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Application of the random coil index to studying protein flexibility

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Abstract

Protein flexibility lies at the heart of many protein–ligand binding events and enzymatic activities. However, the experimental measurement of protein motions is often difficult, tedious and error-prone. As a result, there is a considerable interest in developing simpler and faster ways of quantifying protein flexibility. Recently, we described a method, called Random Coil Index (RCI), which appears to be able to quantitatively estimate model-free order parameters and flexibility in protein structural ensembles using only backbone chemical shifts. Because of its potential utility, we have undertaken a more detailed investigation of the RCI method in an attempt to ascertain its underlying principles, its general utility, its sensitivity to chemical shift errors, its sensitivity to data completeness, its applicability to other proteins, and its general strengths and weaknesses. Overall, we find that the RCI method is very robust and that it represents a useful addition to traditional methods of studying protein flexibility. We have implemented many of the findings and refinements reported here into a web server that allows facile, automated predictions of model-free order parameters, MD RMSF and NMR RMSD values directly from backbone 1H, 13C and 15N chemical shift assignments. The server is available at http://wishart.biology.ualberta.ca/rci.

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References

  • Baber JL, Levens D, Libutti D et al (2000) Chemical shift mapped DNA-binding sites and 15N relaxation analysis of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K. Biochemistry 39:6022–6032

    Article  Google Scholar 

  • Berjanskii MV, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970–14971

    Article  Google Scholar 

  • Berjanskii M, Wishart DS (2006) NMR: prediction of protein flexibility. Nature Protocols 1:683–688

    Article  Google Scholar 

  • Berjanskii MV, Riley MI, Xie A et al (2000) NMR structure of the N-terminal J domain of polyomavirus T antigens: implications for DnaJ-like domains and for T antigen mutations. J Biol Chem 275:36094–36103

    Article  Google Scholar 

  • Berjanskii M, Riley M, Van Doren SR (2002) Hsc70-interacting HPD loop of the J domain of polyomavirus T antigens fluctuates in ps to ns and micros to ms. J Mol Biol 321:503–516

    Article  Google Scholar 

  • Braun D, Wider G, Wuthrich K (1994) Sequence-corrected N-15 random coil chemical-shifts. J Am Chem Soc 116:8466–8469

    Article  Google Scholar 

  • Bundi A, Wuthrich K (1979) H-1-NMR parameters of the common amino-acid residues measured in aqueous-solutions of the linear tetrapeptides H-GLY-GLY-X-L-ALA-OH. Biopolymers 18:285–297

    Article  Google Scholar 

  • Bundi A, Grathwohl C, Hochmann J et al (1975) Proton NMR of protected tetrapeptides TFA-GLY-GLY-L-X-L-ALA-OCH3, where X stands for one of 20 common amino-acids. JMagn Reson 18:191–198

    Google Scholar 

  • Carugo O, Argos P (1999) Reliability of atomic displacement parameters in protein crystal structures. Acta Crystallogr D Biol Crystallogr 55(Pt 2):473–478

    Article  Google Scholar 

  • Case DA (1998) The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 8:624–630

    Article  Google Scholar 

  • Case DA (2002) Molecular dynamics and NMR spin relaxation in proteins. Acc Chem Res 35:325–331

    Article  Google Scholar 

  • Chang SL, Tjandra N (2001) Analysis of NMR relaxation data of biomolecules with slow domain motions using wobble-in-a-cone approximation. J Am Chem Soc 123:11484–11485

    Article  Google Scholar 

  • Chen J, Brooks CL 3rd, Wright PE (2004) Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J Biomol NMR 29:243–257

    Article  Google Scholar 

  • Chou YT, Swain JF, Gierasch LM (2002) Functionally significant mobile regions of Escherichia coli SecA ATPase identified by NMR. J Biol Chem 277:50985–50990

    Article  Google Scholar 

  • Clore GM, Szabo A, Bax A et al (1990) Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 112:4989–4991

    Article  Google Scholar 

  • Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302

    Article  Google Scholar 

  • Dalgarno DC, Levine BA, Williams RJ (1983) Structural information from NMR secondary chemical shifts of peptide alpha C-H protons in proteins. Biosci Rep 3:443–452

