Classification of proteins

Proteins possess quaternary structure if they contain more than one polypeptide chain. The forces that stabilise these aggregates are hydrogen bonds and electrostatic or salt bonds formed between residues on the surfaces of the polypeptide chains. 

All proteins have colloidal properties they differ in their solubility in water, ranging from insoluble keratin to albumins, which are highly soluble. Soluble proteins can be precipitated from solution by the addition of certain salts such as sodium chloride or ammonium sulphate. This is a physical effect and the properties of the proteins are not altered. On dilution the proteins can easily be redissolved. 

Although the amino and carboxyl groups in the peptide linkage are nonfunctional in acid-base reactions, all proteins contain a number of free amino and carboxyl groups, either as terminal units or in the side chain of amino acid residues. Like amino acids, proteins are therefore amphoteric. They exhibit characteristic isoelectric points and have buffering properties. 

Proteins may be classified into two main groups simple proteins and conjugated proteins. 

These proteins produce only amino acids on hydrolysis. They are subdivided into two groups, fibrous and globular proteins, according to shape, solubility and chemical composition. 

2 Classification of Proteins Classification of proteins in terms of the secondary structure may be expressed as follows  

Currendy, classifications tend to have numerous small clusters, all roughly grouped into just a few categories which are still based on the overall secondary structure content and arrangements, such as apoc layers, appa layers, ap barrel. This new classification is quite different from what we have described in Chapter 1. 

---

SCOP Structural Classification of Proteins. Hierarchical protein structure database... 

Murzin A G, S E Brenner, T Hubbard and C Chothia 1995. SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247 536-540. 

TJP Hubbard, B Alley, SE Brenner, AGMurzm, C Chothia. SCOP A stiaictural classification of proteins database. Nucleic Acids Res 27 254-256, 1999. 

CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton. CATH—A hierarchic classification of protein domain structures. Stnrcture 5 1093-1108, 1997. 

Topology diagrams are useful for classification of protein structures... 

Proteins are the agents of biolo ealfunction. Virtually every cellular activity is dependent on one or more particular proteins. Thus, a convenient way to classify the enormous number of proteins is by the biological roles they fill. Table 5.3 summarizes the classification of proteins by function and gives examples of representative members of each class. 

Protein Phosphatases. Figure 3 Classification of protein tyrosine phosphatases. See text for details. Common names for selected PTPs are used according to Ref. [2]. 

Tatusov RL, Natale DA, Garkavtsev IV et al. The COG database new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001 29[l] 22-28. 

Weller M.G., Classification of protein microarrays and related techniques, Anal Bioanal Chem. 2003 375 15-17. 

Classification of Protein Structures Based on Convex Hull Representation by Integrated Neural Network. 

Murzin, A. G. (1996). Structural classification of proteins new superfamilies. Curr. Opin. Struct. Biol. 6, 386-394. 

Murzin, A. G., and Bateman, A. (1997). Distant homology recognition using structural classification of proteins. Proteins Suppl. 1, 105-112. 

Naumann, T. and Matter, H. Structural classification of protein kinases using... 

Contrary to the situation found for the annotation and classification of proteins, where multiple schemes coexist for the different families, it is remarkable to realize that to date, little attention has been paid to the... 

Naumann, T. and Matter, H. (2002) Structural classification of protein kinases using 3d molecular interaction field analysis of their ligand binding sites Target family landscapes../. Med. Chem. 45, 2366-2378. 

FIGURE 4-22 Organization of proteins based on motifs. Shown here are just a small number of the hundreds of known stable motifs. They are divided into four classes all a, all /3, all3, and a + /3. Structural classification data from the SCOP (Structural Classification of Proteins) database (http //scop.mrc-lmb.cam.ac.uk/scop) are also provided. The PDB identifier is the unique number given to each structure archived in the Protein Data Bank (www.rcsb.org/pdb). The a//3 barrel, shown in Figure 4-21, is another particularly common a/fS motif. 

---