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Three-Dimensional Structure Determination of Peptides Using Solution Nuclear Magnetic Resonance Spectroscopy

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Snake and Spider Toxins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2068))

Abstract

Nuclear magnetic resonance (NMR) spectroscopy has over the last few decades proven to be an extremely useful technique for, and indeed an integral part of, investigating the structural features of peptides and small proteins directly in solution, without the need for crystallization. This advantage over X-ray methods is important when dealing with peptides and small proteins that do not readily form crystals. In this chapter we outline what specific NMR experiments are useful, considerations about how to acquire and interpret these experiments, and how information derived from the NMR data can be used to determine solution structures of small peptides.

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References

  1. Rosengren KJ, Daly NL, Craik DJ (2008) NMR of peptide toxins. Annu Rep NMR Spectrosc 68:89–147

    Article  Google Scholar 

  2. Himeno K, Rosengren KJ, Inoue T et al (2015) Identification, characterization, and three-dimensional structure of the novel circular bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium. Biochemistry 54:4863–4876

    Article  CAS  Google Scholar 

  3. Schroeder CI, Rash LD, Vila-Farres X et al (2014) Chemical synthesis, 3D structure, and ASIC binding site of the toxin mambalgin-2. Angew Chem Int Ed Engl 53:1017–1020

    Article  CAS  Google Scholar 

  4. Hwang TL, Shaka AJ (1995) Water suppression that works. Excitation sculpting using arbitrary wave-forms and pulsed-field gradients. J Magn Reson 112:275–279

    Article  CAS  Google Scholar 

  5. Bax A, Davis DG (1985) MLEV-17 based two-dimensional homonuclear magnetization transfer spectroscopy. J Magn Reson 65:355–360

    CAS  Google Scholar 

  6. Jeener J, Meier BH, Bachman P et al (1979) Investigation of chemical exchange processes by two-dimensional NMR spectroscopy. J Chem Phys 71:4546–4553

    Article  CAS  Google Scholar 

  7. Kumar A, Ernst RR, Wüthrich K (1980) A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem Biophys Res Commun 95:1–6

    Google Scholar 

  8. Bax A, Davis DG (1985) Practical aspects of two-dimensional transverse NOE spectroscopy. J Magn Reson 63:207–213

    CAS  Google Scholar 

  9. Bothner-By AA, Stephens RL, Lee J et al (1984) Structure determination of a tetrasaccharide: transient nuclear Overhauser effects in the rotating frame. J Am Chem Soc 106:811–813

    Article  CAS  Google Scholar 

  10. Rance M, Sørenson OW, Bodenhausen G et al (1983) Improved spectral resolution in COSY 1H NMR spectra of proteins via double quantum filtering. Biochem Biophys Res Commun 177:479–485

    Article  Google Scholar 

  11. Greisinger C, Sørenson OW, Ernst RR (1987) Practical aspects of the E. COSY technique. Measurement of scalar spin-spin coupling constants in peptides. J Magn Reson 75:474–492

    Google Scholar 

  12. Palmer AG, Cavanagh J, Wright PE et al (1991) Sensitivity improvement in proton-detected 2-dimensional heteronuclear correlation NMR-spectroscopy. J Magn Reson 93:151–170

    CAS  Google Scholar 

  13. Vuister GW, Bax A (1992) Resolution enhancement and spectral editing of uniformly 13C-enriched proteins by homonuclear broadband 13C decoupling. J Magn Reson 98:428–435

    CAS  Google Scholar 

  14. Wüthrich K (1986) NMR of proteins and Nucleic acids. Wiley-Interscience, New York

    Book  Google Scholar 

  15. Wishart DS, Bigam CG, Yao J et al (1995) 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6:135–140

    Article  CAS  Google Scholar 

  16. Shen Y, Bax A (2013) Protein backbone and side-chain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56:227–241

    Article  CAS  Google Scholar 

  17. Shen Y, Bax A (2015) Protein structural information derived from NMR chemical shift with the neural network program TALOS-N. Methods Mol Biol 1260:17–32

    Article  CAS  Google Scholar 

  18. 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  CAS  Google Scholar 

  19. Wagner G (1990) NMR investigations of protein structure. Prog Nucl Magn Reson Spectrosc 22:101–139

    Article  CAS  Google Scholar 

  20. Armstrong DA, Kaas Q, Rosengren KJ (2018) Prediction of disulfide dihedral angles using chemical shifts. Chem Sci 9:6548–6556

    Article  CAS  Google Scholar 

  21. Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283–298

    Article  Google Scholar 

  22. Güntert P, Buchner L (2015) Combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR 62:453–471

    Article  Google Scholar 

  23. Brünger AT, Adams PD, Clore GM et al (1998) A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921

    Article  Google Scholar 

  24. Nederveen AJ, Doreleijers JF, Vranken W et al (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59:662–672

    Article  CAS  Google Scholar 

  25. Linge JP, Williams MA, Spronk CA et al (2003) Refinement of protein structures in explicit solvent. Proteins 50:496–506

    Article  CAS  Google Scholar 

  26. Chen VB, Arendall WB, Headd JJ et al (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21

    Article  CAS  Google Scholar 

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

    Google Scholar 

  28. Piotto M, Saudek V, Sklenar V (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR 2:661–665

    Article  CAS  Google Scholar 

  29. Cierpicki T, Otlewski J (2001) Amide proton temperature coefficients as hydrogen bond indicators in proteins. J Biomol NMR 21:249–261

