Protein sequence analysis

Fig. 10.22 Hidden Markov model used for protein sequence analysis, are match states (corresponding in this...

Heilman, EJ., Wiksell, E., and Karlsson, B.-M. (1990). A new approach to micropreparative desalting exemplified by desalting a reduction/alkylation mixture, presenred ar Eighr International Conference on Methods in Protein Sequence Analysis, Kiruna, Sweden, July 1-6. 

Protein sequence analysis (PSA) Empirical statistical method... 

J. E. Syka, J. J. Coon, M. J. Schroeder, J. Shabanowitz, and D. F. Hunt. Peptide and Protein Sequence Analysis by Electron Transfer Dissociation Mass Spectrometry. Proc. Natl. Acad. Sci. U.S.A., 101(2004) 9528-9533. 

Evaluation of protein sequence analysis methods based on the use of PSSMs in benchmarking experiments and in a number of test cases shows that these methods are capable of systematically detecting relationships between proteins that previously have been deemed tractable only at the structure-comparison level. Clearly, however, there is still a lot of room for improvement, as many automated procedures missed subtle connections that subsequendy have been revealed on a case-by-case basis, in part thanks to a careful choice of starting points for the PSSM construction. An exhaustive exploration of the sequence space by recursive iterative searching is likely to yield additional, on many occasions unexpected, links between proteins and, in particular, is expected to increase the rate of structure prediction. 

Samyn B., Hardeman K., Van der Eycken J., and Van Beeumen J. (2000), Applicability of the alkylation chemistry for chemical C-terminal protein sequence analysis, Anal. Chem. 72, 1389-1399. 

Wittmann-Liebold, B., Brauer, D., and Dogpiin, J. M. (1977a). In Solid Phase Methods in Protein Sequence Analysis (A. Previero and M. Previero-Coletti, eds.), p. 219. Elsevier, Amsterdam. 

Coon JJ, Syka JEP, Shabanowitz J, Hunt DF. Tandem mass spectrometry for peptide and protein sequence analysis. Biotechniques 38, 519-523, 2005. 

The inability to obtain complete protein sequence analysis of purified bacteriocins has been reason to suspect the presence of N-blocked peptide sequences (34) or lantibiotic residues (14). Recently, Piard et al. (14) have shown from partial sequencing and composition analysis that lacticin 481, a broad spectrum bacteriocin produced by L. lactis 481, also contains lanthionine residues. The early widespread interest in nisin and nisin-producing strains had given the impression that lantibiotics may be characteristic of bacteriocins of lactic acid bacteria. However, recent studies with other LAB bacteriocins suggest that simple peptide bacteriocins may prevail among the LAB. 

The tridecapeptide polydiscamide A (309) was obtained from an unidentified Caribbean species of Discodermia [220], while discodermins A-H (298-305) were isolated from D. kiiensis. The structures deduced previously for discodermins A-E [221, 222] were later revised on the basis of NMR data and protein sequence analysis [223]. A number of closely related compounds, the tetradecapeptides halicylindramides A-C (306-308) [224], the tridecapeptide halicylindramide D (310) [225], and the truncated linear peptide halicylindramide E [225] (311) were obtained from the sponge Halichondria cylindrata. A microbial origin for these compounds was suggested [226]. 

B 2. The new reagent 4-W,W-dimethylaminoazobenzene-4 -isothiocyanate (DABITC) is often used for the Edman method of protein sequence analysis. Write a reaction showing this use of the reagent. 

C. Mathews, K. van Holde, and K. Ahern, Biochemistry, 3rd ed. (2000), Benjamin/ Cummings (San Francisco), pp. 126-160. An introduction to amino acids and protein sequence analysis. 

Croft, L. R (1980) Handbook of Protein Sequence Analysis Wiley-Interscience, Chichester, UK... 

L Stryer, Biochemistry, 4th ed (1995), W H Freeman (New York), pp 18-26, 53-60 A discussion of amino acids and protein sequence analysis... 

Similarity Searching (BLAST) Nucleotide Sequence Analysis Protein Sequence Analysis Molecular Structure Analysis t Genome Analysis Gene Expression... 

Figure 12.6. Secondary structure prediction of duck lysozyme at NPS . The predicted secondary structures of duck lysozyme at Network Protein Sequence Analysis (NPS ) with GOR IV method are depicted in different representations.

The method of Rost and Sander (Rost and Sander, 1993), which combines neural networks with multiple sequence alignments known as PHD, is available from the PredictProtein (Rost, 1996) server of Columbia University (http //cubic.bioc. columbia.edu/predictprotein/). This Web site offers the comprehensive protein sequence analysis and structure prediction (Figure 12.8). For the secondary structure prediction, choose Submit a protein sequence for prediction to open the submission form. Enter e-mail address, paste the sequence, choose options, and then click the... 

Figure 12,7. Secondary structure consensus prediction at NPS . Network Protein Sequence Analysis (NPS ) offers numerous methods for secondary structure prediction of proteins. The secondary structure consensus prediction (Sec.Cons.) of duck lysozyme is derived from simultaneous execution of predictions with more than one methods.

Collections of tools for DNA and Protein sequence analysis, searching and presentation. Supports restriction enzyme mappings, open reading frames, primer design, sequence alignment, property calculations. 

Methods in Protein Sequence Analysis Whittman-Liebold, B. Ed. Springer Verlag.New York, 1989, p 220. 

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