Proteins classification methods

Amino Acid Content. Amino acid content of field pea products is related to protein level, method of processing, and fraction (starch or protein). The protein fraction contains fewer acidic (glu, asp) amino acids than the starch fraction and more basic (lys, his, arg) amino acids than the starch fraction. Also, there are more aromatic (tyr, phe) amino acids, leu, iso, ser, val, and pro in the protein fraction than in the starch fraction (5). An amino acid profile of pea protein concentrate shows relatively high lysine content (7.77 g aa/16 g N) but low sulfur amino acids (methionine and cystine) (1.08-2.4 g aa/16 g N). Therefore, it is recommended that air classification or ultrafiltration be used because acid precipitation results in a whey fraction which contains high levels of sulfur amino acids (12,23). Also, drum drying sodium proteinates decreases lysine content due to the Maillard reaction (33). 

Park, B., Jeong, SK, Lee, WS., Seong, JK, Paik, YK. (2004) A simple pattern classification method for alcohol-responsive proteins that are differentially expressed in mouse brain. Proteomics. 4, 3369-3375... 

The direct sequence encoding methods preserve the order of residues along the sequence string and encode primarily local information. They are, however, not suitable when global sequence features or information content is more important to the application, or when variable length sequences are to be analyzed. This is evident in the intron/exon sequence discrimination (e.g., Uberbacher Mural, 1991 Snyder Stormo, 1993) and protein classification (e.g., Wu et al., 1992 Ferran Ferrara, 1992) problems. 

Hunter, T. Protein kinase classification. Methods EnzymoL, 200, 3-37 (1991)... 

S. Leicester, J. Finney, and R. Bywater, /. Math. Chem., 16, 315 (1994). A Quantitative Representation of Molecular Surface Shape. I. Theory and Development of the Method. S. Leicester, J. Finney, and R. Bywater, /. Math. Chem., 16, 343 (1994). A Quantitative Representation of Molecular Surface Shape. II. Protein Classification Using Fourier Shape Descriptors and Classical Scaling. 

All current structural classification methods are based on the same scheme Protein structures are first divided into discrete, globular domains, which are then classified at the levels of (1) class, (2) folds, (3) superfa-milies, and (4) families. The differences among existing schemes come from the methods that define the domains and the procedures that classify. After reviewing the terms that define a classification, the three main protein structure classifications available, SCOP, CATH, and the DALI Domain Dictionary (DDD), will be described. Links to these databases and related services are listed in Table 7. 

SCOP, CATH, and DDD agree on most of their classifications, despite differences in the classification methods they have implemented, and in the rules of protein structure and taxonomy they are based on. Hadley and Jones were the first to publish a detailed comparison of the fold classifications produced by SCOP, CATH, and FSSP. They showed that the three classification systems tend to agree in most cases, and that the discrepancies and inconsistencies are accounted for by a small number of problems. Among these, the domain assignment plays a crucial role. As mentioned, the separation of proteins into domains is a difficult and often subjective process. Many... 

The above described procedure is quite useftil because it focuses the final classification process on a group of reference strains that are closest relatives of the isolated one. For example, shotgun-proteomic analysis of the whole cell protein extract of a poisonous strain isolated from the Indonesian rice dish followed by the above classification method indicated that it can be classified as Firmicutes... 

In food processing, the major objectives are sometimes achieved at the expense of some loss of recognised nutrients. However, in other cases, important nutrients may become available only after appropriate processing, since inhibitors or other interfering compounds may be destroyed or inactivated. Toxic factors can sometimes be destroyed by denaturation, as with enzymes, protease inhibitors and phyto-haemagglutinins. They can also be physically removed, for example by leaching, solvent extraction or solid classification methods, as in the removal of gossypol from cottonseed protein, or of phytate from cereals. 

Hunter, T. (1991). Protein kinases classification. Methods Enzymol, 200, 3-38. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

A machine-learning method was proposed by Klon et al. [104] as an alternative form of consensus scoring. The method proved unsuccessful for PKB, but showed promise for the phosphatase PTPIB (protein tyrosine phosphatase IB). In this approach, compounds were first docked into the receptor and scored using conventional means. The top scoring compounds were then assumed to be active and used to build a naive Bayes classification model, all compounds were subsequently re-scored and ranked using the model. The method is heavily dependent upon predicting accurate binding... 

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