Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

[1]  A. Annila,et al.  Alignment of chain-like molecules , 2004, Journal of biomolecular NMR.

[2]  István Simon,et al.  Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. , 2004, Journal of molecular biology.

[3]  S. Grzesiek,et al.  Foldon, the natural trimerization domain of T4 fibritin, dissociates into a monomeric A-state form containing a stable beta-hairpin: atomic details of trimer dissociation and local beta-hairpin stability from residual dipolar couplings. , 2004, Journal of molecular biology.

[4]  Pau Bernadó,et al.  A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Lorna J. Smith,et al.  Long-Range Interactions Within a Nonnative Protein , 2002, Science.

[6]  Gottfried Otting,et al.  Alignment of Biological Macromolecules in Novel Nonionic Liquid Crystalline Media for NMR Experiments , 2000 .

[7]  Richard R. Ernst,et al.  Elucidation of cross relaxation in liquids by two-dimensional N.M.R. spectroscopy , 1980 .

[8]  G. Bouvignies,et al.  Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings. , 2006, Journal of the American Chemical Society.

[9]  J. Marsh,et al.  Sensitivity of secondary structure propensities to sequence differences between α‐ and γ‐synuclein: Implications for fibrillation , 2006 .

[10]  I. Landrieu,et al.  Structural impact of heparin binding to full-length Tau as studied by NMR spectroscopy. , 2006, Biochemistry.

[11]  Oleg Jardetzky,et al.  Probability‐based protein secondary structure identification using combined NMR chemical‐shift data , 2002, Protein science : a publication of the Protein Society.

[12]  Ewan W Blanch,et al.  A Raman optical activity study of rheomorphism in caseins, synucleins and tau. New insight into the structure and behaviour of natively unfolded proteins. , 2002, European journal of biochemistry.

[13]  L. Serrano Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation. , 1995, Journal of molecular biology.

[14]  D. Shortle The denatured state (the other half of the folding equation) and its role in protein stability , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[15]  Martin Blackledge,et al.  Quantitative conformational analysis of partially folded proteins from residual dipolar couplings: application to the molecular recognition element of Sendai virus nucleoprotein. , 2008, Journal of the American Chemical Society.

[16]  Michele Vendruscolo,et al.  Protein structure determination from NMR chemical shifts , 2007, Proceedings of the National Academy of Sciences.

[17]  A. Bax,et al.  Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts , 1991 .

[18]  Martin Blackledge,et al.  Amino acid bulkiness defines the local conformations and dynamics of natively unfolded alpha-synuclein and tau. , 2007, Journal of the American Chemical Society.

[19]  W. Eaton,et al.  Protein folding studied by single-molecule FRET. , 2008, Current opinion in structural biology.

[20]  C. Griesinger,et al.  Familial Mutants of α-Synuclein with Increased Neurotoxicity Have a Destabilized Conformation* , 2005, Journal of Biological Chemistry.

[21]  H. Schwalbe,et al.  Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. , 2007, Journal of the American Chemical Society.

[22]  Abhishek K. Jha,et al.  Statistical coil model of the unfolded state: resolving the reconciliation problem. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. Grzesiek,et al.  Solution NMR of proteins within polyacrylamide gels: Diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes , 2000, Journal of biomolecular NMR.

[24]  D. Shortle,et al.  Persistence of Native-Like Topology in a Denatured Protein in 8 M Urea , 2001, Science.

[25]  F. Poulsen,et al.  Short-range, long-range and transition state interactions in the denatured state of ACBP from residual dipolar couplings. , 2004, Journal of molecular biology.

[26]  Arto Annila,et al.  On the origin of residual dipolar couplings from denatured proteins. , 2003, Journal of the American Chemical Society.

[27]  A Keith Dunker,et al.  Characterization of molecular recognition features, MoRFs, and their binding partners. , 2007, Journal of proteome research.

[28]  H. Dyson,et al.  Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.

[29]  V. Uversky Natively unfolded proteins: A point where biology waits for physics , 2002, Protein science : a publication of the Protein Society.

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

[31]  Local dynamic amplitudes on the protein backbone from dipolar couplings: toward the elucidation of slower motions in biomolecules. , 2004, Journal of the American Chemical Society.

[32]  N. Maiti,et al.  Raman spectroscopic characterization of secondary structure in natively unfolded proteins: alpha-synuclein. , 2004, Journal of the American Chemical Society.

[33]  G. Clore,et al.  How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? , 2004, Journal of the American Chemical Society.

[34]  A. Gronenborn,et al.  Insights into conformation and dynamics of protein GB1 during folding and unfolding by NMR. , 2004, Journal of molecular biology.

[35]  R. Kammerer,et al.  Structure and disorder in the ribonuclease S‐peptide probed by NMR residual dipolar couplings , 2003, Protein science : a publication of the Protein Society.

[36]  J. Marsh,et al.  Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation. , 2006, Protein science : a publication of the Protein Society.

