Measuring translational diffusion coefficients of peptides and proteins by PFG-NMR using band-selective RF pulses
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- 作者：Shenggen Yao (1)
Daniel K. Weber (1) (2)
Frances Separovic (1) (2)
David W. Keizer (1) - 关键词：BEST ; Dynamics range ; PFG ; NMR ; Peptides and proteins ; Translational diffusion measurement ; Water suppression
- 刊名：European Biophysics Journal
- 出版年：2014
- 出版时间：July 2014
- 年：2014
- 卷：43
- 期：6-7
- 页码：331-339
- 全文大小：
- 参考文献：1. Ali FE, Separovic F, Barrow CJ, Yao S, Barnham KJ (2006) Copper and zinc mediated oligomerisation of A? peptides. Int J Pept Res Ther 12:153-64 CrossRef
2. Andrec M, Prestegard JH (1997) Quantitation of chemical exchange rates using pulsed-field-gradient diffusion measurements. J Biomol NMR 9:136-50 CrossRef
3. Augustyniak R, Ferrage F, Paquin R, Lequin O, Bodenhausen G (2011) Methods to determine slow diffusion coefficients of biomolecules. Applications to Engrailed 2, a partially disordered protein. J Biomol NMR 50:209-18 CrossRef
4. Barhoum S, Booth V, Yethiraj A (2013) Diffusion NMR study of complex formation in membrane-associated peptides. Eur Biophys J 42:405-14 CrossRef
5. Bocian W, Sitkowski J, Tarnowska A, Bednarek E, Kawecki R, Kozminski W, Kozerski L (2008) Direct insight into insulin aggregation by 2D NMR complemented by PFGSE NMR. Proteins 71:1057-065 CrossRef
6. Brand T, Cabrita EJ, Morris GA, Gunther R, Hofmann HJ, Berger S (2007) Residue-specific NH exchange rates studied by NMR diffusion experiments. J Magn Reson 187:97-04 CrossRef
7. Buevich AV, Baum J (2002) Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. J Am Chem Soc 124:7156-162 CrossRef
8. Callaghan PT, Legros MA, Pinder DN (1983) The measurement of diffusion using deuterium pulse field gradient nuclear magnetic resonance. J Chem Phys 79:6372-381 CrossRef
9. Chou JJ, Baber JL, Bax A (2004) Characterization of phospholipid mixed micelles by translational diffusion. J Biomol NMR 29:299-08 CrossRef
10. Coles M, Bicknell W, Watson AA, Fairlie DP, Craik DJ (1998) Solution structure of amyloid beta-peptide(1-0) in a water-micelle environment. Is the membrane-spanning domain where we think it is? Biochemistry 37:11064-1077 CrossRef
11. Czabotar PE, Westphal D, Dewson G, Ma S, Hockings C, Fairlie WD, Lee EF, Yao S, Robin AY, Smith BJ, Huang DCS, Kluck RM, Adams JM, Colman PM (2013) Bax crystal structures reveal how BH3 Domains activate Bax and nucleate its oligomerization to Induce apoptosis. Cell 152:519-31 CrossRef
12. Dahse K, Garvey M, Kovermann M, Vogel A, Balbach J, Fandrich M, Fahr A (2010) DHPC strongly affects the structure and oligomerization propensity of Alzheimer’s A?(1-40) peptide. J Mol Biol 403:643-59 CrossRef
13. Dehner A, Kessler H (2005) Diffusion NMR spectroscopy: folding and aggregation of domains in p53. Chembiochem 6:1550-565 CrossRef
14. Didenko T, Boelens R, Rudiger SGD (2011) 3D DOSY-TROSY to determine the translational diffusion coefficient of large protein complexes. Protein Eng Des Sel 24:99-03 CrossRef
15. Dingley AJ, Mackay JP, Chapman BE, Morris MB, Kuchel PW, Hambly BD, King GF (1995) Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: application to myosin light chain 2. J Biomol NMR 6:321-28
16. Horst R, Horwich AL, Wuthrich K (2011) Translational diffusion of macromolecular assemblies measured using transverse-relaxation-optimized pulsed field gradient NMR. J Am Chem Soc 133:16354-6357 CrossRef
