Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm

Journal of Biomolecular NMR

Volumn 57, Issue 3, 2013, Pages 281-296

  Yang, Yu ^a   Fritzsching, Keith J ^a   Hong, Mei ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Linewidths; Magic angle spinning; Protein structure determination; Sequential resonance assignment; Solid state NMR

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CLINICAL PROTOCOL; CONTROLLED STUDY; GENETIC ALGORITHM; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION; SOLID STATE; SOLID STATE NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

ALGORITHMS; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; SEQUENCE DELETION;

EID: 84890022105     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-013-9788-9     Document Type: Article

References (34)

1. Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541-3555
2. Bartels C, Billeter M, Guntert P, Wuthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207-213
3. Bertini I, Bhaumik A, De Paëpe G, Griffin RG, Lelli M, Lewandowski JR, Luchinat C (2010) High-resolution solid-state NMR structure of a 17.6 kDa protein. J Am Chem Soc 132:1032-1040
4. Böckmann A, Lange A, Galinier A, Luca S, Giraud N, Juy M, Heise H, Montserret R, Penin F, Baldus M (2003) Solid state NMR sequential resonance assignments and conformational analysis of the 2 × 10.4 kDa dimeric form of the Bacillus subtilis protein Crh. J Biomol NMR 27:323-339
5. Buchler NEG, Zuiderweg ERP, Wang H, Goldstein RA (1997) Protein heteronuclear NMR assignments using mean-field simulated annealing. J Magn Reson 125:34-42
6. Castellani F, vanRossum B, Diehl A, Schubert M, Rehbein K, Oschkinat H (2002) Structure of a protein determined by solid-state magic-angle spinning NMR spectroscopy. Nature 420:98-102
7. Coggins BE, Zhou P (2003) PACES: protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93-111
8. Comellas G, Rienstra CM (2013) Protein structure determination by magic-angle spinning solid-state NMR, and insights into the formation, structure, and stability of amyloid fibrils. Annu Rev Biophys 42:515-536
9. Deb K, Pratap A, Agarwal S, Meyarivan T (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans Evol Comput 6:182-197
10. Franks WT, Zhou DH, Wylie BJ, Money BG, Graesser DT, Frericks HL, Sahota G, Rienstra CM (2005) Magic-angle spinning solid-state NMR spectroscopy of the beta1 immunoglobulin binding domain of protein G (GB1): 15N and 13C chemical shift assignments and conformational analysis. J Am Chem Soc 127:12291-12305
11. Franks WT, Wylie BJ, Schmidt HL, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM (2008) Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR. Proc Natl Acad Sci USA 105:4621-4626
12. Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M (2013) Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information. J Biomol NMR 56:155-167
13. Hong M, Zhang Y, Hu F (2012) Membrane protein structure and dynamics from NMR spectroscopy. Annu Rev Phys Chem 63:1-24
14. Hu KN, McGlinchey RP, Wickner RB, Tycko R (2011a) Segmental polymorphism in a functional amyloid. Biophys J 101:2242-2250
15. Hu KN, Qiang W, Tycko R (2011b) A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers. J Biomol NMR 50:267-276
16. Hyberts SG, Wagner G (2003) IBIS - a tool for automated sequential assignment of protein spectra from triple resonance experiments. J Biomol NMR 26:335-344
17. Igumenova TI, McDermott AE, Zilm KW, Martin RW, Paulson EK, Wand AJ (2004) Assignments of carbon NMR resonances for microcrystalline ubiquitin. J Am Chem Soc 126:6720-6727
18. Knowles JD, Corne DW (2000) Approximating the nondominated front using the Pareto archived evolution strategy. Evol Comput 8:149-172
19. Lee W, Yu W, Kim S, Chang I, Lee W, Markley JL (2012) PACSY, a relational database management system for protein structure and chemical shift analysis. J Biomol NMR 54:169-179
20. 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
21. Li Y, Berthold DA, Gennis RB, Rienstra CM (2008) Chemical shift assignment of the transmembrane helices of DsbB, a 20-kDa integral membrane enzyme, by 3D magic-angle spinning NMR spectroscopy. Protein Sci 17:199-204
22. Li S, Zhang Y, Hong M (2010) 3D 13C-13C-13C correlation NMR for de novo distance determination of solid proteins and application to a human alpha defensin. J Magn Reson 202:203-210
23. Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A (2012) Atomic model of the type III secretion system needle. Nature 486:276-279
24. Luca S, Heise H, Baldus M (2003) High-resolution solid-state NMR applied to polypeptides and membrane proteins. Acc Chem Res 36:858-865
25. McDermott AE (2009) Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR. Annu Rev Biophys 38:385-403
26. Moseley HNB, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 339:91-108
27. Olson JB, Markley JL (1994) Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package. J Biomol NMR 4:385-410
28. Schmidt E, Guntert P (2012) A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 134:12817-12829
29. Shi L, Ahmed MA, Zhang W, Whited G, Brown LS, Ladizhansky V (2009) Three-dimensional solid-state NMR study of a seven-helical integral membrane proton pump - structural insights. J Mol Biol 386:1078-1093
30. Shi L, Kawamura I, Jung KH, Brown LS, Ladizhansky V (2011) Conformation of a seven-helical transmembrane photosensor in the lipid environment. Angew Chem Int Ed Engl 50:1302-1305
31. Tycko R (2011) Solid-state NMR studies of amyloid fibril structure. Annu Rev Phys Chem 62:279-299
32. 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 205:304-314
33. Wasmer C, Lange A, Van Melckebeke H, Siemer AB, Riek R, Meier BH (2008) Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core. Science 319:1523-1526
34. Zhang Y, Doherty T, Li J, Lu W, Barinka C, Lubkowski J, Hong M (2010) Resonance assignment and three-dimensional structure determination of a human alpha-defensin, HNP-1, by solid-state NMR. J Mol Biol 397:408-422