    Article  CAS  Google Scholar 

  30. Gottlieb HE, Kotlyar V, Nudelman A (1997) NMR chemical shifts of common laboratory solvents as trace impurities. J Org Chem 62:7512–7515

    Article  CAS  Google Scholar 

  31. Bartels C, Xia TH, Billeter M et al (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1–10

    Article  CAS  Google Scholar 

  32. Goddard TD, Kneller DG (2004) SPARKY 3. University of California, San Francisco

    Google Scholar 

  33. Vranken WF, Boucher W, Stevens TJ et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696

    Article  CAS  Google Scholar 

  34. Marion D, Wuthrich K (1983) Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteins. Biochem Biophys Res Commun 113:967–974

    Article  CAS  Google Scholar 

  35. Pardi A, Billeter M, Wüthrich K (1984) Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHNa, in a globular protein. Use of 3JHNa, for identification of helical secondary structure. J Mol Biol 180:741–751

    Article  CAS  Google Scholar 

  36. Clubb RT, Ferguson SB, Walsh CT et al (1994) Three-dimensional solution structure of Escherichia coli periplasmic cyclophilin. Biochemistry 33:2761–2772

    Article  CAS  Google Scholar 

  37. Ludvigsen S, Poulsen FM (1992) Positive theta-angles in proteins by nuclear magnetic resonance spectroscopy. J Biomol NMR 2:227–233

    Article  CAS  Google Scholar 

  38. Wagner G, Braun W, Havel TF et al (1987) Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J Mol Biol 196:611–639

    Article  CAS  Google Scholar 

  39. Rosengren KJ, Daly NL, Plan MR et al (2003) Twists, knots, and rings in proteins. J Biol Chem 278:8606–8616

    Article  CAS  Google Scholar 

  40. Clore GM, Gronenborn AM (1989) Determination of the three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. CRC Crit Rev Biochem Mol Biol 24:479–564

    Article  CAS  Google Scholar 

  41. Braun W, Go N (1985) Calculation of protein conformation by proton-proton distance constraints: a new efficient algorithm. J Mol Biol 186:611–626

    Article  CAS  Google Scholar 

  42. Nilges M, Gronenborn AM, Brunger AT et al (1988) Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine protease inhibitor 2. Protein Eng 2:27–38

    Article  CAS  Google Scholar 

  43. Brünger AT, Clore GM, Gronenborn AM et al (1986) Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc Natl Acad Sci U S A 83:3801–3805

    Article  Google Scholar 

  44. Clore GM, Nilges M, Sakuraman DK et al (1986) The three-dimensional structure of a1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J 5:2729–2735

    Article  CAS  Google Scholar 

  45. Kaptein R, Zuiderweg ERP, Scheck RM et al (1985) A protein structure from nuclear magnetic resonance data: lac repressor headpiece. J Mol Biol 182:179–182

    Article  CAS  Google Scholar 

  46. Montelione GT, Nilges M, Bax A et al (2013) Recommendations of the wwPDB NMR validation task force. Structure 21:1563–1570

    Article  CAS  Google Scholar 

  47. Henriques ST, Deplazes E, Lawrence N et al (2016) Interaction of tarantula venom peptide ProTx-II with lipid membranes is a prerequisite for its inhibition of human voltage-gated sodium channel NaV1.7. J Biol Chem 291:17049–17065

    Article  CAS  Google Scholar 

  48. Luo S, Zhangsun D, Schroeder CI et al (2014) A novel alpha4/7-conotoxin LvIA from Conus lividus that selectively blocks alpha3beta2 vs. alpha6/alpha3beta2beta3 nicotinic acetylcholine receptors. FASEB J 28:1842–1853

    Article  CAS  Google Scholar 

  49. 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  CAS  Google Scholar 

  50. Sutcliffe MJ (1993) Structure determination from NMR data II. Computational approaches. In: Roberts GCK (ed) NMR of macromolecules, a practical approach. Oxford University Press, New York, pp 359–390

    Google Scholar 

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Acknowledgments

This work was supported by a National Health and Medical Research (NHMRC) project grant (APP1080405) awarded to CIS. CIS is an Australian Research Council (ARC) Future Fellow (FT160100055) and an Institute for Molecular Bioscience Industry Fellow and KJR is an ARC Future Fellow (FT130100890).

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Authors and Affiliations

  1. Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia

    Christina I. Schroeder

  2. School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia

    K. Johan Rosengren

Authors
  1. Christina I. Schroeder
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  2. K. Johan Rosengren
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Corresponding authors

Correspondence to Christina I. Schroeder or K. Johan Rosengren .

Editor information

Editors and Affiliations

  1. Faculty of Medicine, School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel

    Avi Priel

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Schroeder, C.I., Rosengren, K.J. (2020). Three-Dimensional Structure Determination of Peptides Using Solution Nuclear Magnetic Resonance Spectroscopy. In: Priel, A. (eds) Snake and Spider Toxins. Methods in Molecular Biology, vol 2068. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9845-6_7

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  • DOI: https://doi.org/10.1007/978-1-4939-9845-6_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9844-9

  • Online ISBN: 978-1-4939-9845-6

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