Predicting 13Cα chemical shifts for validation of protein structures

Journal of Biomolecular NMR

Volumn 38, Issue 3, 2007, Pages 221-235

  Vila, Jorge A ^a,b   Villegas, Myriam E ^b   Baldoni, Hector A ^b   Scheraga, Harold A ^a  

^a Cornell University ^*  (United States)

^b UNIVERSIDAD NACIONAL DE SAN LUIS   (Argentina)

Author keywords

13C chemical shift prediction; Protein structure validation; Solution structure; Ubiquitin; X ray and NMR structures

Indexed keywords

CARBON; HISTIDINE; PHOSPHOPROTEIN; PROTEIN; UBIQUITIN;

ARTICLE; CHEMISTRY; HUMAN; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION; REPRODUCIBILITY;

CARBON; CARBON ISOTOPES; HISTIDINE; HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHOSPHOPROTEINS; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; UBIQUITIN;

EID: 34748921707     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-007-9162-x     Document Type: Review

References (71)

1. Allerhand A, Childers RF, Oldfield E (1973) Natural-abundance carbon-13 nuclear magnetic resonance studies in 20-mm sample tubes. Observation of numerous single-carbon resonances of Hen Egg-White Lysozyme. Biochem 12:1335-1241
2. 3His zincbinding domain from Nup475/Tristetraprolin: a novel fold with a disklike structure. Biochem 42:217-221 (Pubitemid 36083869)
3. Babini E, Bertini I, Capozzi F, Del Bianco C, Hollender D, Kiss T, Luchinat C, Quattrone A (2004) Solution structure of human β-parvalbumin and structural comparison with its paralog α-parvalbumin and with their rat orthologs. Biochem 43:16076-16085 (Pubitemid 40041021)
4. Ban Y-E, Rudolph J, Zhou P, Edelsbrunner H (2006) Evaluating the quality of NMR structures by local density of protons. Proteins 62:852-864 (Pubitemid 43364151)
5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242 (Pubitemid 30047768)
6. Biological Magnetic Resonance Data Bank (http://www.bmrb.wisc. edu)
7. Case DA (2000) Interpretation of chemical shifts and coupling constants in macromolecules. Curr Opin Struct Biol 10:197-203 (Pubitemid 30198946)
8. Case DA, Dyson HJ, Wright PE (1994) Use of chemical shifts and coupling constant in nuclear magnetic resonance structural studies on peptides and proteins. Methods Enzymol 239:392-416
9. α heteronuclear NOE data in monitoring a protein NMR structure refinement. J Biomol NMR 5:161-172
10. Chakrabarti P, Pal D (1998) Main-chain conformational features at different conformations of the side-chains in proteins. Protein Eng 11:631-647 (Pubitemid 28389154)
11. Chesnut DB, Moore KD (1989) Locally dense basis sets for chemical shift calculations. J Comp Chem 10:648-659
12. Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a diluite liquid crystalline phase. J Am Chem Soc 120:6836-6837 (Pubitemid 28347351)
13. 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 (Pubitemid 29143535)
14. de Dios AC, Pearson JG, Oldfield E (1993a) Chemical shifts in proteins: ab initio study of carbon-13 nuclear magnetic resonance chemical shielding in glycine, alanine and valine residues. J Am Chem Soc 115:9768-9773
15. de Dios AC, Pearson JG, Oldfield E (1993b) Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science 260:1491-1496 (Pubitemid 23273262)
16. Doreleijers JF, Rullmann J A C, Kaptein R (1998) Quality assessment of NMR structures: a statistical survey. J Mol Biol 281:149-164 (Pubitemid 28360678)
17. Dunbrack RL Jr, Karplus M (1994) Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nat Struct Biol 1:334-340
18. Dyson HJ, Wright PE (2005) Elucidation of the protein folding landscape by NMR. Methods Enzymol 394:299-321 (Pubitemid 40460920)
19. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE Jr, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill P M W, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98. Revision A.7, Inc., Pittsburgh, PA
