Fundamentals of Biochemistry - Filippovich, Y. B. 1999

Proteins
Nomenclature and Classification of Proteins

Despite the fact that the primary, secondary, and quaternary structures of Proteins have been studied extensively and progress in this field continues, neither a rigorous nomenclature nor a scientific Classification of Proteins has yet been established. Proteins are named based on incidental features, most frequently taking into consideration the source from which the protein was isolated (for example, the name Avidin—an egg protein—comes from the Latin avis, meaning bird; casein—a milk protein—from the Latin caseus, meaning cheese; phaseolin—the main storage protein of the common bean, Phaseolus vulgaris, and so forth) or accounting for the protein's solubility in various agents, molecular shape, Amino Acid Composition, and the like.

The classification of proteins is equally imperfect. Depending on the criterion chosen as the basis for classification, various narrow or broad groups of proteins are distinguished. For instance, when characterizing proteins by their degree of complexity, two major groups are identified: simple and complex proteins. Simple proteins, or proteinins, are defined as proteins that yield only Amino Acids upon Hydrolysis. Complex proteins are substances composed of a protein (a simple protein) and an additional non-protein group. Therefore, it was previously customary to refer to complex proteins as proteinids, meaning protein-like substances. However, this term has now been abandoned, and depending on the Chemical Nature of the prosthetic group, these proteins are designated as Chromoproteins, Lipoproteins, Glycoproteins, Nucleoproteins, Metalloproteins, and so on. Simple proteins are frequently denoted as single-component, while complex ones are denoted as two-component.

Based on the shape of their particles, proteins are divided into fibrillar (fibrous) and globular (corpuscular) types. Fibrillar Proteins are characterized by a very high b/a axial ratio (several tens of units); their molecules are thread-like and typically assembled into bundles that subsequently form fibers. Examples of fibrillar proteins include Silk Fibroin, Hair keratin, Skin Collagen, and others. Proteins with a low b/a ratio (within the range of a few units) and, consequently, a rod-like molecular shape are termed corpuscular (from corpuscle, meaning particle) or globular. The overwhelming majority of natural proteins belong to the corpuscular type.

Depending on their behavior toward certain conventionally chosen Solvents, proteins are subdivided into proteinoids, albumins, globulins, and prolamins.

Proteinoids include proteins that are insoluble in conventional protein solvents: Water, saline solutions, and aqueous-alcoholic mixtures. This property is inherent to almost all fibrillar proteins. However, proteinoids dissolve readily in specific agents; for example, silk fibroin passes completely into solution upon Treatment with dichloroacetic acid, anhydrous hydrofluoric acid, concentrated lithium thiocyanate or potassium bromide solutions, and the like.

Albumins comprise proteins that are highly soluble in water and strong salt solutions; in the latter case, albumins are considered characteristically soluble in an aqueous (NH₄)₂SО₄ solution where the sulfate concentration exceeds 50% saturation. When transitioning to very concentrated (NH₄)₂SО₄ solutions, up to full saturation, albumins undergo salting-out.

Globulins belong to proteins that are insoluble in water but soluble in salt solutions of moderate concentrations. A characteristic feature of globulins is their complete precipitation at half-saturation with (NH₄)₂SО₄.

Prolamins represent a group of proteins soluble in 60–80% aqueous ethyl alcohol.

In terms of their amino acid composition, certain proteins exhibit distinct peculiarities, which also provides a basis for grouping them. Thus, proteins containing 80–90% arg in their molecules alongside a limited set (6–8) of Other Amino Acids are classified as protamines (the simplest proteins). They are abundantly found in fish milt. A typical representative is salmine from salmon milt, which contains (in %) 85.2 arg, 9.1 ser, 5.8 pro, 3.1 val, 3.0 gly, 1.6 ile, 1.1 ala, and lacks all other amino acids commonly encountered in proteins. Another group of proteins with a peculiar amino acid composition is Histones. These proteins are distinguished by a high content of basic amino acids: arg, lys, and his (at least 30%) and are found in significant quantities in Cell nuclei. Alcohol-soluble proteins—prolamins—also possess a characteristic amino acid composition: they are rich in glu (20–50%) and pro (10–15%), which is how they earned their name. Prolamins have been isolated exclusively from plant sources.

