Applications - Protein Sequence Analysis

Sequence similarity database searching and protein sequence analysis constitute one of the most important computational approaches to understanding protein structure and function. Although most computational methods used for nucleic acid sequence analysis are also applicable to protein sequence studies, how to capture the enriched features of amino acid alphabets (Chapter 6) poses a special challenge for protein analysis. 

Reference Application Neural Network Input/Output Encoding  

Ladungaer al., 1991 Signal Peptide Prediction 4L/FF/Tiling BIN20/1(Y,N) 

Nielsen et al., 1997 Signal Peptide Prediction 2x3L/FF/BP BIN21/1(Y,N) 

Wrede et al., 1998 Site Feature/Peptide Design 2L/FF/GA Real2/1(Y,N) 

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Iwai, K., Fukuoka, S.-I., Fushiki, T., Kido, K., Sengoku, Y., and Semba, T. (1988) Preparation of a verifiable peptide-protein immunogen direction-controlled conjugation of a synthetic fragment of the monitor peptide with myoglobin and application for sequence analysis. Anal. Biochem. 171, 277-282. 

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. 

Table 11.1 Neural network applications for protein sequence analysis.

Neural network applications for protein sequence analysis are summarized in Table 11.1. Like the DNA coding region recognition problem, signal peptide prediction (11.2) involves both search for content and search for signal tasks. An effective means for protein sequence analysis is reverse database searching to detect functional motifs or sites (11.3) and identify protein families (11.4). Most of the functional motifs are also... 

How have neural networks been used in genome informatics applications In Part II, we have summarized them based on the types of applications for DNA sequence analysis, protein structure prediction and protein sequence analysis. Indeed, the development of neural network applications over the years has resulted in many successful and widely used systems. Current state-of-the-art systems include those for gene recognition, secondary structure prediction, protein classification, signal peptide recognition, and peptide design, to name just a few. 

Moritz R L, Simpson R J (1992). Application of capillary reversed-phase high-performance liquid chromatography to high-sensitivity protein sequence analysis. J. Chromatogr. 599(1-2) 119-130. 

Application of tandem mass spectrometry (MS-MS) in protein sequence analysis... 

Dinitrophenylamino acids (DNP-amino acids) and phenylthio-hydantoins (PTH-amino acids) are formed when proteins or peptides are treated with dinitrofluorobenzene [151—154] or phenyl isothiocyanate [155], respectively, and the reaction product suitably broken down. Their separation from the reaction mixture and their identification is of considerable practical importance since systematic application enables sequence analysis of peptide structures to be performed. Numerous investigators have worked on this problem... 

Mann, M., and Wilm, M., 1995. Electro.spray ma.ss. spectrometry for protein characterization. Trends in Biochemical Sciences 20 219-224. A review of die ba.sic application of ma.ss. spectrometric methods to the analysis of protein. sequence and. structure. 

This overview presents some cases in which sequence profile-based methods have been able to predict nontrivial structural and evolutionary relationships between proteins and then discusses the current state of structural genomics as assesed using these methods. This discussion is not a comprehensive review of profile-based methods for sequence analysis and their application in structural genomics rather observations made with PSI-BLAST-constructed PSSMs are emphasized, and results produced by other methods are cited only as needed for discussion. 

Whilst chymotrypsin and trypsin are especially useful in peptide sequence analysis, they also have medicinal applications. Their ability to hydrolyse proteins makes them valuable for wound and ulcer cleansing (trypsin) or during cataract removal (chymotrypsin). 

Simple Peptide Bacteriocins. Interest in LAB bacteriocins has prompted the application of molecular analyses to identify the genetic and/or protein sequences of these compounds. Such efforts have demonstrated the absence of lanthionine-related residues in leucocin A-UAL 187 (22) and lactacin F (35), for which the first 13 and 25 amino acid residues, respectively, were determined by sequence analysis the absence of lanthionine-related residues was confirmed by composition analysis. Similarly, the entire 54- and 39-amino acid sequences of lactococcin A (15) and Gcxi (16a), respectively, were also obtained by direct sequencing. 

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