    Article  Google Scholar 

  • Damberg P, Jarvet J, Graslund A (2005) Limited variations in 15N CSA magnitudes and orientations in ubiquitin are revealed by joint analysis of longitudinal and transverse NMR relaxation. J Am Chem Soc 127:1995–2005

    Article  Google Scholar 

  • Dedios AC, Oldfield E (1994) Chemical-shifts of carbonyl carbons in peptides and proteins. J Am Chem Soc 116:11485–11488

    Article  Google Scholar 

  • Dyson HJ, Wright PE (1998) Equilibrium NMR studies of unfolded and partially folded proteins. Nat Struct Biol 5(Suppl):499–503

    Article  Google Scholar 

  • Eghbalnia HR, Wang L, Bahrami A et al (2005) Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements. J Biomol NMR 32:71–81

    Article  Google Scholar 

  • Elofsson A, Nilsson L (1993) How consistent are molecular-dynamics simulations - comparing structure and dynamics in reduced and oxidized Escherichia-Coli thioredoxin. J Mol Biol 233:766–780

    Article  Google Scholar 

  • Farrow NA, Zhang O, Forman-Kay JD et al (1997) Characterization of the backbone dynamics of folded and denatured states of an SH3 domain. Biochemistry 36:2390–2402

    Article  Google Scholar 

  • Fiaux J, Bertelsen EB, Horwich AL et al (2002) NMR analysis of a 900K GroEL GroES complex. Nature 418:207–211

    Article  ADS  Google Scholar 

  • Fushman D, Cahill S, Cowburn D (1997) The main-chain dynamics of the dynamin pleckstrin homology (Ph) domain in solution – analysis of N-15 relaxation with monomer/dimer equilibration. J Mol Biol 266:173–194

    Article  Google Scholar 

  • Glushka J, Lee M, Coffin S et al (1989) N-15 chemical-shifts of backbone amides in bovine pancreatic trypsin-Inhibitor and apamin. J Am Chem Soc 111:7716–7722

    Article  Google Scholar 

  • Grathwoh C, Wuthrich K (1974) C-13 NMR of protected tetrapeptides TFA-GLY-GLY-L-X-L-ALA-OCH3, where X stands for 20 common amino-acids. J Magn Reson 13:217–225

    Google Scholar 

  • Halle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci USA 99:1274–1279

    Article  ADS  Google Scholar 

  • Horita DA, Zhang W, Smithgall TE et al (2000) Dynamics of the Hck-SH3 domain: comparison of experiment with multiple molecular dynamics simulations. Protein Sci 9:95–103

    Article  Google Scholar 

  • Huang X, Peng JW, Speck NA et al (1999) Solution structure of core binding factor beta and map of the CBF alpha binding site. Nat Struct Biol 6:624–627

    Article  Google Scholar 

  • Ishima R, Torchia DA (2000) Protein dynamics from NMR. Nat Struct Biol 7:740–743

    Article  Google Scholar 

  • Jin DQ, Andrec M, Montelione GT et al (1998) Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics. J Biomol NMR 12:471–492

    Article  Google Scholar 

  • Kay LE (1998) Protein dynamics from NMR. Nat Struct Biol 5(Suppl):513–517

    Article  Google Scholar 

  • Koradi R, Billeter M, Wüthrich K (1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 14:51–55

    Article  Google Scholar 

  • Korzhnev DM, Orekhov VY, Arseniev AS (1997) Model-free approach beyond the borders of its applicability. J Magn Reson 127:184–191

    Article  ADS  Google Scholar 

  • Lacroix E, Bruix M, Lopez-Hernandez E et al (1997) Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli. J Mol Biol 271:472–487

    Article  Google Scholar 

  • Le HB, Oldfield E (1996) Ab initio studies of amide-N-15 chemical shifts in dipeptides: Applications to protein NMR spectroscopy. J Phys Chem 100:16423–16428

    Article  Google Scholar 

  • Lecroisey A, Martineau P, Hofnung M et al (1997) NMR studies on the flexibility of the poliovirus C3 linear epitope inserted into different sites of the maltose-binding protein. J Biol Chem 272:362–368