17. Hwang T-L, Shaka AJ (1995) Water suppression that works. Excitation sculpting using arbitrary wave-forms and pulsed-field gradients. J Magn Reson A 112:275-79 CrossRef
18. Jansma AL, Kirkpatrick JP, Hsu AR, Handel TM, Nietlispach D (2010) NMR analysis of the structure, dynamics, and unique oligomerization properties of the chemokine CCL27. J Biol Chem 285:14424-4437 CrossRef
19. Johnson CS (1999) Diffusion ordered nuclear magnetic resonance spectroscopy: principles and applications. Prog Nucl Magn Reson Spectrosc 34:203-56 CrossRef
20. Kallick DA, Tessmer MR, Watts CR, Li CY (1995) The use of dodecylphosphocholine micelles in solution NMR. J Magn Reson Ser B 109:60-5 CrossRef
21. Khera S, Grillo M, Schnier P, Hollis S (2010) Application of diffusion-edited NMR spectroscopy for the structural characterization of drug metabolites in mixtures. J Pharmaceut Biomed 51:164-69 CrossRef
22. Kuchel PW, Chapman BE (1991) Translational diffusion of hemoglobin in human erythrocytes and hemolysates. J Magn Reson 94:574-80
23. Kuipers BJ, Gruppen H (2007) Prediction of molar extinction coefficients of proteins and peptides using UV absorption of the constituent amino acids at 214?nm to enable quantitative reverse phase high-performance liquid chromatography–mass spectrometry analysis. J Agric Food Chem 55:5445-451 CrossRef
24. Lee CD, Sun HC, Hu SM, Chiu CF, Homhuan A, Liang SM, Leng CH, Wang TF (2008) An improved SUMO fusion protein system for effective production of native proteins. Protein Sci 17:1241-248 CrossRef
25. Malakhov MP, Mattern MR, Malakhova OA, Drinker M, Weeks SD, Butt TR (2004) SUMO fusions and SUMO-specific protease for efficient expression and purification of proteins. J Struct Funct Genomics 5:75-6 CrossRef
26. Mandal PK, Pettegrew JW (2004a) Alzheimer’s disease: NMR studies of asialo (GM1) and trisialo (GT1b) ganglioside interactions with A beta(1-0) peptide in a membrane mimic environment. Neurochem Res 29:447-53 CrossRef
27. Mandal PK, Pettegrew JW (2004b) Alzheimer’s disease: soluble oligomeric A beta(1-0) peptide in membrane mimic environment from solution NMR and circular dichroism studies. Neurochem Res 29:2267-272 CrossRef
28. Mansfield P (1977) Multi-planar image-formation using NMR spin echos. J Phys C—Solid State Phys 10:L55–L58 CrossRef
29. Manzo G, Carboni M, Rinaldi AC, Casu M, Scorciapino MA (2013) Characterization of sodium dodecylsulphate and dodecylphosphocholine mixed micelles through NMR and dynamic light scattering. Magn Reson Chem 51:176-83 CrossRef
30. McLachlan AS, Richards JJ, Bilia AR, Morris GA (2009) Constant time gradient HSQC-iDOSY: practical aspects. Magn Reson Chem 47:1081-085 CrossRef
31. Momot KI, Kuchel PW (2004) Convection-compensating PGSE experiment incorporating excitation-sculpting water suppression (CONVEX). J Magn Reson 169:92-01 CrossRef
32. Park KD, Lee YJ (2006) Slice-selected LED and BPPLED: application of slice selection to DOSY. Magn Reson Chem 44:887-91 CrossRef
33. Pelta MD, Morris GA, Stchedroff MJ, Hammond SJ (2002) A one-shot sequence for high-resolution diffusion-ordered spectroscopy. Magn Reson Chem 40:S147–S152 CrossRef
34. Piotto M, Saudek V, Sklenar V (1992) Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR 2:661-65 CrossRef
35. Price WS, Elwinger F, Vigouroux C, Stilbs P (2002) PGSE-WATERGATE, a new tool for NMR diffusion-based studies of ligand-macromolecule binding. Magn Reson Chem 40:391-95 CrossRef
