Journal of Biomolecular NMR

, Volume 54, Issue 3, pp 237–243 | Cite as

Improved chemical shift prediction by Rosetta conformational sampling

  • Ye Tian
  • Stanley J. Opella
  • Francesca M. Marassi
Communication

Abstract

Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.

Keywords

Chemical shift Prediction Rosetta Ensemble averaging Structure Membrane protein Solid-state NMR Conformational ensemble 

References

  1. Asbury T, Quine JR, Achuthan S, Hu J, Chapman MS, Cross TA, Bertram R (2006) PIPATH: an optimized algorithm for generating alpha-helical structures from PISEMA data. J Magn Reson 183(1):87–95ADSCrossRefGoogle Scholar
  2. Berardi MJ, Shih WM, Harrison SC, Chou JJ (2011) Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature 476(7358):109–113. doi:10.1038/nature10257 CrossRefGoogle Scholar
  3. Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D (2001) Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins Suppl 5:119–126. doi:10.1002/prot.1170 CrossRefGoogle Scholar
  4. Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309(5742):1868–1871. doi:10.1126/science.1113801 ADSCrossRefGoogle Scholar
  5. Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104(23):9615–9620. doi:10.1073/pnas.0610313104 ADSCrossRefGoogle Scholar
  6. Clayden NJ, Williams RJP (1982) Peptide group shifts. J Magn Reson 49(3):383–396. doi:10.1016/0022-2364(82)90252-9 Google Scholar
  7. 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(3):289–302CrossRefGoogle Scholar
  8. Dalgarno DC, Levine BA, Williams RJ (1983) Structural information from NMR secondary chemical shifts of peptide alpha C-H protons in proteins. Biosci Rep 3(5):443–452CrossRefGoogle Scholar
  9. Das R, Baker D (2008) Macromolecular modeling with Rosetta. Annu Rev Biochem 77:363–382. doi:10.1146/annurev.biochem.77.062906.171838 CrossRefGoogle Scholar
  10. Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmstrom L, Wollacott AM, Wang C, Andre I, Baker D (2007) Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta at home. Proteins 69(Suppl 8):118–128. doi:10.1002/prot.21636 CrossRefGoogle Scholar
  11. Das BB, Nothnagel HJ, Lu GJ, Son WS, Tian Y, Marassi FM, Opella SJ (2012) Structure determination of a membrane protein in proteoliposomes. J Am Chem Soc 134(4):2047–2056. doi:10.1021/ja209464f CrossRefGoogle Scholar
  12. De Angelis AA, Howell SC, Nevzorov AA, Opella SJ (2006) Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy. J Am Chem Soc 128(37):12256–12267. doi:10.1021/ja063640w CrossRefGoogle Scholar
  13. de Dios AC, Pearson JG, Oldfield E (1993) Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science 260(5113):1491–1496ADSCrossRefGoogle Scholar
  14. Delaglio F, Kontaxis G, Bax A (2000) Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J Am Chem Soc 122:2142–2143CrossRefGoogle Scholar
  15. Gross K-H, Kalbitzer HR (1988) Distribution of chemical shifts in 1H nuclear magnetic resonance spectra of proteins. J Magn Reson 76(1):87–99. doi:10.1016/0022-2364(88)90203-x Google Scholar
  16. Han B, Liu Y, Ginzinger SW, Wishart DS (2011) SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR 50(1):43–57. doi:10.1007/s10858-011-9478-4 CrossRefGoogle Scholar
  17. Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C, Marks DS (2012) Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149(7):1607–1621. doi:10.1016/j.cell.2012.04.012 CrossRefGoogle Scholar
  18. Howell SC, Mesleh MF, Opella SJ (2005) NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system. Biochemistry 44(13):5196–5206. doi:10.1021/bi048095v CrossRefGoogle Scholar
  19. Iwadate M, Asakura T, Williamson MP (1999) C alpha and C beta carbon-13 chemical shifts in proteins from an empirical database. J Biomol NMR 13(3):199–211CrossRefGoogle Scholar