20. 1 on shielding. J Am Chem Soc 119:11951-11958 (Pubitemid 28012761)
21. Hehre WJ, Radom L, Schleyer P, Pople JA (1986) Ab initio molecular orbital theory. Wiley, New York
22. Howard OW, Lilley D M J (1978) Carbon-13-NMR of peptides and proteins. Prog Nucl Magn Reson Spectrosc 12:1-40
23. Hunter C, Packer MJ, Zonta C (2005) From structure to chemical shift and vice-versa. Prog Nucl Magn Reson Spectrosc 47:27-39 (Pubitemid 41446975)
24. β carbon-13 chemical shifs in protein from an empirical database. J Biomol NMR 13:199-211 (Pubitemid 29143528)
25. Jameson CJ (1996) Understanding NMR chemical shifts. Annu Rev Phys Chem 47:135-169 (Pubitemid 126416963)
26. β chemical shifts on protein structure determination by NMR. J Magn Reson Ser B 106:92-96
27. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283-291
28. Laskowski RA, Rullmann J A C, MacArthur MW, Kaptein R, Thornton J (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8:477-486 (Pubitemid 126706801)
29. Laws DD, Le H, de Dios AC, Havlin RH, Oldfield E (1995) A basis size dependence study of Carbon-13 nuclear magnetic resonance spectroscopic shielding in Alanyl and Valyl fragments: toward protein shielding hypersurfaces. J Am Chem Soc 117:9542-9546
30. Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 433:128-132
31. α chemical shifts in protein structure determination. Magn Resn B 109:220-233
32. 13C NMR of enzymes. Prog Nucl Magn Reson Spectrosc 18:1-59
33. Meiler JJ (2003) PROSHIFT: protein chemical shift prediction using artificial neural networks. J Biomol NMR 26:25-37
34. Melnik BS, Garbuzynskiy SO, Lobanov MYu, Galzitskaya OV (2005) The difference between protein structures obtained by X-ray analysis and nuclear magnetic resonance. J Mol Biol 39:113-122 (Pubitemid 40941316)
35. Moon S, Case DA (2006) A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: mixed basis set and ONION methods combined with a complete basis set extrapolation. J Comp Chem 27:825-836
36. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992) Stereochemical quality of protein structure coordinates. Proteins 12:345-364
37. Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin A M JJ, Vuister GW, Vriend G, Spronk C A EM (2004) DRESS: a database of Refined solution NMR structures. Proteins 55:483-486 (Pubitemid 38620072)
38. Napper S, Delbaere L T J, Waygood B E J (1999) Histidine-containing protein, HPr, of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system can accept and donate a phosphoryl group. J Biol Chem 274:21776-21782
39. 15N chemical shifts. J Biomol NMR 26:215-240 (Pubitemid 36758442)
40. Némethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA (1992) Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 96:6472-6484
41. Oldfield E (2002) Chemical shifts in amino acids, peptides and proteins: from quantum chemistry to drug design. Annu Rev Phys Chem 53:349-378
42. Oldfield E, Allerhand A (1975) Identification of tryptophan resonances in natural abundance C-13 nuclear magnetic-resonance spectra of protein. Application of partially relaxed fouriertransform spectroscopy. J Am Chem Soc 97:221-224
43. Pearson JG, Le H, Sanders LK, Godbout N, Havlin RH, Oldfield EJ (1997) Predicting chemical shifts in proteins: structure refinement of valine residues by using ab initio and empirical geometry optimizations. J Am Chem Soc 119:11941-11950 (Pubitemid 28012760)
44. Pearson JG, Wang J-F, Markley JL, Le H, Oldfield E (1995) Protein structure refinement using carbon-13 nuclear magnetic resonance spectroscopic chemical shifts and quantum chemistry. J Am Chem Soc 117:8823-8829
45. Pontius J, Richelle J, Wodak SJ (1996) Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 264:121-136 (Pubitemid 26399998)