36. Ryan TM, Caine J, Mertens HD, Kirby N, Nigro J, Breheney K, Waddington LJ, Streltsov VA, Curtain C, Masters CL, Roberts BR (2013) Ammonium hydroxide treatment of A? produces an aggregate free solution suitable for biophysical and cell culture characterization. Peer J 1:e73 CrossRef
37. Schanda P (2009) Fast-pulsing longitudinal relaxation optimized techniques: enriching the toolbox of fast biomolecular NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 55:238-65 nmrs.2009.05.002" target="_blank" title="It opens in new window">CrossRef
38. Schanda P, Brutscher B (2005) Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. J Am Chem Soc 127:8014-015 CrossRef
39. Shukla M, Dorai K (2011) Resolving overlaps in diffusion encoded spectra using band-selective pulses in a 3D BEST-DOSY experiment. J Magn Reson 213:69-5 CrossRef
40. Sibille N, Bellot G, Wang J, Demene H (2012) Low concentration of a Gd-chelate increases the signal-to-noise ratio in fast pulsing BEST experiments. J Magn Reson 224:32-7 CrossRef
41. Sigmund EE, Cho H, Song Y-Q (2007) Multiple-modulation-multiple-echo magnetic resonance. Concepts Magn Reson A 30A:358-77 CrossRef
42. Sillerud LO, Larson RS (2012) Advances in nuclear magnetic resonance for drug discovery. Methods Mol Biol 910:195-66 CrossRef
43. Sklenar V, Piotto M, Leppik R, Saudek V (1993) Gradient-tailored water suppression for 1H-15N HSQC experiments optimized to retain full sensitivity. J Magn Reson Ser A 102:241-45 CrossRef
44. Stamps JP, Ottink B, Visser JM, van Duynhoven JP, Hulst R (2001) Difftrain: a novel approach to a true spectroscopic single-scan diffusion measurement. J Magn Reson 151:28-1 CrossRef
45. Theillet FX, Binolfi A, Liokatis S, Verzini S, Selenko P (2011) Paramagnetic relaxation enhancement to improve sensitivity of fast NMR methods: application to intrinsically disordered proteins. J Biomol NMR 51:487-95 CrossRef
46. Wahlstrom A, Hugonin L, Peralvarez-Marin A, Jarvet J, Graslund A (2008) Secondary structure conversions of Alzheimer’s A?(1-40) peptide induced by membrane-mimicking detergents. FEBS J 275:5117-128 CrossRef
47. Wahlstrom A, Cukalevski R, Danielsson J, Jarvet J, Onagi H, Rebek J, Linse S, Graslund A (2012) Specific binding of a beta-cyclodextrin dimer to the amyloid ? peptide modulates the peptide aggregation process. Biochemistry 51:4280-289 CrossRef
48. Wang YQ, Li CG, Pielak GJ (2010) Effects of proteins on protein diffusion. J Am Chem Soc 132:9392-397 CrossRef
49. Williamson MP, Suzuki Y, Bourne NT, Asakura T (2006) Binding of amyloid ?-peptide to ganglioside micelles is dependent on histidine-13. Biochem J 397:483-90 CrossRef
50. Wu DH, Chen AD, Johnson CS (1995) An improved diffusion-ordered spectroscopy experiment incorporating bipolar-gradient pulses. J Magn Reson Ser A 115:260-64 CrossRef
51. Wu DH, Chen AD, Johnson CS (1996) Heteronuclear-detected diffusion-ordered NMR spectroscopy through coherence transfer. J Magn Reson Ser A 123:215-18 CrossRef
52. Yan JL, Kline AD, Mo HP, Zartler ER, Shapiro MJ (2002) Epitope mapping of ligand-receptor interactions by diffusion NMR. J Am Chem Soc 124:9984-985 CrossRef
53. Yao S, Keizer DW (2014) Nutation frequency modulation on NMR signal of nuclear spins in chemical exchange with solvent water under the BEST conditions. Magn Reson Chem 52:190-94 CrossRef