    Article  Google Scholar 

  • Levitt MH (2001) Spin dynamics: basics of nuclear magnetic resonance. Wiley, Chichester

    Google Scholar 

  • Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317

    Google Scholar 

  • Lindorff-Larsen K, Best RB, Depristo MA et al (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128–132

    Article  ADS  Google Scholar 

  • Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104:4546–4559

    Article  Google Scholar 

  • Lukin JA, Gove AP, Talukdar SN et al (1997) Automated probabilistic method for assigning backbone resonances of (C-13,N-15)-labeled proteins. J Biomol NMR 9:151–166

    Article  Google Scholar 

  • McConnell HM (1958) Reaction Rates by Nuclear Magnetic Resonance. J Chem Phys 28:430–431

    Article  ADS  Google Scholar 

  • Merutka G, Dyson HJ, Wright PE (1995) Random Coil H-1 Chemical-Shifts Obtained as a Function of Temperature and Trifluoroethanol Concentration for the Peptide Series Ggxgg. J Biomol NMR 5:14–24

    Article  Google Scholar 

  • Mielke SP, Krishnan VV (2004) An evaluation of chemical shift index-based secondary structure determination in proteins: influence of random coil chemical shifts. J Biomol NMR 30:143–153

    Article  Google Scholar 

  • Neal S, Nip AM, Zhang H et al (2003) Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR 26:215–240

    Article  Google Scholar 

  • Oldfield E (1995) Chemical shifts and three-dimensional protein structures. J Biomol NMR 5:217–225

    Article  Google Scholar 

  • Osapay K, Case DA (1994) Analysis of proton chemical shifts in regular secondary structure of proteins. J Biomol NMR 4:215–230

    Article  Google Scholar 

  • Palmer AG 3rd (2001) NMR probes of molecular dynamics: overview and comparison with other techniques. Annu Rev Biophys Biomol Struct 30:129–155

    Article  Google Scholar 

  • Palmer AG 3rd, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 339:204–238

    Article  Google Scholar 

  • Pang Y, Buck M, Zuiderweg ER (2002) Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15)N and (13)CO) NMR relaxation and computational molecular dynamics. Biochemistry 41:2655–2666

    Article  Google Scholar 

  • Pardi A, Wagner G, Wuthrich K (1983) Protein conformation and proton nuclear-magnetic-resonance chemical shifts. Eur J Biochem 137:445–454

    Article  Google Scholar 

  • Penkett CJ, Redfield C, Jones JA et al (1998) Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococcus aureus. Biochemistry 37:17054–17067

    Article  Google Scholar 

  • Petsko GA, Ringe D (1984) Fluctuations in protein structure from X-ray diffraction. Annu Rev Biophys Bioeng 13:331–371

    Article  Google Scholar 

  • Richarz R, Wuthrich K (1978) C-13 Nmr Chemical-Shifts of Common Amino-Acid Residues Measured in Aqueous-Solutions of Linear Tetrapeptides H-Gly-Gly-X-L-Ala-Oh. Biopolymers 17:2133–2141

    Article  Google Scholar 

  • Sahu SC, Bhuyan AK, Udgaonkar JB et al (2000) Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study. J Biomol NMR 18:107–118

    Article  Google Scholar 

  • Sanders CR, Landis GC (1994) Facile acquisition and assignment of oriented sample NMR-spectra for bilayer surface-associated proteins. J Am Chem Soc 116:6470–6471

    Article  Google Scholar 

  • Schwarzinger S, Kroon GJ, Foss TR et al (2001) Sequence-dependent correction of random coil NMR chemical shifts. J Am Chem Soc 123:2970–2978

    Article  Google Scholar 

  • Schwarzinger S, Kroon GJ, Foss TR et al (2000) Random coil chemical shifts in acidic 8 M urea: implementation of random coil shift data in NMRView. J Biomol NMR 18:43–48

    Article  Google Scholar 

  • Scott WRP, Hunenberger PH, Tironi IG et al (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596–3607

    Article  Google Scholar 

  • Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and C-alpha and C-beta C-13 nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490–5492

