A maximum entropy approach to the study of residue‐specific backbone angle distributions in α‐synuclein, an intrinsically disordered protein

α‐Synuclein is an intrinsically disordered protein of 140 residues that switches to an α‐helical conformation upon binding phospholipid membranes. We characterize its residue‐specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential HNHα and HNHN NOEs, values for 3JHNHα, 1JHαCα, 2JCαN, and 1JCαN, as well as chemical shifts of 15N, 13Cα, and 13C′ nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20–30%) of the PPII region and a somewhat higher population of the potentially aggregation‐prone β region (20–40%) than seen in the database. A generally lower population of the αR region (10–20%) is found. Analysis of 1H1H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein.

[1]  Zhengshuang Shi,et al.  Polyproline II propensities from GGXGG peptides reveal an anticorrelation with beta-sheet scales. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  A. Gronenborn,et al.  Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination. , 2004, Journal of the American Chemical Society.

[3]  P. Lansbury,et al.  Phosphorylation at Ser-129 but Not the Phosphomimics S129E/D Inhibits the Fibrillation of α-Synuclein* , 2008, Journal of Biological Chemistry.

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

[5]  D. Eliezer,et al.  Residual Structure and Dynamics in Parkinson's Disease-associated Mutants of α-Synuclein* , 2001, The Journal of Biological Chemistry.

[6]  D. Shortle,et al.  Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. , 1997, Journal of molecular biology.

[7]  Martin Blackledge,et al.  Mapping the potential energy landscape of intrinsically disordered proteins at amino acid resolution. , 2012, Journal of the American Chemical Society.

[8]  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.

[9]  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.

[10]  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.

[11]  Jory Z. Ruscio,et al.  Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations. , 2008, Journal of the American Chemical Society.

[12]  H. Schwalbe,et al.  Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I' band profiles and NMR scalar coupling constants. , 2010, Journal of the American Chemical Society.

[13]  A. Bax,et al.  Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology , 2007, Journal of biomolecular NMR.

[14]  A. Bax,et al.  Limits on variations in protein backbone dynamics from precise measurements of scalar couplings. , 2007, Journal of the American Chemical Society.

[15]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[16]  A. Bax,et al.  An empirical correlation between 1JC.alpha.H.alpha. and protein backbone conformation , 1992 .

[17]  D. Eliezer,et al.  Conformational properties of alpha-synuclein in its free and lipid-associated states. , 2001, Journal of molecular biology.

[18]  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.

[19]  C. Hogue,et al.  A fast method to sample real protein conformational space , 2000, Proteins.

[20]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[21]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[22]  B. Brutscher,et al.  Recovering lost magnetization: polarization enhancement in biomolecular NMR , 2011, Journal of biomolecular NMR.

[23]  Ronald M Levy,et al.  Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. , 2009, Journal of molecular biology.

[24]  Xavier Salvatella,et al.  Identification of fibril-like tertiary contacts in soluble monomeric α-synuclein. , 2013, Biophysical journal.

[25]  Kang Chen,et al.  Conformation of the backbone in unfolded proteins. , 2006, Chemical reviews.

[26]  R. Schweitzer‐Stenner Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants. , 2009, The journal of physical chemistry. B.

[27]  R. Tycko,et al.  Biopolymer Conformational Distributions from Solid-State NMR: α-Helix and 310-Helix Contents of a Helical Peptide , 1998 .

[28]  A. Bax,et al.  Measurement of 15N relaxation rates in perdeuterated proteins by TROSY-based methods , 2012, Journal of Biomolecular NMR.

[29]  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.

[30]  Joseph A Marsh,et al.  Improved structural characterizations of the drkN SH3 domain unfolded state suggest a compact ensemble with native-like and non-native structure. , 2007, Journal of molecular biology.

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

[32]  W. The use of 1 Jcaua coupling constants as a probe for protein backbone conformation * , 2022 .

[33]  W F van Gunsteren,et al.  Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations , 2001, Journal of biomolecular NMR.

[34]  Ad Bax,et al.  Impact of N-Terminal Acetylation of α-Synuclein on Its Random Coil and Lipid Binding Properties , 2012, Biochemistry.

[35]  H. Kalbitzer,et al.  Protein NMR Spectroscopy. Principles and Practice , 1997 .

[36]  A. Palmer,et al.  Protein NMR Spectroscopy: principles and practice, 2nd ed. , 2006 .

[37]  A. Bax,et al.  Measurement of15N-13C J couplings in staphylococcal nuclease , 1991, Journal of biomolecular NMR.

[38]  Nicolas L. Fawzi,et al.  Homogeneous and heterogeneous tertiary structure ensembles of amyloid-β peptides. , 2011, Biochemistry.

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

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

[41]  H. Schwalbe,et al.  Motional properties of unfolded ubiquitin: a model for a random coil protein , 2006, Journal of biomolecular NMR.

[42]  Ad Bax,et al.  Multiple tight phospholipid-binding modes of alpha-synuclein revealed by solution NMR spectroscopy. , 2009, Journal of molecular biology.

[43]  A. Bax,et al.  Mixed-time parallel evolution in multiple quantum NMR experiments: sensitivity and resolution enhancement in heteronuclear NMR , 2007, Journal of biomolecular NMR.

[44]  Ad Bax,et al.  Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis. , 2008, The journal of physical chemistry. B.

[45]  Paul A. Keifer,et al.  Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity , 1992 .

[46]  Ad Bax,et al.  Improved Cross Validation of a Static Ubiquitin Structure Derived from High Precision Residual Dipolar Couplings Measured in a Drug-Based Liquid Crystalline Phase , 2014, Journal of the American Chemical Society.

