Chemical shifts in biomolecules

Current Opinion in Structural Biology

Volumn 23, Issue 2, 2013, Pages 172-176

  Case, David A ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULE; MACROMOLECULE; MOLECULE; PHYSICAL MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; STRUCTURE ANALYSIS;

EID: 84878537787     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2013.01.007     Document Type: Review

References (54)

1. Case D.A. The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 1998, 8:624-630.
2. Buckingham A.D., Schaefer T., Schneider W.G. Solvent effects in nuclear magnetic resonance spectra. J Chem Phys 1960, 32:1227-1233.
3. Sitkoff D., Case D.A. Theories of chemical shift anisotropies in proteins and nucleic acids. Prog NMR Spectrosc 1998, 32:165-190.
4. Wishart D.S., Case D.A. Use of chemical shifts in macromolecular structure determination. Methods Enzymol 2001, 338:3-34.
5. Ulrich E.L., Akutsu H., Doreleijers J.F., Harano Y., Ioannidis Y.E., Lin J., Livny M., Mading S., Maziuk D., Miller Z., et al. BioMagResBank. Nucleic Acids Res 2008, 36:D402-D408.
6. Markley J.L. In support of the BMRB. Nat Struct Mol Biol 2012, 19:854-860.
7. McConnell H.M. Theory of nuclear magnetic shielding in molecules. I. Long-range dipolar shielding of protons. J Chem Phys 1957, 27:226-229.
8. Bertini I., Turano P., Vila A.J. Nuclear magnetic resonance of paramagnetic metalloproteins. Chem Rev 1993, 93:2833-2932.
9. Schmitz C., Vernon R., Otting G., Baker D., Huber T. Protein structure determination from pseudocontact shifts using Rosetta. J Mol Biol 2012, 416:668-677.
10. ösapay K., Case D.A. A new analysis of proton chemical shifts in proteins. J Am Chem Soc 1991, 113:9436-9444.
11. Xu X.P., Case D.A. Automated prediction of N, Cα, Cβ and C' chemical shifts in proteins using a density functional database. J Biomol NMR 2001, 21:321-333.
12. Shen Y., Bax A. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 2007, 38:289-302.
13. Shen Y., Bax A. SPARTA plus: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 2010, 48:13-22.
14. 15N chemical shifts. J Biomol NMR 2003, 26:215-240.
15. Han B., Liu Y., Ginzinger S.W., Wishart D.S. SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR 2011, 50:43-57.
16. Kohlhoff K.J., Robustelli P., Cavalli A., Salvatella X., Vendruscolo M. Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 2009, 131:13894-13895.
17. Sahakyan A.B., Vranken W.F., Cavalli A., Vendruscolo M. Structure-based prediction of methyl chemical shifts in proteins. J Biomol NMR 2011, 50:331-346.
18. Sahakyan A.B., Cavalli A., Vranken W.F., Vendruscolo M. Protein structure validation using side-chain chemical shifts. J Phys Chem B 2012, 116:4754-4759.
19. Li D.-W., Brüschweiler R. PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. J Biomol NMR 2012, 54:257-265.
20. Lehtivarjo J., Hassinen T., Korhonen S.P., Perakyla M., Laatikainen R. 4D prediction of protein H-1 chemical shifts. J Biomol NMR 2009, 45:413-426.
21. Lehtivarjo J., Tuppurainen K., Hassinen T.T., Laatikainen R., Perakyla M. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction. J Biomol NMR 2012, 52:257-267.
22. Nielsen J.T., Eghbalnia H.R., Nielsen N.C. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field. Prog NMR Spectrosc 2012, 60:1-28.
23. ösapay K., Theriault Y., Wright P.E., Case D.A. Solution structure of carbonmonoxy myoglobin determined from NMR distance and chemical shift constraints. J Mol Biol 1994, 244:183-197.
24. Schwieters C.D., Kuszewski J.J., Tjandra N., Clore G.M. The Xplor-NIH NMR molecular structure determination package. J Magn Res 2003, 160:66-74.
25. Cavalli A., Salvatella X., Dobson C.M., Vendruscolo M. Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 2007, 104:9615-9620.
26. Shen Y., Lange O., Delaglio F., Rossi P., Aramini J.M., Liu G.H., Eletsky A., Wu Y.B., Singarapu K.K., Lemak A., et al. Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 2008, 105:4685-4690.
27. Sgourakis N.G., Lange O.F., DiMaio F., Andre I., Fitzkee N.C., Rossi P., Montelione G.T., Bax A., Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. J Am Chem Soc 2011, 133:6288-6298.
