De novo sequencing of nonribosomal peptides

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4955 LNBI, Issue , 2008, Pages 181-195

  Bandeira, Nuno ^a   Ng, Julio ^a   Meluzzi, Dario ^a   Linington, Roger G ^b   Dorrestein, Pieter ^a   Pevzner, Pavel A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cyclic peptides; De novo algorithm; Sequencing

Indexed keywords

AMINES; ARSENIC COMPOUNDS; BIOCHEMISTRY; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; PEPTIDES; PROTEINS;

COMPUTATIONAL MOLECULAR BIOLOGY; DE NOVO SEQUENCING; GENETIC CODING; HIGH-THROUGHPUT (HT); INTERNATIONAL CONFERENCES; MULTI-STAGE; NATURAL COMPOUNDS; SCREENING PROGRAMS;

BIOLOGY;

EID: 47249143245     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-78839-3_16     Document Type: Conference Paper

References (33)

1. Sieber, S.A., Marahiel, M.A.: Molecular Mechanisms Underlying Nonribosomal Peptide Synthesis: Approaches to New Antibiotics. Chem. Rev. 105, 715-738 (2005)
2. Dorrestein, P.C., Kelleher, N.L.: Dissecting Non-ribosomal and Polyketide Biosynthetic Machineries Using Electrospray Ionization Fourier-Transform Mass Spectrometry. Natural Product Reports 23, 893-918 (2006)
3. Welker, M., Von Doehren, H.: Cyanobacterial Peptides - Nature's Own Combinatorial Biosynthesis. FEMS Microbiology Reviews 30, 530-563 (2006)
4. Butcher, B.G., Helmann, J.D.: Identification of Bacillus subtilis Sigma-dependent Genes that Provide Intrinsic Resistance to Antimicrobial Compounds Produced by Bacilli. Mol. Microbiol. 60, 765-782 (2006)
5. Williams, D., Austin, P., Diaz-Marrero, A., Soest, R., Matainaho, T., Roskelley, C., Roberge, M., Andersen, R.: Neopetrosiamides, Peptides from the Marine Sponge Neopetrosia sp. That Inhibit Amoeboid Invasion by Human Tumor Cells. Organic Letters 7, 4173-4176 (2005)
6. Luesch, H., Williams, P., Yoshida, W., Moore, R., Paul, V.: Ulongamides A-F, New Beta-Amino Acid-Containing Cyclodepsipeptides from Palauan Collections of the Marine Cyanobacterium Lyngbya sp. Journal of Natural Products 65, 996-1000 (2002)
7. Hamada, T., Matsunaga, S., Yano, G., G nd Fusetani, N.: Polytheonamides A and B, Highly Cytotoxic, Linear Polypeptides with Unprecedented Structural Features, from the Marine Sponge, Theonella swinhoei. J Am. Chem. Soc. 127, 110-118 (2005)
8. Ireland, C.M., Durso, A.R., Newman, R.A., Hacker, M.P.: Antineoplastic Cyclic Peptides from the Marine Tunicate Lissoclinum patella. J. Org. Chem. 47, 360-361 (1982)
9. Kurosawa, K., Matsuura, K., Chida, N.: Total Synthesis of Stevastelins B3 and C3: Structure Confirmation of Stevastelin B3 and Revision of Stevastelin C3. Tetrahedron Letters 46, 389-392 (2005)
10. Li, J., Burgett, A., Esser, L., Amezcua, C., G.Harran, P.: Total synthesis of nominal diazonamides: Part 2. on the true structure and origin of natural isolates. Angew. Chem Intl. Ed. Engl., 4771-4773 (2001)
11. Ikeda, H., Nonomiya, T., Ōmura, S.: Organization of Biosynthetic Gene Cluster for Avermectin in Streptomyces avermitilis: Analysis of Enzymatic Domains in Four Polyketide Synthases. Journal of Industrial Microbiology and Biotechnology 27, 170-176 (2001)
12. Watanabe, K., Hotta, K., Praseuth, A.P., Koketsu, K., Migita, A., Boddy, C.N., Wang, C.C., Oguri, H., Oikawa, H.: Total Biosynthesis of Antitumor Nonribosomal Peptides in Escherichia coli. Nat. Chem. Biol. 2, 423-428 (2006)
13. Barber, M., Bell, D.J., Morris, M.R., Tetler, L.W., Monaghan, J.J., Morden, W.E., Bycroft, B.W., Green, B.N.: An Investigation of the Tyrothricin Complex by Tandem Mass Spectrometry. International Journal of Mass Spectrometry and Ion Processes 122, 143-151 (1992)
