Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.
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Christian Griesinger | Pau Bernadó | Martin Blackledge | Markus Zweckstetter | Malene Ringkjøbing Jensen | S. Grzesiek | M. Blackledge | P. Markwick | M. R. Jensen | C. Griesinger | P. Bernadó | S. Meier | M. Zweckstetter | Sebastian Meier | Stephan Grzesiek | Phineus R L Markwick
[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.