies catalysis , 2005, Nature.

[17]  I. Ayala,et al.  Stereospecific isotopic labeling of methyl groups for NMR spectroscopic studies of high-molecular-weight proteins. , 2010, Angewandte Chemie.

[18]  Yujin E. Kim,et al.  Molecular chaperone functions in protein folding and proteostasis. , 2013, Annual review of biochemistry.

[19]  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.

[20]  F. Hartl,et al.  SnapShot: Molecular Chaperones, Part I , 2007, Cell.

[21]  H. Dyson,et al.  Intrinsically disordered proteins in cellular signalling and regulation , 2014, Nature Reviews Molecular Cell Biology.

[22]  F. Allain,et al.  Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins , 2010, Journal of biomolecular NMR.

[23]  K Wüthrich,et al.  NMR spectroscopy of large molecules and multimolecular assemblies in solution. , 1999, Current opinion in structural biology.

[24]  Markus Mund,et al.  LEGO-NMR Spectroscopy: A Method to Visualize Individual Subunits in Large Heteromeric Complexes , 2013, Angewandte Chemie.

[25]  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 .

[26]  L. Kay,et al.  Dynamic Regulation of Archaeal Proteasome Gate Opening As Studied by TROSY NMR , 2010, Science.

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

[28]  A. Feigl,et al.  Convergent evolution of clamp-like binding sites in diverse chaperones , 2006, Nature Structural &Molecular Biology.

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

[30]  Patrik Lundström,et al.  Isotope labeling methods for studies of excited protein states by relaxation dispersion NMR spectroscopy , 2009, Nature Protocols.

[31]  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.

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

[33]  G. Wagner,et al.  Increased resolution of aromatic cross peaks using alternate 13C labeling and TROSY , 2015, Journal of biomolecular NMR.

[34]  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.

[35]  L. Kay,et al.  Bringing dynamic molecular machines into focus by methyl-TROSY NMR. , 2014, Annual review of biochemistry.

[36]  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.

[37]  P. Goloubinoff,et al.  Molecular chaperones are nanomachines that catalytically unfold misfolded and alternatively folded proteins , 2014, Cellular and Molecular Life Sciences.

[38]  Sukyeong Lee,et al.  Molecular chaperones in protein quality control. , 2005, Journal of biochemistry and molecular biology.

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

[40]  Y. Ishida,et al.  Exploiting E. coli auxotrophs for leucine, valine, and threonine specific methyl labeling of large proteins for NMR applications , 2016, Journal of biomolecular NMR.

[41]  S. Tans,et al.  SecB--a chaperone dedicated to protein translocation. , 2010, Molecular bioSystems.

[42]  L. Kay,et al.  New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy. , 2016, Journal of molecular biology.

[43]  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 .

[44]  I. Shimada,et al.  Perdeuteration and methyl-selective 1H, 13C-labeling by using a Kluyveromyces lactis expression system , 2013, Journal of Biomolecular NMR.

[45]  H. Saibil.  Chaperone machines in action. , 2008, Current opinion in structural biology.

[46]  D. Boehr,et al.  The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis , 2006, Science.

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

[48]  Maya A. Wright,et al.  Biophysical approaches for the study of interactions between molecular chaperones and protein aggregates , 2015, Chemical communications.

[49]  Samuel Karlin,et al.  Protein length in eukaryotic and prokaryotic proteomes , 2005, Nucleic acids research.

[50]  Shoeib Moradi,et al.  Unraveling the Mechanism of Protein Disaggregation Through a ClpB-DnaK Interaction , 2013, Science.

[51]  H. Saibil.  Chaperone machines for protein folding, unfolding and disaggregation , 2013, Nature Reviews Molecular Cell Biology.

[52]  R. Sharan,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[53]  H. Dyson,et al.  Mechanism of coupled folding and binding of an intrinsically disordered protein , 2007, Nature.

[54]  S. Karamanou,et al.  Bacterial protein secretion through the translocase nanomachine , 2007, Nature Reviews Microbiology.

[55]  C. Kalodimos,et al.  Structural basis for the antifolding activity of a molecular chaperone , 2016, Nature.

[56]  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.

[57]  Andreas Bracher,et al.  Molecular chaperones in protein folding and proteostasis , 2011, Nature.

[58]  Zhaohui Xu,et al.  Crystal structure of the bacterial protein export chaperone SecB , 2000, Nature Structural Biology.

[59]  Stefan Günther,et al.  Structural features and evolution of protein-protein interactions. , 2010, Genome informatics. International Conference on Genome Informatics.

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

[61]  I. Shimada,et al.  Functional dynamics of deuterated β2 -adrenergic receptor in lipid bilayers revealed by NMR spectroscopy. , 2014, Angewandte Chemie.

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

[63]  C. Kalodimos,et al.  Structures of Large Protein Complexes Determined by Nuclear Magnetic Resonance Spectroscopy. , 2017, Annual review of biophysics.

[64]  Patrik Lundström,et al.  Biosynthetic 13C labeling of aromatic side chains in proteins for NMR relaxation measurements. , 2006, Journal of the American Chemical Society.

[65]  C. Kalodimos,et al.  Structural Basis for Protein Antiaggregation Activity of the Trigger Factor Chaperone , 2014, Science.

[66]  P. Genevaux,et al.  Multitasking SecB chaperones in bacteria , 2014, Front. Microbiol..

[67]  A. Wand,et al.  A 13C labeling strategy reveals a range of aromatic side chain motion in calmodulin. , 2013, Journal of the American Chemical Society.

[68]  L. Kay,et al.  ClpB N-terminal domain plays a regulatory role in protein disaggregation , 2015, Proceedings of the National Academy of Sciences.