    Article  Google Scholar 

  • Sun HH, Sanders LK, Oldfield E (2002) Carbon-13 NMR shielding in the twenty common amino acids: Comparisons with experimental results in proteins. J Am Chem Soc 124:5486–5495

    Article  Google Scholar 

  • Szilagyi L (1995) Chemical-shifts in proteins come of age. Prog Nucl Magn Reson Spectrosc 27:325–443

    Article  Google Scholar 

  • Thanabal V, Omecinsky DO, Reily MD et al (1994) The 13C chemical shifts of amino acids in aqueous solution containing organic solvents: application to the secondary structure characterization of peptides in aqueous trifluoroethanol solution. J Biomol NMR 4:47–59

    Article  Google Scholar 

  • van Gunsteren WF, Mark AE (1998) Validation of molecular dynamics simulation. J Chem Phys 108:6109–6116

    Article  ADS  Google Scholar 

  • Vila JA, Ripoll DR, Baldoni HA et al (2002) Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study. J Biomol NMR 24:245–262

    Article  Google Scholar 

  • Wand AJ (2001) Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat Struct Biol 8:926–931

    Article  Google Scholar 

  • Wang Y, Jardetzky O (2002a) Investigation of the neighboring residue effects on protein chemical shifts. J Am Chem Soc 124:14075–14084

    Article  Google Scholar 

  • Wang Y, Jardetzky O (2002b) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852–861

    Article  Google Scholar 

  • Wang Y, Jardetzky O (2004) Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from PHI, PSI i-1, and CHI-1 torsion angles. J Biomol NMR 28:327–340

    Article  Google Scholar 

  • Wang Y, Wishart DS (2005) A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins. J Biomol NMR 31:143–148

    Article  MATH  Google Scholar 

  • Wang T, Cai S, Zuiderweg ER (2003) Temperature dependence of anisotropic protein backbone dynamics. J Am Chem Soc 125:8639–8643

    Article  Google Scholar 

  • Wishart DS, Nip AM (1998) Protein chemical shift analysis: a practical guide. Biochem Cell Biol 76:153–163

    Article  Google Scholar 

  • Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:171–180

    Article  Google Scholar 

  • Wishart DS, Sykes BD (1994) Chemical shifts as a tool for structure determination. Methods Enzymol 239:363–392

    Google Scholar 

  • Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222:311–333

    Article  Google Scholar 

  • Wishart DS, Sykes BD, Richards FM (1992) The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31:1647–1651

    Article  Google Scholar 

  • Wishart DS, Bigam CG, Holm A et al (1995) 1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J Biomol NMR 5:67–81

    Article  Google Scholar 

  • Wolf-Watz M, Grundstrom T, Hard T (2001) Structure and backbone dynamics of Apo-CBFbeta in solution. Biochemistry 40:11423–11432

    Article  Google Scholar 

  • Xu XP, Case DA (2002) Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65:408–423

    Article  Google Scholar 

  • Zhang F, Bruschweiler R (2002) Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc 124:12654–12655

    Article  Google Scholar 

  • Zhang H, Neal S, Wishart DS (2003) RefDB: a database of uniformly referenced protein chemical shifts. J Biomol NMR 25:173–195

    Article  Google Scholar 

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Acknowledgements

This work was supported by the Natural Sciences and Engineering Research Council (NSERC), the National Research Council’s National Institute for Nanotechnology (NINT), the Protein Engineering Network of Centres of Excellence (PENCE), Alberta Prion Research Institute, and PrioNet Canada.

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  1. Department of Computing Science, University of Alberta, Edmonton, AB, Canada

    Mark V. Berjanskii & David S. Wishart

  2. NRC National Institute for Nanotechnology, University of Alberta, 2-21 Athabasca Hall, T6G 2E8, Edmonton, AB, Canada

    David S. Wishart

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  1. Mark V. Berjanskii
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Correspondence to David S. Wishart.

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Berjanskii, M.V., Wishart, D.S. Application of the random coil index to studying protein flexibility. J Biomol NMR 40, 31–48 (2008). https://doi.org/10.1007/s10858-007-9208-0

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