54. Yao S, Howlett GJ, Norton RS (2000) Peptide self-association in aqueous trifluoroethanol monitored by pulsed field gradient NMR diffusion measurements. J Biomol NMR 16:109-19 CrossRef
55. Yao S, Cherny RA, Bush AI, Masters CL, Barnham KJ (2004) Characterizing bathocuproine self-association and subsequent binding to Alzheimer’s disease amyloid ?-peptide by NMR. J Pept Sci 10:210-17 CrossRef
56. Yao S, Babon JJ, Norton RS (2008) Protein effective rotational correlation times from translational self-diffusion coefficients measured by PFG-NMR. Biophys Chem 136:145-51 CrossRef
57. Yao S, Hinds MG, Murphy JM, Norton RS (2011) Exchange enhanced sensitivity gain for solvent-exchangeable protons in 2D 1H-15N heteronuclear correlation spectra acquired with band-selective pulses. J Magn Reson 211:243-47 CrossRef
58. Yao S, Westphal D, Babon JJ, Thompson GV, Robin AY, Adams JM, Colman PM, Czabotar PE (2014) NMR studies of interactions between Bax and BH3 domain-containing peptides in the absence and presence of CHAPS. Arch Biochem Biophys 545:33-3 CrossRef
59. Yu LP, Edalji R, Harlan JE, Holzman TF, Lopez AP, Labkovsky B, Hillen H, Barghorn S, Ebert U, Richardson PL, Miesbauer L, Solomon L, Bartley D, Walter K, Johnson RW, Hajduk PJ, Olejniczak ET (2009) Structural characterization of a soluble amyloid ?-peptide oligomer. Biochemistry 48:1870-877 CrossRef
60. Zhang S (2006) Quantitative measurement of molecular diffusion coefficients by NMR spectroscopy. J Am Chem Soc 128:4974-975 CrossRef
61. Zheng G, Price WS (2010) Solvent signal suppression in NMR. Prog Nucl Magn Reson Spectrosc 56:267-88 nmrs.2010.01.001" target="_blank" title="It opens in new window">CrossRef - 作者单位：Shenggen Yao (1)
Daniel K. Weber (1) (2)
Frances Separovic (1) (2)
David W. Keizer (1)
1. Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
2. School of Chemistry, The University of Melbourne, Melbourne, VIC, 3010, Australia - ISSN：1432-1017
文摘
Molecular translational self-diffusion, a measure of diffusive motion, provides information on the effective molecular hydrodynamic radius, as well as information on the properties of media or solution through which the molecule diffuses. Protein translational diffusion measured by pulsed-field gradient nuclear magnetic resonance (PFG-NMR) has seen increased application in structure and interaction studies, as structural changes or protein–protein interactions are often accompanied by alteration of their effective hydrodynamic radii. Unlike the analysis of complex mixtures by PFG-NMR, for monitoring changes of protein translational diffusion under various conditions, such as different stages of folding/unfolding, a partial region of the spectrum or even a single resonance is sufficient. We report translational diffusion coefficients measured by PFG-NMR with a modified stimulated echo (STE) sequence where band-selective pulses are employed for all three 1H RF pulses. Compared with conventional non-selective sequence, e.g. the BPP-LED sequence, the advantage of this modified band-selective excitation short transient (BEST) version of STE (BEST-STE) sequence is multi-fold, namely: (1) potential sensitivity gain as in generalized BEST-based sequences, (2) water suppression is no longer required as the magnetization of solvent water is not perturbed during the measurement, and (3) dynamic range problems due to the presence of intense resonances from molecules other than the protein or peptide of interest, such as non-deuterated detergent micelles, are avoided.