Protein nomenclature

The discovery of this evolutionary activity has reeked havoc with the accepted PTS protein nomenclature. Instead of the time-honored E-I, E-II, E-III and HPr, we must resort to cumbersome phrases such as the E-III-like domain of E-IT etc. To alleviate the problem, Saier Jr and Reizer [3] have proposed a new nomenclature (Fig. 2) based on the original IIA/IIB nomenclature of Kundig and Roseman [4]. The old nomenclature is given above the bars representing the permeases in Fig. 2 and the new nomenclature below the bars. H and I still represent HPr and E-I, respectively, but IIA replaces E-IIl. IIC represents the hydrophobic domain of E-... 

During the nineteenth and early twentieth centuries, separation of the proteins was limited to casein and the classical lactalbumin and lacto-globulin fractions of the whey proteins. Subsequent work has resulted in the identification and characterization of numerous proteins from each of these fractions. A classification system of the known proteins in milk developed by the American Dairy Science Association s (ADSA) Committee on Milk Protein Nomenclature, Classification, and Methodology (Eigel et al 1984) is summarized and enlarged to include the minor proteins and enzymes in Table 3.1. 

The ADSA Protein Nomenclature Committee (Eigel et al. 1984) recommends that these minor K-caseins be identified temporarily according to their genetic variant and numbered consecutively in their order of increasing relative electrophoretic mobility in alkaline urea gels in the presence of mercaptoethanol (Yaguchi et al 1968) as K-casein A-l or K-casein B-l, etc. 

The ADSA Committee on Milk Protein Nomenclature (Eigel et al. 1984) presented a tentative nomenclature for the new enzyme membrane proteins. While the primary structures of these proteins have not been established, sufficient information exists to obtain an operational definition. The total protein complement of the membrane as observed is dependent upon the past history of the membrane from its formation to its analysis. Both the temperature and the time of storage before analysis can alter the membrane composition and physical state (Wooding 1971). In addition, plasmin has been shown to be associated with preparations of the membrane, and proteolytic products of the membrane protein have been observed in milk (Hoffman et al. 1979 Kanno and Yamauchi 1979). Therefore, one should use fresh warm raw milk for the study of the native MFGM protein. 

The protein nomenclature adopted in this review is partly that recommended by a committee of the American Dairy Science Association in their two most recent reports (Eigel etal., 1984 Whitney et al, 1976) and partly the nomenclature of the source literature. The relation of the new nomenclature to that in the earlier literature has been summarized, with some simplifications, in Fig. 1. 

Fundel K, Zimmer R. 2006. Gene and protein nomenclature in public databases. BMC Bioinformatics. 7 372. 

Fig. 10.2 Human FK506-binding proteins. Protein nomenclature is according to Fischer [3], The gene name and the molecular mass ofthe unprocessed proteins are shown in the brackets. In the second row, the accession number of the SWISS-PROT/TREMBL database and an example of an alternative name ofthe protein is given. The amino acid...

Prion protein nomenclature or Abandon hope all ye who enter here . There is no doubt that the nomenclamre of the TSE field can be confusing to outside observers and seasoned researchers alike. Part of this confusion arises from the genuine uncertainty that exists about the normal function (s) of PrP, the nature of TSE infectivity, and the various and variable abnormal properties of PrP most relevant to infectivity and/or TSE pathogenesis. No attempt has been made to unify the terminology used in the different chapters of this volume for two reasons. Eirst, this seems like a hopeless task. Second, it is my belief that the nomenclature in any rapidly changing field should evolve with the facts as they are revealed. This state of flux will naturally require that authors carefully define and redefine their usage of terminology from time to time. Unfortunately, it also may require that readers of literature have the patience of Job and the semantic acumen of Supreme Court justices. 

Determined in the SDS-urea electrophoresis system described in [8] " Polarity index = D+N+E+Q+K+R+S+T+H/total amino acids, mol Z [9] lumenal side / stromal side / intrinsic membrane protein Nomenclature according to [10] and [11]. 

As with all macromolecules, protein nomenclature predominantly uses trivial names. Proteins can be classified from a variety of perspectives, which reflect their importance in nutrition, origin, structure, chemical and biochemical properties and other attributes. 

Proteins Nomenclature of main subunits Molecular Weight (kDa) Ref... 

---