14. Hitzeroth, G., Vater, J., Franke, P., Gebhardt, K., Fiedler, H.P.: Whole Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and in situ Structure Analysis of Streptocidins, a Family of Tyrocidine-like Cyclic Peptides. Rapid Communications in Mass Spectrometry 19, 2935-2942 (2005)
15. Gebhardt, K., Pukall, R., Fiedler, H.P.: Streptocidins A-D, Novel Cyclic Decapeptide Antibiotics Produced by Streptomyces sp. Tü 6071. I. Taxonomy, Fermentation, Isolation and Biological Activities. Antibiot. 54, 428-433 (2001)
16. Höltzel, A., Jack, R.W., Nicholson, G.J., Jung, G., Gebhardt, K., Fiedler, H.P., Süssmuth, R.D.: Streptocidins A-D, Novel Cyclic Decapeptide Antibiotics Produced by Streptomyces sp. Tü 6071. II. Structure elucidation. Antibiot. 54, 434-440 (2005)
17. Redman, J., Wilcoxen, K., Ghadiri, M.: Automated Mass Spectrometric Sequence Determination of Cyclic Peptide Library Members. Journal of Combinatorial Chemistry 5, 33-40 (2003)
18. Olsen, J.V., Mann, M.: Improved Peptide Identification in Proteomics by Two Consecutive Stages of Mass Spectrometric Fragmentation. Proc. Natl. Acad. Sci. 101, 13417-13422 (2004)
19. Ulintz, P.J., Bodenmiller, B., Andrews, P.C., Aebersold, R., Nesvizhskii, A.I.: Investigating MS2-MS3 Matching Statistics: A Model for Coupling Consecutive Stage Mass Spectrometry Data for Increased Peptide Identification Confidence. In: Molecular Cellular Proteomics, pp. M700128-MCP200 (2007)
20. Skiena, S.S., Sundaram, G.: A Partial Digest Approach to Restriction Site Mapping. Bulletin of Mathematical Biology 56, 275-294 (1994)
21. Rosenblatt, J., Seymour, P.D.: The Structure of Homometric Sets. SIAM Journal on Algebraic and Discrete Methods 3, 343-350 (1982)
22. Cieliebak, M., Eidenbenz, S., Penna, P.: Partial Digest Problem is Hard to Solve for Erroneous Input Data. Theoretical Computer Science 349, 361-381 (2005)
23. Xu, C., Ma, B.: Complexity and Scoring Function of MS/MS Peptide De Novo Sequencing. Computational Systems Bioinformatics 5, 361-369 (2006)
24. Pevzner, P.A., Dancik, V., Tang, C.: Mutation-Tolerant Protein Identification by Mass Spectrometry. J Comput. Biol. 7, 777-787 (2000)
25. Bandeira, N., Clauser, K.R., Pevzner, P.A.: Shotgun Protein Sequencing: Assembly of Peptide Tandem Mass Spectra from Mixtures of Modified Proteins. Mol. Cell Proteomics 6, 1123-1134 (2007)
26. Bandeira, N., Tsur, D., Frank, A., Pevzner, P.A.: Protein Identification by Spectral Networks Analysis. Proceedings of the National Academy of Sciences 104, 6140-6145 (2007)
27. Bern, M., Goldberg, D.: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. Journal of Computational Biology 13, 364-378 (2006)
28. Chen, T., Kao, M.Y., Tepel, M., Rush, J., Church, G.M.: A Dynamic Programming Approach to De Novo Peptide Sequencing via Tandem Mass Spectrometry. J Comput. Biol. 8, 325-337 (2001)
29. B'Hymer, C., Montes-Bayon, M., Caruso, J.A.: Marfey's Reagent: Past, Present, and Future Uses of 1-Fluoro-2,4-Dinitrophenyl-5-L-Alanine Amide. Journal of Separation Science 26, 7-19 (2003)
30. Bandeira, N., Tang, H., Bafna, V., Pevzner, P.: Shotgun Protein Sequencing by Tandem Mass Spectra Assembly. Analytical Chemistry 76, 7221-7233 (2004)
31. Dancik, V., Addona, T., Clauser, K., Vath, J., Pevzner, P.: De Novo Peptide Sequencing via Tandem Mass Spectrometry. J Comput. Biol. 6, 327-342 (1999)
32. Frank, A.M., Pevzner, P.A.: PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Anal. Chem. 77, 964-973 (2005)
33. Mo, L., Dutta, D., Wan, Y., Chen, T.: MSNovo: A Dynamic Programming Algorithm for De Novo Peptide Sequencing via Tandem Mass Spectrometry. Anal. Chem. 79, 4870-4878 (2007)