The aforementioned classification is extremely imperfect. It is based on incidental traits that frequently lead to contradictions and confusion. For instance, the division of proteins into simple and complex becomes increasingly difficult with The Development of Analytical Methods and the refinement of protein composition, as sensitive analysis in many cases reveals minor yet stable impurities of non-amino acid compounds (metals, amino sugars, etc.) within the composition of typical simple proteins. Egg albumin, for example, was long considered a typical simple protein, but approximately 2% mannose was recently discovered in it. As noted above, globulins are classified as proteins insoluble in water and salted out at 50% (NH₄)₂SО₄ saturation. However, a large group of proteins exists that are soluble in water like albumins, yet salt out like globulins (referred to as pseudoglobulins). The number of such examples could easily be multiplied. Therefore, attempts have been made, building upon the advances of Protein Chemistry and biochemistry, to provide a scientifically substantiated classification.

The first attempt consists in classifying proteins According to the features of their secondary and tertiary structures. According to this classification, Globular proteins are divided into 4 classes: α, β, α+β, and α/β. The α-Class comprises globular proteins containing exclusively α-helical Conformations accounting for at least 60% of their constituent polypeptide chain; the β-class comprises proteins containing only β-structures, typically in the form of at least two antiparallel strands; the α+β-class comprises proteins containing both structures within the same polypeptide chain, where one domain is assembled from α-structures and the other from β-structures; the α/β-class comprises proteins containing numerous α- and β-structures, either alternating along the polypeptide chain or arranged such that one or more β-sheets are surrounded by several α-helices each. Domains in α/ß-proteins are typically composed of α- and β-structures (Fig. 40).

Fig. 40. Classification of globular proteins according to the representation and arrangement of α- and β-structures in their molecules:

A — arrangement of α- and β-structures (denoted by circles and rectangles, respectively) in α-, β-, α+β-, and α/β-proteins; arrows indicate the direction of the polypeptide chain from the N-terminus to the C-terminus of the molecule; Myoglobin is a Muscle protein responsible for oxygen binding; rubredoxin is an iron protein participating in redox processes; Ribonuclease is an enzyme accelerating the hydrolysis of Ribonucleic Acids; Triosephosphate isomerase is an enzyme catalyzing The conversion of phosphoglyceraldehyde to phosphodihydroxyacetone; B — Structure of three representatives of α-, β-, and α/β-proteins, where the α-structure is depicted as helices and the β-structure as arrows; myohemerythrin is an iron protein that binds oxygen, similar to myo-globin (two iron atoms are shown as hatched circles located between double α-helices); erabutoxin is a proteinaceous neurotoxin isolated from sea snake venom (dashed lines indicate 4 disulfide bridges in its molecule, which is represented by a polypeptide chain of 61 amino acid residues); flavodoxin is a protein functioning as a hydrogen atom carrier (the HEAD portion of the figure shows the grouping responsible for hydrogen atom transfer depicted as three condensed six-membered rings)

Most globular proteins evaluated from this perspective belong to the α/β-class, which is only slightly surpassed in number by the β-class; the α-class and α+β-class of globular proteins are less widespread than the first two. It should be borne in mind that there are extremely rare globular proteins completely devoid of any canonical Secondary structure and belonging to none of the aforementioned classes.

The second approach amounts to classifying proteins according to the Functions they perform. According to this classification, proteins are divided into the following groups: 1) catalytically active proteins; 2) hormone proteins; 3) regulatory proteins; 4) protective proteins; 5) toxic proteins; 6) transport proteins; 7) structural proteins; 8) contractile proteins; 9) receptor proteins; 10) enzyme inhibitor proteins; 11) viral coat proteins; 12) proteins with other functions.

Of course, dividing proteins into the groups listed above represents a classification still far from perfection, and in the case of bifunctional proteins, one must naturally give preference to a single primary function. Nonetheless, within each of the enumerated categories, it is already possible to discern certain common features of structure, properties, and functional activity among the specific proteins included therein. This allows for a deeper understanding of the structure-function relationship in protein molecules, opens up possibilities for generalizing data concerning the interaction of proteins with compounds of other classes (Nucleic Acids, Lipids, etc.), and provides a basis for discussing the regularities of Introduction/18.html">Protein Evolution, the structural and Genetic foundations of their species Specificity, and other pressing problems in protein chemistry and biology as a whole.