Spectral fitting for signal assignment and structural analysis of uniformly 13C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

Journal of Biomolecular NMR

Volumn 38, Issue 4, 2007, Pages 325-339

  Matsuki, Yoh ^a,b   Akutsu, Hideo ^b   Fujiwara, Toshimichi ^a  

^a OSAKA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Chemical shift; Magic angle spinning; Signal assignment; Spectral simulation

Indexed keywords

CARBON 13; MASTOPARAN; MASTOPARAN X; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; CALCULATION; CARBON NUCLEAR MAGNETIC RESONANCE; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN STRUCTURE; SIGNAL PROCESSING; SIMULATION; STRUCTURE ANALYSIS;

CARBON ISOTOPES; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE; TIME FACTORS;

EID: 34547215825     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-007-9170-x     Document Type: Article

References (63)

1. 15N labeled peptides and proteins. J Magn Reson 158:157-163
2. Baldus M, Petkova AT, Herzfeld J, Griffin RG (1998) Cross polarization in the tilted frame: Assignment and spectral simplification in heteronuclear spin systems. Mol Phys 95:1197-1207
3. Bak M, Rasmussen JT, Nielsen NC (2000) SIMPSON: A general simulation program for solid-state NMR spectroscopy. J Magn Reson 147:296-330
4. Bennett AE, Rienstra CM, Griffiths JM, Zhen W, Lansbury PT Jr, Griffin RG (1998) Homonuclear radio frequency-driven recoupling in rotating solids. J Chem Phys 108:9463-9479
5. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR System: A new software suite for macromolecular structure determination. Acta Crystallogr D54:905-921
6. Buchler NEG, Zuiderweg ERP, Wang H, Goldstein RA (1997) Protein heteronuclear NMR assignments using mean-field simulated annealing. J Magn Reson 125:34-42
7. Cadars S, Lesage A, Emsley L (2005) Chemical shift correlations in disordered solids. J Am Chem Soc 127:4466-4476
8. 13C dipolar correlation spectroscopy and chemical shift analysis. Biochemistry 42:11476-11483
9. 1H NMR spectra. J Magn Reson 80:119-127
10. 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
11. de Dios AC, Pearson JG, Oldfield E (1993) Chemical shifts in proteins: an ab initio study of carbon-13 nuclear magnetic resonance chemical shielding in glycine, alanine, and valine residues. J Am Chem Soc 115:9768-9773
12. Eccles C, Güntert P, Billeter M, Wüthrich K (1991) Efficient analysis of protein 2D NMR spectra using the software package EASY. J Biomol NMR 1:111-130
13. Egawa A, Fujiwara T, Mizoguchi T, Kakitani Y, Koyama Y, Akutsu H (2007) Structure of the light-harvesting bacteriochlorophyll c assembly in chlorosomes from Chlorobium limicola determined by solid-state NMR. Proc Natl Acad Sci USA 104:790-795
14. Elena B, Pintacuda G, Mifsud N, Emsley L (2006) Molecular structure determination in powders by NMR crystallography from proton spin diffusion. J Am Chem Soc 128:9555-9560
15. Etzkorn M, Martell S, Andronesi OC, Seidel K, Engelhard M, Baldus M (2007) Secondary structure, dynamics, and topology of a seven-helix receptor in native membranes, studied by solid-state NMR spectroscopy. Angew Chem Int Ed 46:459-462
16. 13C chemical shift assignments and conformational analysis. J Am Chem Soc 127:12291-12305
17. 15N-labeled peptide, mastoparan-X, by multidimensional solid-state NMR under magic-angle spinning. J Biomol NMR 28:311-325
18. Grommek A, Meier BH, Ernst M (2006) Distance information from proton-driven spin diffusion under MAS. Chem Phys Lett 427:404-409
19. 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
20. 1H-depolarization under magic-angle spinning. J Am Chem Soc 128:10654-10655
21. Havlin RH, Tycko R (2005) Probing site-specific conformational distributions in protein folding with solid-state NMR. Proc Natl Acad Sci USA 102:3284-3289
22. Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M (2005) Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J 89:2113-2120
23. Hohwy M, Jakobsen HJ, Edén M, Levitt MH, Nielsen NC (1998) Broadband dipolar recoupling in the nuclear magnetic resonance of rotating solids: A compensated C7 pulse sequence. J Chem Phys 108:2686-2694
24. Hong M (1999) Solid-state dipolar INADEQUATE NMR spectroscopy with a large double-quantum spectral width. J Magn Reson 136:86-91
25. Hughes CE, Luca S, Baldus M (2004) Radio-frequency driven polarization transfer without heteronuclear decoupling in rotating solids. Chem Phys Lett 385:435-440
26. Jakeman DL, Mitchell DJ, Shuttleworth WA, Evans JNS (1998) Effects of sample preparation conditions on biomolecular solid-state NMR lineshapes. J Biomol NMR 12:417-421
27. Kainosho M, Torizawa T, Iwashita Y, Terauchi T, Ono AM, Güntert P (2006) Optimal isotope labelling for NMR protein structure determinations. Nature 440:52-57
28. Kleywegt GJ (2000) Validation of protein crystal structures. Acta Cryst D56:249-265
