Protein alignment using cellulose nanocrystals: Practical considerations and range of application

Journal of Biomolecular NMR

Volumn 47, Issue 3, 2010, Pages 195-204

  Denisov, Alexey Y ^a   Kloser, Elisabeth ^a   Gray, Derek G ^a   Mittermaier, Anthony K ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

Cellulose nanocrystals; Liquid crystals; Residual dipolar couplings; SH3 domains

Indexed keywords

CELLULOSE; NANOCRYSTAL; PROTEIN KINASE FYN; PROTEIN SH3;

AQUEOUS SOLUTION; ARTICLE; BACTERIOPHAGE; IONIC STRENGTH; LIQUID CRYSTAL; MACROMOLECULE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PH; PRIORITY JOURNAL;

ANIMALS; CELLULOSE; CHICKENS; DETERGENTS; HYDROGEN-ION CONCENTRATION; NANOPARTICLES; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTO-ONCOGENE PROTEINS C-FYN; SRC HOMOLOGY DOMAINS; WATER;

EID: 77954759927     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9423-y     Document Type: Article

References (48)

1. Araki J, Wada M, Kuga S, Okano T (1998) Flow properties of microcrystalline cellulose suspension prepared by acid treatment of native cellulose. Colloids Surf A Physicochem Eng Asp 142:75-82
2. Bax A (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 12:1-16
3. Bax A, Grishaev A (2005) Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr Opin Struct Biol 15:563-570
4. Clore G (2000) Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear Overhauser enhancement data and dipolar couplings by rigid body minimization. Proc Natl Acad Sci USA 97:9021-9025
5. Cornilescu G, Marquardt J, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836-6837
6. Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A (1995) NMRpipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293
7. DeLano W, Hus J (2002) The PyMOL molecular graphic system. DeLano Scientific, San Carlos
8. Dong X, Kimura T, Revol J-F, Gray D (1996) Effects of ionic strength on the phase separation of suspensions of cellulose crystallites. Langmuir 12:2076-2082
9. Dong X, Revol J-F, Gray D (1998) Effect of microcrystallite preparation conditions on the formation of colloid crystals of cellulose. Cellulose 5:19-32
10. Dosset P, Hus J, Marion D, Blackledge M (2001) A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings. J Biomol NMR 20:223-231
11. 15N NMR relaxation. Biochemistry 33:5984-6003
12. Fleming K, Gray D, Prasannan S, Matthews S (2000) Cellulose crystallites: a new and robust liquid crystalline medium for the measurement of residual dipolar couplings. J Am Chem Soc 122:5224-5225
13. Fleming K, Gray D, Matthews S (2001) Cellulose crystallites. Chem Eur J 7:1831-1836
14. Habibi Y, Lucia L, Rojas O (2010) Cellulose nanocrystals: chemistry, self-assembly, and applications. Chem Rev. doi:10.1021/cr900 339w
15. Hansen M, Mueller L, Pardi A (1998) Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol 5:1065-1074
16. Jensen M, Markwick P, Meier S, Griesinger C, Zweckstetter M, Grzesiek S, Bernado P, Blackledge M (2009) Quantitative determination of the conformational properties of partially and intristically disordered proteins using NMR dipolar couplings. Structure 17:1169-1185
17. Johnson B, Blevins R (1994) NMR View: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
18. Koenig W, Hu J-S, Ottiger M, Bose S, Hendler R, Bax A (1999) NMR measurement of dipolar couplings in proteins aligned by transient binding to purple membrane fragments. J Am Chem Soc 121:1385-1386
19. Lange O, Lakomek N, Fares C, Schroder G, Walter K, Becker S, Meiler J, Grubmuller H, Griesinger C, deGroot B (2008) Recognition dynamics up to microseconds revealed from RDC-derived ubiquitin ensemble in solution. Science 320:1471-1475
20. Liepinsh E, Otting G, Wuthrich K (1992) NMR spectroscopy of hydroxyl protons in aqueous solutions of peptides and proteins. J Biomol NMR 2:447-465
21. Lipsitz R, Tjandra N (2004) Residual dipolar couplings in NMR structure analysis. Annu Rev Biophys Biomol Struct 33:387-413
22. Lorieau J, Yao L, Bax A (2008) Liquid crystalline phase of G-tetrad DNA for NMR study of detergent-solubilized proteins. J Am Chem Soc 130:7536-7537