[47]  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.

[48]  G. Hummer,et al.  Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. , 2009, The journal of physical chemistry. B.

[49]  V. Pande,et al.  Unusual compactness of a polyproline type II structure. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[50]  A. Liwo,et al.  Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[51]  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.

[52]  H. Schwalbe,et al.  Angular dependence of 1J(Ni,Cα i) and 2J(Ni,Cα (i − 1)) coupling constants measured in J-modulated HSQCs , 2002, Journal of biomolecular NMR.

[53]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[54]  Joseph A Marsh,et al.  Ensemble modeling of protein disordered states: Experimental restraint contributions and validation , 2011, Proteins.

[55]  Chris Neale,et al.  Characterization of disordered proteins with ENSEMBLE , 2013, Bioinform..

[56]  A. Gronenborn,et al.  Detection of nuclear Overhauser effects between degenerate amide proton resonances by heteronuclear three-dimensional NMR spectroscopy , 1990 .

[57]  K. Lindorff-Larsen,et al.  Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease , 2006 .

[58]  G. Rose,et al.  Is protein folding hierarchic? I. Local structure and peptide folding. , 1999, Trends in biochemical sciences.

[59]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[60]  Dmitri I. Svergun,et al.  pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins , 2013, Nucleic Acids Res..

[61]  A Keith Dunker,et al.  Intrinsic disorder and protein function. , 2002, Biochemistry.

[62]  Céline Charavay,et al.  Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables , 2012, Bioinform..

[63]  S. Teichmann,et al.  Probing the diverse landscape of protein flexibility and binding. , 2012, Current opinion in structural biology.

[64]  C. Dobson,et al.  Protein misfolding, functional amyloid, and human disease. , 2006, Annual review of biochemistry.

[65]  P E Wright,et al.  Defining solution conformations of small linear peptides. , 1991, Annual review of biophysics and biophysical chemistry.

[66]  J. Forman-Kay,et al.  Calculation of ensembles of structures representing the unfolded state of an SH3 domain. , 2001, Journal of molecular biology.

[67]  Junmei Wang,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..

[68]  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.

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

[70]  A. Bax,et al.  SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network , 2010, Journal of biomolecular NMR.

[71]  L. Kay,et al.  Spectral density function mapping using 15N relaxation data exclusively , 1995, Journal of biomolecular NMR.

[72]  S. F. Lienin,et al.  Anisotropic Intramolecular Backbone Dynamics of Ubiquitin Characterized by NMR Relaxation and MD Computer Simulation , 1998 .

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

[74]  Carlo Camilloni,et al.  Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts. , 2012, Biochemistry.

[75]  G. Hummer,et al.  SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. , 2011, Structure.

[76]  F. Löhr,et al.  Correlation of 2J couplings with protein secondary structure , 2010, Proteins.

[77]  Martin Blackledge,et al.  Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings. , 2009, Journal of the American Chemical Society.

[78]  B. Sykes,et al.  Quantification of the calcium‐induced secondary structural changes in the regulatory domain of troponin‐C , 1994, Protein science : a publication of the Protein Society.

[79]  H. Schwalbe,et al.  Disentangling the coil: modulation of conformational and dynamic properties by site-directed mutation in the non-native state of hen egg white lysozyme. , 2012, Biochemistry.

[80]  A. Bax,et al.  Homonuclear decoupling for enhancing resolution and sensitivity in NOE and RDC measurements of peptides and proteins. , 2014, Journal of magnetic resonance.

[81]  F. Poulsen,et al.  Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH , 2011, Journal of biomolecular NMR.

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

[83]  Ad Bax,et al.  The use of 1JCαHα coupling constants as a probe for protein backbone conformation , 1993 .

[84]  Sheena E. Radford,et al.  Conformational Properties of the Unfolded State of Im7 in Nondenaturing Conditions , 2012, Journal of molecular biology.

[85]  Nicholas C Fitzkee,et al.  The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB , 2005, Proteins.

[86]  P. Tompa,et al.  Structural and dynamic characterization of intrinsically disordered human securin by NMR spectroscopy. , 2008, Journal of the American Chemical Society.

[87]  A. Bax,et al.  Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks , 2013, Journal of Biomolecular NMR.

[88]  Jane R. Allison,et al.  Determination of the free energy landscape of alpha-synuclein using spin label nuclear magnetic resonance measurements. , 2009, Journal of the American Chemical Society.

[89]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[90]  Martin Blackledge,et al.  NMR characterization of long-range order in intrinsically disordered proteins. , 2010, Journal of the American Chemical Society.

[91]  J. Baum,et al.  Backbone assignment and dynamics of human α-synuclein in viscous 2 M glucose solution , 2011, Biomolecular NMR assignments.

[92]  M. Parrinello,et al.  Crystal structure and pair potentials: A molecular-dynamics study , 1980 .

[93]  M. Blackledge,et al.  Conformational propensities of intrinsically disordered proteins from NMR chemical shifts. , 2013, Chemphyschem : a European journal of chemical physics and physical chemistry.

[94]  J. Danielsson,et al.  Cooperative formation of native-like tertiary contacts in the ensemble of unfolded states of a four-helix protein , 2010, Proceedings of the National Academy of Sciences.

[95]  K. Griebenow,et al.  Preferred peptide backbone conformations in the unfolded state revealed by the structure analysis of alanine-based (AXA) tripeptides in aqueous solution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[96]  F. Mulder,et al.  Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins. , 2012, Biochemical Society transactions.