29. 1H NMR spectra of proteins: Basic algorithms and application to phoratoxin B. J Biomol NMR 1:23-47
30. +-ATP synthase subunit c, by magic-angle spinning solid-state NMR. J Biomol NMR 36:279-293
31. Lange A, Giller K, Hornig S, Martin-Eauclaire M-F, Pongs O, Becker S, Baldus M (2006) Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR. Nature 440:959-962
32. Le HB, Pearson JG, de Dios AC, Oldfield E (1995) Protein structure refinement and prediction via NMR chemical shifts and quantum chemistry. J Am Chem Soc 117:3800-3807
33. 15N NMR chemical shifts in proteins and secondary structure. J Biomol NMR 4:341-348
34. Leopold MF, Urbauer JK, Wand AJ (1994) Resonance assignment strategies for the analysis of NMR spectra of proteins. Mol Biotechnol 2:61-93
35. Leutner M, Gschwind RM, Liermann J, Schwarz C, Gemmecker G, Kessler H (1998) Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J Biomol NMR 11:31-43
36. Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szypersk T (2005) NMR data collection and analysis protocol for high-throughput protein structure determination. Proc Natl Acad Sci USA 102:10487-10492
37. Marulanda D, Tasayco ML, McDermott A, Cataldi M, Arriaran V, Polenova T (2004) Magic angle spinning solid-state NMR spectroscopy for structural studies of protein interfaces Resonance assignments of differentially enriched Escherichia coli thioredoxin reassembled by fragment complementation. J Am Chem Soc 126:16608-16620
38. 1H double-quantum dipolar interactions recoupled under magic angle spinning conditions. Magn Reson Chem 42:291-300
39. Mertens HDT, Gooley PR (2005) Validating the use of database potentials in protein structure determination by NMR. FEBS Lett 579:5542-5548
40. Meiler J (2003) PROSHIFT: Protein chemical shift prediction using artificial neural networks. J Biomol NMR 26:25-37
41. Morcombe CR, Zilm KW (2003) Chemical shift referencing in MAS solid state NMR. J Magn Reson 162:479-486
42. Moseley HNB, Montelione GT (1999) Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol 9:635-642
43. Neal S, Berjanskii M, Zhang H, Wishart DS (2006) Accurate prediction of protein torsion angles using chemical shifts and sequence homology. Magn Reson Chem 44:S158-S167
44. 15N chemical shifts. J Biomol NMR 26:215-240
45. Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, Güntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJ (2005) RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59:662-672
46. Nilges M, O'Donoghue SI (1998) Ambiguous NOEs and automated NOE assignment. Prog Nucl Magn Reson 32:107-139
47. Oas TG, Hartzell CJ, Dahlquist FW, Drobny GP (1987) The amide nitrogen-15 chemical shift tensors of four peptides determined from carbon-13 dipole-coupled chemical shift powder patterns. J Am Chem Soc 109:5962-5966
48. Oldfield E (2002) Chemical shifts in amino acids, peptides, and proteins: From quantum chemistry to drug design. Annu Rev Phys Chem 53:349-378
49. Ösapay K, Case DA (1994) Analysis of proton chemical shifts in regular secondary structure of proteins. J Biomol NMR 4:215-230
50. 13CO chemical shift anisotropy tensors in solution. J Am Chem Soc 122:4841-4842
51. 15N NMR. J Mol Struct 441:251-266
52. Sun H, 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
53. Thomas PD, Basus VJ, James TL (1991) Protein solution structure determination using distances from two-dimensional nuclear overhauser effect experiments: Effect of approximations on the accuracy of derived structures. Proc Natl Acad Sci USA 88:1237-1241
54. Todokoro Y, Yumen I, Fukushima K, Kang SW, Park JS, Kohno T, Wakamatsu K, Akutsu H, Fujiwara T (2006) Structure of tightly membrane-bound mastoparan-X, a g-protein-activating peptide, determined by solid-state NMR. Biophys J 91:1368-1379
55. Veshtort M, Griffin RG (2006) SPINEVOLUTION: A powerful tool for the simulation of solid and liquid state NMR experiments. J Magn Reson 178:248-282
56. Wagner G, Pardi A, Wüthrich K (1983) Hydrogen bond length and proton NMR chemical shifts in proteins. J Am Chem Soc 105:5948-5949
57. 1 torsion angles. J Biomol NMR 28:327-340
58. 13C NMR chemical shift anisotropy tensors of polypeptides. J Am Chem Soc 123:6118-6126
59. Wishart DS, Case DA (2001) Use of chemical shifts in macromolecular structure determination. Meth Enzymol 338:3-34
60. Wishart DS, Nip AM (1998) Protein chemical shift analysis: A practical guide. Biochem Cell Biol 76:153-163
61. 13C′ chemical shifts in peptides using density functional theory. Biopolymers 65:408-423
62. Xu Y, Wang X, Yang J, Vaynberg J, Qin J (2006) PASA - A program for automated protein NMR backbone signal assignment. J Biomol NMR 34:41-56
63. Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien CY, Powers R, Montelione GT (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592-610