[37]  Christopher J. Oldfield,et al.  Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. , 2007, Journal of proteome research.

[38]  Y. Ishii,et al.  Alignment of Biopolymers in Strained Gels: A New Way To Create Detectable Dipole−Dipole Couplings in High-Resolution Biomolecular NMR , 2000 .

[39]  D. Shortle,et al.  Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. , 1997, Journal of molecular biology.

[40]  Christian Griesinger,et al.  Structural Polymorphism of 441-Residue Tau at Single Residue Resolution , 2009, PLoS biology.

[41]  Rafael Brüschweiler,et al.  Protein conformational flexibility from structure-free analysis of NMR dipolar couplings: quantitative and absolute determination of backbone motion in ubiquitin. , 2009, Angewandte Chemie.

[42]  Zoran Obradovic,et al.  DisProt: a database of protein disorder , 2005, Bioinform..

[43]  J. Axelsen,et al.  Physical interpretation of residual dipolar couplings in neutral aligned media. , 2002, Journal of the American Chemical Society.

[44]  Arash Bahrami,et al.  Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications , 2005, Journal of biomolecular NMR.

[45]  Martin von Bergen,et al.  Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation. , 2007, Journal of the American Chemical Society.

[46]  P. Tompa,et al.  Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. , 2008, Trends in biochemical sciences.

[47]  G M Clore,et al.  Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[48]  J. Lindon,et al.  NMR Spectroscopy Using Liquid Crystal Solvents , 1975 .

[49]  Martin Blackledge,et al.  Mapping the conformational landscape of urea-denatured ubiquitin using residual dipolar couplings. , 2007, Journal of the American Chemical Society.

[50]  J Meiler,et al.  Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. , 2001, Journal of the American Chemical Society.

[51]  A. Bax Weak alignment offers new NMR opportunities to study protein structure and dynamics , 2003, Protein science : a publication of the Protein Society.

[52]  Christian Griesinger,et al.  The “Jaws” of the Tau-Microtubule Interaction* , 2007, Journal of Biological Chemistry.

[53]  Zoran Obradovic,et al.  DisProt: the Database of Disordered Proteins , 2006, Nucleic Acids Res..

[54]  Ad Bax,et al.  Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. , 2003, Journal of the American Chemical Society.

[55]  Ad Bax,et al.  Prediction of Sterically Induced Alignment in a Dilute Liquid Crystalline Phase: Aid to Protein Structure Determination by NMR , 2000 .

[56]  Dominique Marion,et al.  Interaction of the C-Terminal Domains of Sendai Virus N and P Proteins: Comparison of Polymerase-Nucleocapsid Interactions within the Paramyxovirus Family , 2007, Journal of Virology.

[57]  L. Mueller,et al.  Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions , 1998, Nature Structural Biology.

[58]  J. Prestegard,et al.  Residual Dipolar Couplings in Structure Determination of Biomolecules , 2004 .

[59]  E. Mandelkow,et al.  Tau in Alzheimer's disease. , 1998, Trends in cell biology.

[60]  J M Thornton,et al.  Analysis of main chain torsion angles in proteins: prediction of NMR coupling constants for native and random coil conformations. , 1996, Journal of molecular biology.

[61]  C. Dobson,et al.  Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea. , 1997, Biochemistry.

[62]  G. Marius Clore,et al.  Use of dipolar 1H–15N and 1H–13C couplings in the structure determination of magnetically oriented macromolecules in solution , 1997, Nature Structural Biology.

[63]  Benjamin A. Shoemaker,et al.  Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.

[65]  C. Griesinger,et al.  Familial mutants of alpha-synuclein with increased neurotoxicity have a destabilized conformation. , 2005, Journal of Biological Chemistry.

[66]  Martin Blackledge,et al.  Charge-induced molecular alignment of intrinsically disordered proteins. , 2006, Angewandte Chemie.

[67]  C. Griesinger,et al.  Release of long-range tertiary interactions potentiates aggregation of natively unstructured alpha-synuclein. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Martin Tollinger,et al.  Calculation of residual dipolar couplings from disordered state ensembles using local alignment. , 2008, Journal of the American Chemical Society.

[69]  C. Dobson,et al.  Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations. , 2005, Journal of the American Chemical Society.

[70]  P. Tompa Intrinsically unstructured proteins. , 2002, Trends in biochemical sciences.

[71]  G. Wider,et al.  NMR determination of residual structure in a urea-denatured protein, the 434-repressor. , 1992, Science.

[72]  Patrick Aloy,et al.  Ten thousand interactions for the molecular biologist , 2004, Nature Biotechnology.

[73]  Oliver F. Lange,et al.  Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics , 2008, Journal of biomolecular NMR.

[74]  Oliver F. Lange,et al.  Consistent blind protein structure generation from NMR chemical shift data , 2008, Proceedings of the National Academy of Sciences.

