Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

Abstract

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness.

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References

  1. Atreya HS, Chary KVR, Govil G (2002) Automated NMR assignments of proteins for high throughput structure determination: TATAPRO II. Curr Sci 83:1372–1376

    Google Scholar 

  2. Bartels C, Xia C-H, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 5:1–10

    Article  Google Scholar 

  3. Bartels C, Billeter M, Güntert P, Wüthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207–213

    Article  Google Scholar 

  4. Billeter M, Basus VJ, Kuntz ID (1988) ID: a program for semi-automatic sequential resonance assignments in protein 1H nuclear magnetic resonance spectra. J Magn Reson 76:400–415

    Google Scholar 

  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

    Article  ADS  Google Scholar 

  6. Coggins BE, Zhou P (2003) PACES: protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93–111

    Article  Google Scholar 

  7. Corne D, Dorigo M, Glover F (1999) New ideas in optimization. McGraw-Hill

  8. Eghbalnia HR, Bahrami A, Wang L, Assadi A, Markley JL (2005) Probabilistic identification of spin systems and their assignments including coil-helix inference output (PISTACHIO). J Biomol NMR: 219–233

  9. Etezady-Esfarjani T, Peti W, Wüthrich K (2003) NMR assignment of the conserved hypothetical protein TM1290 of Thermotoga maritima. J Biomol NMR 25:167–168

    Article  Google Scholar 

  10. Fiorito F, Hiller S, Wider G, Wüthrich K (2006) Automated resonance assignment of proteins: 6D APSY-NMR. J Biomol NMR 35:27–37

    Article  Google Scholar 

  11. Garey MR, Johnson DS (1979) Computers and intractability. A guide to the theory of NP-completeness. Freeman, New York

    Google Scholar 

  12. Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS, Sönnichsen FD, Sykes BD (1998) CAMRA, chemical shift based computer aided protein NMR assignment. J Biomol NMR 12:395–405

    Article  Google Scholar 

  13. Güntert P, Salzmann M, Braun D, Wüthrich K (2000) Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR 18:129–137

    Article  Google Scholar 

  14. Hare BJ, Prestegard H (1994) Application of neural networks to automated assignment of NMR spectra of proteins. J Biomol NMR 4:35–46

    Article  Google Scholar 

  15. Hart WE, Krasnogor N, Smith JE (2005) Recent advances in memetic algorithms series: studies in fuzziness and soft computing, vol 166. Springer, Berlin and Heidelberg

    Google Scholar 

  16. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189

    Article  Google Scholar 

  17. Herrmann T, Güntert P, Wüthrich K (2002b) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227

    Article  Google Scholar 

  18. Hiller S, Fiorito F, Wüthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102:10876–10881

    Article  ADS  Google Scholar 

  19. Hiller S, Wasmer W, Wider G, Wüthrich K (2007) Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR spectroscopy. J Am Chem Soc 129:10823–10828

    Article  Google Scholar 

  20. 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

    Article  Google Scholar 

  21. Ikura M, Kay LE, Bax A (1990) A novel approach for sequential assignment of 1H, 13C, and 15N spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Biochemistry 29:4659–4667

    Article  Google Scholar 

  22. Kay LE, Ikura M, Tschudin R, Bax A (1990) Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins. J Magn Reson 89:496–514

    Google Scholar 

  23. Kraulis PJ (1994) Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real space ab initio approach. J Mol Biol 243:696–718

    Article  Google Scholar 

  24. Leutner M, Gschwind RM, Liermann J, Schwarz C, Gemmecker G, Kessler H (1998) Automated backbone assignment of labelled proteins using the threshold accepting algorithm. J Biomol NMR 11:31–43

    Article  Google Scholar 

  25. Lin HN, Wu KP, Chang JM, Sung TY, Hsu WL (2005) GANA—a genetic algorithm for NMR backbone resonance assignment. Nucleic Acids Res 33:4593–4601

    Article  Google Scholar 

  26. Lukin JA, Gove AP, Talukdar SN, Ho C (1997) Automated probabilistic method for assigning backbone resonances of (13C, 15N)-labeled proteins. J Biomol NMR 9:151–166

    Article  Google Scholar 

  27. Montelione GT, Wagner G (1989) Accurate measurements of homonuclear HN-Hα coupling constants in polypeptides using heteronuclear 2D NMR experiments. J Am Chem Soc 111:5474–5475

    Article  Google Scholar 

  28. Montelione GT, Wagner G (1990) Conformation independent sequential NMR connections in isotope-enriched polypeptides by 1H–13C-15N triple-resonance experiments. J Magn Reson 83:183–188

    Google Scholar 

  29. Moscato P (1989) On evolution, search, optimization, genetic algorithms and martial arts: Towards memetic algorithms. Caltech Concurrent Computation Program, C3P Report

  30. Olson JB Jr, 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

    Article  Google Scholar 

  31. Ong YS, Krasnogor N, Ishibuchi H (2007) Special Isssue on Memetic Algorithms. IEEE Trans Syst, Man, Cybernet, Part B 37(1):2–5

    Article  Google Scholar 

  32. Ullman JD (1976) An algorithm for subgraph isomorphism. J ACM 23:31–42

    Article  MATH  Google Scholar 

  33. Wand AJ, Nelson SJ (1991) Refinement of the main chain directed assignment strategy for the analysis of 1H NMR spectra of proteins. Biophysics 59:1101–1112

    Article  Google Scholar 

  34. Wüthrich K (1983) Sequential individual resonance assignments in the 1H-NMR spectra of polypeptides and proteins. Biopolymers 22:131–138

    Article  Google Scholar 

  35. Wüthrich K (1986) NMR of Proteins and Nucleic Acids. Wiley, New York

    Google Scholar 

  36. Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610

    Article  Google Scholar 

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Acknowledgments

We thank Dr. B. Pedrini for sharing his experience with applications of MATCH for backbone resonance assignments in a variety of proteins. Financial support by the Schweizerischer Nationalfonds (project 3100-AO-113838) is gratefully acknowledged.

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Correspondence to Kurt Wüthrich.

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Volk, J., Herrmann, T. & Wüthrich, K. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH. J Biomol NMR 41, 127 (2008). https://doi.org/10.1007/s10858-008-9243-5

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Keywords

  • Protein NMR
  • Sequence-specific resonance assignment
  • Genetic algorithm
  • Automation