28. Lange O.F., Rossi P., Sgourakis N.G., Song Y., Lee H.-W., Aramini J.M., Ertekin A., Xiao R., Acton T.B., Montelione G.T., Baker D. Determination of solution structures of proteins up to 40kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proc Natl Acad Sci USA 2012, 109:10873-10878.
29. Hansen D.F., Vallurupalli P., Lundstrom P., Neudecker P., Kay L.E. Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: how well can we do?. J Am Chem Soc 2008, 130:2667-2675.
30. Korzhnev D.M., Religa T.L., Banachewicz W., Fersht A.R., Kay L.E. A transient and low-populated protein-folding intermediate at atomic resolution. Science 2010, 329:1312-1316.
31. Camilloni C., Robustelli P., Simone A.D., Cavalli A., Vendruscolo M. Characterization of the conformational equilibrium between the two major substrates of RNase A using NMR chemical shifts. J Am Chem Soc 2012, 134:3968-3971.
32. 1H probes. J Am Chem Soc 2012, 134:3178-3189.
33. Ban D., Funk M., Gulich R., Egger D., Sabo T.M., Walter K.F.A., Fenwick R.B., Giller K., Kree R., et al. Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed 2011, 50:11437-11440.
34. Beauchamp K.A., Lin Y., Das R., Pande V.S. Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements. J Chem Theory Comput 2012, 8:1409-1414.
35. Robustelli P., Stafford K.A., Palmer A.G. Interpreting protein structural dynamics from NMR chemical shifts. J Am Chem Soc 2012, 134:6365-6374.
36. Li D.-W., Brüschweiler R. NMR-based protein potentials. Angew Chem Int Ed 2010, 49:6778-6780.
37. 1H chemical shift calculations for use in structure refinement. J Biomol NMR 1997, 10:337-350.
38. Dejaegere A., Bryce R.A., Case D.A. An empirical analysis of proton chemical shifts in nucleic acids. Modeling NMR Chemical Shifts 1999, 194-206. American Chemical Society, Washington, DC. J.C. Facelli, A.C. de Dios (Eds.).
39. 1H chemical shifts: an accurate and balanced predictive empirical scheme. Magn Reson Chem 2000, 38:95-107.
40. Helgaker T., Jaszunski M., Ruud K. Ab initio methods for the calculation of NMR shielding and indirect spin-spin coupling constants. Chem Rev 1999, 99:293-352.
41. Wolinski K., Hinton J.F., Pulay P. Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. J Am Chem Soc 1990, 112:8324-8328.
42. Malkin V.G., Malkina O.L., Casida M.E., Salahub D.R. Nuclear magnetic resonance shielding tensors calculated with a sum-over-states density functional perturbation theory. J Am Chem Soc 1994, 116:5898-5908.
43. Casabianca L.B., deDios A.C. Ab initio calculations of NMR chemical shifts. J Chem Phys 2008, 128:052201.
44. Vila J.A., Scheraga H.A. Assessing the accuracy of protein structures by quantum mechanical computations of C-13(alpha) chemical shifts. Acc Chem Res 2009, 42:1545-1553.
45. Gao Q., Yokojima S., Fedorov D.G., Kitaura K., Sakurai M., Nakamura S. Fragment-molecular-orbital-method-based ab initio NMR chemical-shift calculations for large molecular systems. J Chem Theory Comput 2010, 6:1428-1444.
46. Frank A., Onila I., Möller H.M., Exner T.E. Toward the quantum chemical calculation of nuclear magnetic resonance chemical shifts of proteins. Proteins 2011, 79:2189-2202.
47. Frank A., Möller H.M., Exner T.E. Toward the quantum chemical calculation of NMR chemical shifts of proteins. 2. Level of theory. Basis set, and solvents model dependence. J Chem Theory Comput 2012, 8:1480-1492.
48. Flaig D., Beer M., Ochsenfeld C. Convergence of electronic structure with the size of the QM region: example of QM/MM NMR shieldings. J Chem Theory Comput 2012, 8:2260-2271.
49. Zhu T., He X., Zhang J.Z.H. Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys Chem Chem Phys 2012, 14:7837-7845.
50. He X., Wang B., Merz K.M. Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. J Phys Chem B 2009, 113:10380-10388.
51. Tang S., Case D.A. Calculation of chemical shift anisotropy in proteins. J Biomol NMR 2011, 51:303-312.
52. Tian Y., Opella S.J., Marassi F.M. Improved chemical shift prediction by Rosetta conformational sampling. J Biomol NMR 2012, 54:237-243.
53. Cornlescu G., Marquardt J.L., Ottiger M., Bax A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 1998, 120:6836-6837.
54. Fenwick R.B., Esteban-Martin S., Richter B., Lee D., Walter K.F.A., Milovanovic D., Becker S., Lakomek N.A., Griesinger C., Salvatella X. Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition. J Am Chem Soc 2011, 133:10336-10339.