  20. Kohlhoff KJ, Robustelli P, Cavalli A, Salvatella X, Vendruscolo M (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131(39):13894–13895. doi:10.1021/ja903772t CrossRefGoogle Scholar
  21. Li D-W, Bruschweiler R (2009) Certification of molecular dynamics trajectories with NMR chemical shifts. J Phys Chem Lett 1(1):246–248. doi:10.1021/jz9001345 CrossRefGoogle Scholar
  22. London RE, Wingad BD, Mueller GA (2008) Dependence of amino acid side chain 13C shifts on dihedral angle: application to conformational analysis. J Am Chem Soc 130(33):11097–11105. doi:10.1021/ja802729t CrossRefGoogle Scholar
  23. Luginbuhl P, Szyperski T, Wuthrich K (1995) Statistical basis for the use of 13C chemical shifts in protein structure determination. J Magn Reson B 109(2):229–233. doi:10.1006/jmrb.1995.0016 CrossRefGoogle Scholar
  24. Marassi FM, Opella SJ (2003) Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints. Protein Sci 12(3):403–411. doi:10.1110/ps.0211503 CrossRefGoogle Scholar
  25. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS ONE 6(12):e28766. doi:10.1371/journal.pone.0028766 CrossRefGoogle Scholar
  26. Markwick PR, Cervantes CF, Abel BL, Komives EA, Blackledge M, McCammon JA (2010) Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. J Am Chem Soc 132(4):1220–1221. doi:10.1021/ja9093692 CrossRefGoogle Scholar
  27. Meiler J (2003) PROSHIFT: protein chemical shift prediction using artificial neural networks. J Biomol NMR 26(1):25–37. doi:5121785 CrossRefGoogle Scholar
  28. Mittag T, Forman-Kay JD (2007) Atomic-level characterization of disordered protein ensembles. Curr Opin Struct Biol 17(1):3–14. doi:10.1016/j.sbi.2007.01.009 CrossRefGoogle Scholar
  29. Moseley HN, Sperling LJ, Rienstra CM (2010) Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of beta1 immunoglobulin binding domain of protein G (GB1). J Biomol NMR 48(3):123–128. doi:10.1007/s10858-010-9448-2 CrossRefGoogle Scholar
  30. Mulder FA (2009) Leucine side-chain conformation and dynamics in proteins from 13C NMR chemical shifts. ChemBioChem 10(9):1477–1479. doi:10.1002/cbic.200900086 CrossRefGoogle Scholar
  31. Neal S, Nip AM, Zhang H, Wishart DS (2003) Rapid and accurate calculation of protein 1H, 13C and 15 N chemical shifts. J Biomol NMR 26(3):215–240CrossRefGoogle Scholar
  32. Nielsen JT, Eghbalnia HR, Nielsen NC (2012) Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field. Prog Nucl Magn Reson Spectrosc 60:1–28. doi:10.1016/j.pnmrs.2011.05.002 CrossRefGoogle Scholar
  33. Osapay K, Case DA (1991) A new analysis of proton chemical shifts in proteins. J Am Chem Soc 113(25):9436–9444. doi:10.1021/ja00025a002 CrossRefGoogle Scholar
  34. Park SH, Das BB, Casagrande F, Tian Y, Nothnagel HJ, Chu M, Kiefer H, Maier K, De Angelis A, Marassi FM, Opella SJ (2012) Structure of the chemokine receptor CXCR1 in phospholipid bilayers. Nature (in press)Google Scholar
  35. Pastore A, Saudek V (1990) The relationship between chemical shift and secondary structure in proteins. J Magn Reson 90(1):165–176. doi:10.1016/0022-2364(90)90375-j Google Scholar
  36. Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D (2010) NMR structure determination for larger proteins using backbone-only data. Science 327(5968):1014–1018. doi:10.1126/science.1183649 ADSCrossRefGoogle Scholar
  37. Saito H (1986) Conformation-dependent 13C chemical shifts: a new means of conformational characterization as obtained by high-resolution solid-state 13C NMR. Magn Reson Chem 24(10):835–852. doi:10.1002/mrc.1260241002 CrossRefGoogle Scholar
  38. Sharma M, Yi M, Dong H, Qin H, Peterson E, Busath DD, Zhou HX, Cross TA (2010) Insight into the mechanism of the influenza A proton channel from a structure in a lipid bilayer. Science 330(6003):509–512. doi:10.1126/science.1191750 ADSCrossRefGoogle Scholar
