Globular proteins classification

Proteins are often referred to as globular and fibrous proteins according to their conformation. Globular proteins are usually soluble in water, whilst fibrous proteins are usually insoluble. The complex nature of their structures has resulted in the use of a sub-classification, sometimes referred to as the order of protein structures. This classification divides the structure into into primary, secondary, tertiary and quaternary orders of structures. 

One difficulty in characterizing the CD for a typical p turn has been the lack of well characterized model compounds and the variability of the p turn structure in terms of allowable backbone dihedral angles. Early classification schemes described three general classes of p turns, termed types I, n, and III (see Table I). Type III turns resemble a single turn of a 3jo helix (see below), while types I and II are the most common structures for chain reversal found in globular proteins. Types I and IT have also been identified, with the prime symbols indicating an approximate 180° rotation of the peptide group of the i+lth residue. 

Various schemes have been developed for the classification of protein three-dimensional structures. One common scheme is the classification based on the four tertiary super classes, namely, all a (proteins having mainly a-helix secondary structure), all P (mainly P-sheet secondary structure), a+p (segment of a-helices followed by segment of P-sheets), and o/p (alternating or mixed a-helix and P-sheet segments) (Levitt, 1976). A fifth class is often added to account for globular proteins with irregular secondary... 

Ans. This classification is based on solubility in the aqueous environment. Fibrous proteins are insoluble while globular proteins are soluble. Globular proteins are globe-shaped, i.e., more or less spherical. Fibrous proteins have shapes in which one dimension is much longer than the other dimensions, i.e., they are elongated. Fibrous proteins function as structural and contractile proteins (Table 20-1). The functions of globular proteins are those such as the transport, enzyme, defense, and regulatory functions which require solubility in the aqueous environment. 

Describe proteins in terms of the following characteristics size, function, classification as fibrous or globular, and classification as simple or conjugated. (Section 9.5)... 

Table 1. Classification of internal motions of globular proteins...

In the past, globular proteins were classified according to their solubilities and some of their chemical characteristics. This classification is no longer satisfactory, especially because the classes cannot be defined precisely enough. We want to distinguish only among (1) histones, (2) albumins, and (3) globulins. 

As already mentioned, classification of globular proteins according to the structural patterns, has been introduced by Levitt and Chothia (1976). The proteins which contain Pctfi units pertain to class IV the proteins which pertain to one of the three first classes do not have any pap folds. Figure 2.27 displays several examples of proteins which pertain to the different categories according to the simplified representation. (Examples of all —a proteins in... 

Cholesterol, which is largely insoluble in aqueous m a, travels through the blood circulation in the form of Upoprotein complexes. The plasma lipoproteins are a family of globular particles that share common structural features. A core of hydrophobic lipid, principally triacylglycerols (triglycerides) and cholesterol esters, is surrounded by a hydrophilic monolayer of phospholipid and protein (the apolipoproteins) [1-3]. Lipid-apolipoprotein interactions, facihtated byi amphi-pathic protein helices that segregate polar from nonpolar surfaces [2,3], provide the mechanism by which cholesterol can circulate in a soluble form. In addition, the apolipoproteins modulate the activities of certain enzymes involved in Upoprotein metabolism and interact with specific cell surface receptors which take up Upopro-teins by receptor-mediated endocytosis. Differences in the Upid and apoUpoprotein compositions of plasma Upoproteins determine their target sites and classification based on buoyant density. 

Problem 20.25. Describe the classification of proteins as fibrous or globular. What is the relationship of this classification to physiological function ... 

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. 

The first complication associated with structure classification involves the fact that protein structures are often composed of distinct globular domains. Because these domains can function individually, with distinct functional roles, proteins are usually separated into domains before classification. 

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