[75]  H. Schwalbe,et al.  Theoretical framework for NMR residual dipolar couplings in unfolded proteins , 2007, Journal of biomolecular NMR.

[76]  M. Blackledge Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings , 2005 .

[77]  P E Wright,et al.  Sequence-dependent correction of random coil NMR chemical shifts. , 2001, Journal of the American Chemical Society.

[78]  D. Shortle,et al.  Structure and dynamics of a denatured 131-residue fragment of staphylococcal nuclease: a heteronuclear NMR study. , 1994, Biochemistry.

[79]  A. Gronenborn,et al.  Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of a Colloidal Suspension of Rod-Shaped Viruses , 1998 .

[80]  G. Maret,et al.  Fibres of highly oriented Pf1 bacteriophage produced in a strong magnetic field. , 1979, Journal of molecular biology.

[81]  Joel R Tolman,et al.  De novo determination of bond orientations and order parameters from residual dipolar couplings with high accuracy. , 2003, Journal of the American Chemical Society.

[82]  V. Uversky,et al.  The Saccharomyces cerevisiae Nucleoporin Nup2p Is a Natively Unfolded Protein* , 2002, The Journal of Biological Chemistry.

[83]  Andrew L. Lee,et al.  Direct Demonstration of Structural Similarity between Native and Denatured Eglin C † , 2004 .

[84]  I. Landrieu,et al.  NMR investigation of the interaction between the neuronal protein tau and the microtubules. , 2007, Biochemistry.

[85]  A. Fersht,et al.  Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain , 2008, Proceedings of the National Academy of Sciences.

[86]  S. Grzesiek,et al.  Direct observation of dipolar couplings and hydrogen bonds across a beta-hairpin in 8 M urea. , 2007, Journal of the American Chemical Society.

[87]  H. Steinhoff,et al.  Global hairpin folding of tau in solution. , 2006, Biochemistry.

[88]  A. Bax,et al.  Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. , 1997, Science.

[89]  Gerard J A Kroon,et al.  Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. , 2004, Journal of molecular biology.

[90]  Martin Blackledge,et al.  Conformational distributions of unfolded polypeptides from novel NMR techniques. , 2008, The Journal of chemical physics.

[91]  Peter E Wright,et al.  Modeling transient collapsed states of an unfolded protein to provide insights into early folding events , 2008, Proceedings of the National Academy of Sciences.

[92]  G. Bouvignies,et al.  Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. , 2007, Journal of the American Chemical Society.

[93]  M. Blackledge,et al.  Structure and dynamics of the nucleocapsid-binding domain of the Sendai virus phosphoprotein in solution. , 2004, Virology.

[94]  J. R. Tolman A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. , 2002, Journal of the American Chemical Society.

[95]  H. Dyson,et al.  Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.

[96]  M. Blackledge,et al.  Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex , 2009, Nucleic acids research.

[97]  T. Masaki Structure and Dynamics , 2002 .

[98]  A. Fink Natively unfolded proteins. , 2005, Current opinion in structural biology.

[99]  Martin T. Dove Structure and Dynamics , 2003 .

[100]  M. Blackledge,et al.  Structural characterization of flexible proteins using small-angle X-ray scattering. , 2007, Journal of the American Chemical Society.

[101]  K. Plaxco,et al.  Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. , 2002, Advances in protein chemistry.

[102]  S. Grzesiek,et al.  High-accuracy residual 1HN-13C and 1HN-1HN dipolar couplings in perdeuterated proteins. , 2003, Journal of the American Chemical Society.

[103]  M. Blackledge,et al.  Defining long-range order and local disorder in native alpha-synuclein using residual dipolar couplings. , 2005, Journal of the American Chemical Society.

[104]  H. Dyson,et al.  Unfolded proteins and protein folding studied by NMR. , 2004, Chemical reviews.

[105]  E. Mandelkow,et al.  Characterization of Alzheimer's-like paired helical filaments from the core domain of tau protein using solid-state NMR spectroscopy. , 2008, Journal of the American Chemical Society.

[106]  F. Richards,et al.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. , 1992, Biochemistry.

[107]  M. Bolognesi,et al.  Function and Structure of Inherently Disordered Proteins This Review Comes from a Themed Issue on Proteins Edited Prediction of Non-folding Proteins and Regions Frequency of Disordered Regions Protein Evolution Partitioning Unstructured Proteins and Regions into Groups Involvement of Inherently Diso , 2022 .

[108]  D. Eliezer,et al.  Residual structure, backbone dynamics, and interactions within the synuclein family. , 2007, Journal of molecular biology.

[109]  Martin Blackledge,et al.  Residual dipolar couplings in short peptides reveal systematic conformational preferences of individual amino acids. , 2006, Journal of the American Chemical Society.

[110]  R. Hodges,et al.  1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects , 1995, Journal of biomolecular NMR.

[111]  On the interpretation of residual dipolar couplings as reporters of molecular dynamics. , 2004, Journal of the American Chemical Society.