  39. Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38(4):289–302. doi:10.1007/s10858-007-9166-6 CrossRefGoogle Scholar
  40. Shen Y, Bax A (2010) modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network. J Biomol NMR 48(1):13–22. doi:10.1007/s10858-010-9433-9 CrossRefGoogle Scholar
  41. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105(12):4685–4690. doi:10.1073/pnas.0800256105 ADSCrossRefGoogle Scholar
  42. Shen Y, Vernon R, Baker D, Bax A (2009) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43(2):63–78. doi:10.1007/s10858-008-9288-5 CrossRefGoogle Scholar
  43. Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and C. alpha. and C. beta. 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113(14):5490–5492. doi:10.1021/ja00014a071 CrossRefGoogle Scholar
  44. Steele RA, Opella SJ (1997) Structures of the reduced and mercury-bound forms of MerP, the periplasmic protein from the bacterial mercury detoxification system. Biochemistry 36(23):6885–6895. doi:10.1021/bi9631632 CrossRefGoogle Scholar
  45. Szilagyi L, Jardetzky O (1989) Proton chemical shifts and secondary structure in proteins. J Magn Reson 83(3):441–449. doi:10.1016/0022-2364(89)90341-7 Google Scholar
  46. Tian F, Valafar H, Prestegard JH (2001) A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. J Am Chem Soc 123(47):11791–11796CrossRefGoogle Scholar
  47. Tycko R, Hu KN (2010) A Monte Carlo/simulated annealing algorithm for sequential resonance assignment in solid state NMR of uniformly labeled proteins with magic-angle spinning. J Magn Reson 205(2):304–314. doi:10.1016/j.jmr.2010.05.013 ADSCrossRefGoogle Scholar
  48. Vila JA, Villegas ME, Baldoni HA, Scheraga HA (2007) Predicting 13Calpha chemical shifts for validation of protein structures. J Biomol NMR 38(3):221–235. doi:10.1007/s10858-007-9162-x CrossRefGoogle Scholar
  49. Vila JA, Aramini JM, Rossi P, Kuzin A, Su M, Seetharaman J, Xiao R, Tong L, Montelione GT, Scheraga HA (2008) Quantum chemical 13C(alpha) chemical shift calculations for protein NMR structure determination, refinement, and validation. Proc Natl Acad Sci USA 105(38):14389–14394. doi:10.1073/pnas.0807105105 ADSCrossRefGoogle Scholar
  50. Vila JA, Arnautova YA, Martin OA, Scheraga HA (2009) Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation. Proc Natl Acad Sci USA 106(40):16972–16977. doi:10.1073/pnas.0908833106 ADSCrossRefGoogle Scholar
  51. Villegas ME, Vila JA, Scheraga HA (2007) Effects of side-chain orientation on the 13C chemical shifts of antiparallel beta-sheet model peptides. J Biomol NMR 37(2):137–146. doi:10.1007/s10858-006-9118-6 CrossRefGoogle Scholar
  52. Wang Y, Jardetzky O (2004) Predicting 15 N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from phi, psi i-1, and chi 1 torsion angles. J Biomol NMR 28(4):327–340. doi:10.1023/B:JNMR.0000015397.82032.2a CrossRefGoogle Scholar
  53. Wishart DS, Sykes BD, Richards FM (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 222(2):311–333CrossRefGoogle Scholar
  54. Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res 36(Web Server issue):496–502. doi:10.1093/nar/gkn305 CrossRefGoogle Scholar
  55. Xu XP, Case DA (2001) Automated prediction of 15 N, 13Calpha, 13Cbeta and 13C′ chemical shifts in proteins using a density functional database. J Biomol NMR 21(4):321–333CrossRefGoogle Scholar
  56. Yarov-Yarovoy V, Schonbrun J, Baker D (2006) Multipass membrane protein structure prediction using Rosetta. Proteins 62(4):1010–1025. doi:10.1002/prot.20817 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  • Ye Tian
    • 1
    • 2
  • Stanley J. Opella
    • 2
  • Francesca M. Marassi
    • 1
  1. 1.Sanford Burnham Medical Research InstituteLa JollaUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of California San DiegoLa JollaUSA

Personalised recommendations