46. Press HW, Teukolsky SA, Vetterling WT, Flannery BP (1992) In: Numerical recipes in Fortran 77. The art of scientific computing, 2nd edn. Cambridge University Press, Ch. 14, pp 630-633
47. Ripoll DR, Vorobjev YN, Liwo A, Vila JA, Scheraga HA (1996) Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. J Mol Biol 264:770-783 (Pubitemid 27013560)
48. Ripoll DR, Vila JA, Scheraga HA (2005) On the Orientation of the Backbone Dipoles in Native Folds. Proc Natl Acad Sci USA 102:7559-7564 (Pubitemid 40741010)
49. Ripoll DR, Vila JA, Scheraga HA (2004) Folding of the Villin headpiece subdomain from random structures. Análisis of the charge distribution as function of pH. J Mol Biol 339:915-925 (Pubitemid 38686353)
50. Simon K, Xu J, Kim C, Skrynnikov NR (2005) Estimating the accuracy of protein structures using residual dipolar couplings. J Biomol NMR 33:83-93 (Pubitemid 41662431)
51. 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490-5492
52. Schubert M, Laudde D, Oschkinat H, Schmieder P (2002) A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistic. J Biomol NMR 24:149-154 (Pubitemid 35414678)
53. 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 (Pubitemid 34506947)
54. van Nuland N A J, Hangyi IW, van Schaik RC, Berendsen H J C, van Gunsteren WF, Scheek RM, Robillard GT (1994) The highresolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from nuclear magnetic resonance nuclear Overhauser effect data. J Mol Biol 237:544-559
55. Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 194:531-544
56. Vila JA, Baldoni HA, Ripoll DR, Scheraga HA (2003) Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts. J Biomol NMR 26:113-130 (Pubitemid 36609044)
57. Vila JA, Baldoni HA, Ripoll DR, Ghosh A, Scheraga HA (2004a) Polyproline II helix conformation in a proline-rich enviroment: a theoretical study. Biophys J 86:731-742 (Pubitemid 38209521)
58. 13C chemical shifts for an alaninerich peptide. Proteins 57:87-98 (Pubitemid 39195885)
59. Vila JA, Ripoll DR, Baldoni HA, Scheraga HA (2002) Unblocked statistical-coil tetrapeptides and pentapeptides in aqueous solution: a theoretical study. J Biomol NMR 24:245-262 (Pubitemid 36118824)
60. α chemical shifts in protein structure determination. J Phys Chem B (in press)
61. 13C chemical shifts of antiparallel β-sheet model peptides. J Biomol NMR 37:137-146 (Pubitemid 46157978)
62. Vriend GJ (1990) A molecular modeling and drug design. Mol Graph 8:52-56
63. Vriend G, Sander C (1993) Quality control of protein models: directional atomic contact analysis. J Appl Crystallogr 26:47-60 (Pubitemid 23611937)
64. Wang Y, Jardetzky O (2002) Probability-based protein secondary structure identification using combined NMR chemical-shift data. Protein Sci 11:852-861 (Pubitemid 34241293)
65. Wilson KS, Dauter Z, Lamzin VS, Walsh M, Wodak S, Richelle J, Pontius J, Vaguine A, Laskowski JM, MacArthur MW, Dodson E, Murshudov G, Oldfield TJ, Kaptein R, Rullmann J A C (1998) Who checks the checkers? Four validation tools applied to eight atomic resolution structures. J Mol Biol 276:417-436 (Pubitemid 28085330)
66. Wishart DS, Case DA (2001) Use of chemical shifts in macromolecular structure determination. Methods Enzymol 338:3-34 (Pubitemid 32666573)
67. 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6:135-140
68. Wishart DS, Nip AM (1998) Protein chemical shift analysis: a practical guide. Biochem Cell Biol 76:153-163 (Pubitemid 29102000)
69. 13C' chemical shifts in proteins using a density functional database. J Biomol NMR 21:321-333 (Pubitemid 34071387)
70. 13C' chemical shifts in peptides using density functional theory. Biopolymers 65:408-423 (Pubitemid 35423737)
71. Zhao D, Jardetzky O (1994) An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance erros. J Mol Biol 239:601-607