23. Marley J, Lu M, Bracken C (2001) A method for efficient isotopic labeling of recombinant proteins. J Biomol NMR 20:71-75
24. McConnell H (1958) Reaction rates by nuclear magnetic resonance. J Chem Phys 28:430-431
25. Mittermaier A (2003) Studying excited states of proteins by NMR spectroscopy. PhD thesis, Department of Biochemistry, University of Toronto, Toronto
26. Mittermaier A, Kay L (2004) The response of internal dynamics to hydrophobic core mutations in the SH3 domain from the Fyn tyrosine kinase. Protein Sci 13:1088-1099
27. Mohana-Borges R, Goto N, Kroon G, Dyson H, Wright P (2004) Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings. J Mol Biol 340:1131-1142
28. Musacchio A, Wilmanns M, Saraste M (1994) Structure and function of the SH3 domain. Prog Biophys Mol Biol 61:283-297
29. Noble M, Musacchio A, Saraste M, Courtneidge S, Wierenga R (1993) Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin. EMBO J 12:2617-2624
30. Ottiger M, Bax A (1998) Characterization of magnetically oriented phospholipid micelles for measurement of dipolar couplings in macromolecules. J Biomol NMR 12:361-372 (Pubitemid 128511302)
31. Ottiger M, Bax A (1999) Bicelle-based liquid crystals for NMRmeasurement of dipolar couplings at acidic and basic pH values. J Biomol NMR 13:187-191
32. Ottiger M, Delaglio F, Bax A (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J Magn Reson 131:373-378
33. Prestegard J, Bougault C, Kishore A (2004) Residual dipolar couplings in structure determination of biomolecules. Chem Rev 104:3519-3540
34. Prosser R, Losonczi J, Shiyanovskaya I (1998) Use of a novel aqueous liquid crystalline medium for high-resolution NMR of macromolecules in solution. J Am Chem Soc 120:11010-11011
35. Ranby B (1951) Fibrous macromolecular systems. Cellulose and muscle. The colloidal properties of cellulose micelles. Discuss Faraday Soc 11:158-164
36. Revol J-F, Bradford H, Giasson J, Marchessault R, Gray D (1992) Helicoidal self-ordering of cellulose microfibrils in aqueous suspension. Int J Biol Macromol 14:170-172
37. Revol J-F, Godbout L, Dong X, Gray D, Chanzy H, Maret G (1994) Chiral nematic suspensions of cellulose crystallites: phase separation and magnetic field orientation. Liq Cryst 16:127-134
38. Ruckert M, Otting G (2000) Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J Am Chem Soc 122:7793-7797
39. Salmon L, Bouvignies G, Markwick P, Lakomek N, Showalter S, Li D-W, Walter K, Griesinger C, Bruschweiler R, Blackledge M (2009) Protein conformational flexibility from structure-free analysis of NMR dipolar couplings: quantitative and absolute determination of backbone motion in ubiquitin. Angew Chem Int Ed 48:4154-4157
40. Sass J, Cordier F, Hoffmann A, Rogowski M, Cousin A, Omichinski J, Lowen H, Grzesiek S (1999) Purple membrane induced alignment of biological macromolecules in the magnetic field. J Am Chem Soc 121:2047-2055
41. Sass H-J, Musco G, Stahl S, Wingfield P, Grzesiek S (2000) Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes. J Biomol NMR 18:303-309
42. Skrynnikov N, Goto N, Yang D, Choy W, Tolman J, Mueller G, Kay L (2000) Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with betacyclodextrin. J Mol Biol 295:1265-1273
43. Tolman J, Ruan K (2006) NMR residual dipolar couplings as probes of biomolecular dynamics. Chem Rev 106:1720-1736
44. Torbet J, Maret G (1981) High-field magnetic birefringence study of the structure of rodlike phages Pf1 and fd in solution. Biopolymer 20:2657-2669
45. Trempe J-F, Gehring K (2003) Observation and interpretation of residual dipolar couplings in biomolecules. In: Burnell E, de Lange C (eds) NMR of ordered liquids. Kluwer Academic, Dordrecht, pp 163-190
46. Wierenga A, Philipse A, Lekkerkerker H (1998) Aqueous dispersions of colloidal Boehmite: structure, dynamics, and yield stress of rod gels. Langmuir 14:55-65
47. Wu K-P, Weinstock D, Narayanan C, Levy R, Baum J (2009) Structural reorganization of α-synuclein at low pH observed by NMR and REMD simulations. J Mol Biol 391:784-796
48. Zhang Q, Stelzer A, Fisher C, Al-Hashimi H (2007) Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450:1263-1267