SUATARON, SARAH MARIE C.

CLASSIFICATION OF PROTEINS A Simple Proteins

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Albumins: blood (serumbumin); milk (lactalbumin); egg white (ovolbumin); lentils (legumelin); kidney beans (phaseolin); wheat (leucosin). Globular protein; soluble in water and dilute salt solution; precipitated by saturation with ammonium sulfate solution; coagulated by heat; found in plant and animal tissues. Globulins: blood (serum globulins); muscle (myosin); potato (tuberin); Brazil nuts (excelsin); hemp (edestin); lentils (legumin). Globular protein; sparingly soluble in water; soluble in neutral solutions; precipitated by dilute ammonium sulfate and coagulated by heat; distributed in both plant and animal tissues. Glutelins: wheat (glutenin); rice (oryzenin). Insoluble in water and dilute salt solutions; soluble in dilute acids; found in grains and cereals. Prolamines: wheat and rye (gliadin); corn (zein); rye (secaline); barley (hordein). Insoluble in water and absolute alcohol; soluble in 70% alcohol; high in amide nitrogen and proline; occurs in grain seeds. Protamines: sturgeon (sturine); mackerel (scombrine); salmon (salmine); herring (clapeine). Soluble in water; not coagulated by heat; strongly basic; high in arginine; associate with DNA; occurs in sperm cells. Histones: Thymus gland; pancreas; nucleoproteins (nucleohistone). Soluble in water, salt solutions, and dilute acids; insoluble in ammonium hydroxide; yields large amounts of lysine and arginine; combined with nucleic acids within cells. Scleroproteins: Connective tissues and hard tissues. Fibrous protein; insoluble in all solvents and resistant to digestion.

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3. 4. 5. 6. 7.

a. b. c.

Collagen: connective tissues, bones, cartilage, and gelatin. Resistant to digestive enzymes but altered to digest gelatin by boiling water, acid, or alkali; high in hydroxylrpline. Elastin: Ligaments, tendons, and arteries. Similar to collagen but cannot be converted to gelatin.

B.

Keratin: Hair, nails, hooves, horns, and feathers. Partially resistant to digestive enzymes; contains large amounts of sulfur, as cystine. Conjugated Proteins

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Nucleoproteins: cytoplasm of cells (ribonucleoprotein); nucleas of chromosomes (deoxyribonucleoprotein) viruses, and bacteriophages. Contains nucleic acids, nitrogen, and phosphorus. Present in chromosomes and in all living forms as a combination of protein with either RNA or DNA. Mucoprotein: saliva (mucin); egg white (ovomucoid). Proteins combined with amino sugars, sugar acids, and sulfates. Glycoprotein: bone (osseomucoid); tendons (tendomucoid); carilage (chondromucoid). Containing more than 4% hexosamine, mucoproteins; if less than 4%, then glycoproteins. Phosphoproteins: milk (casein); egg yolk (ovovitellin). Phosphoric acid joined in ester linkage to protein. Chromoproteins: hemoglobin; myoglobin; flavoproteins; respiratory pigments; cytochromes. Protein compounds with such nonprotein pigments as heme; colored proteins. Lipoproteins: serum lipoprotein; brain, nerve tissues, milk, and eggs. Water-soluble protein conjugated with lipids; found dispersed widely in all cells and all living forms.

2. 3. 4. 5. 6. 7.

C.

Metallo proteins: ferritin; carbonic anhydrase; ceruloplasmin. Proteins combined with metallic atoms that are not parts of a nonprotein prosthetic group. Derived Proteins

1. 2. 3. 4.

Proteans: edestan (from elastin) and myosan (from myosin). Results from short action of acids or enzymes; insolvent in water. Proteases: intermediate products of protein digestion. Soluble in water; uncoagulated by heat; and precipitated by saturated ammonium sulfate; result from partial digestion of protein by pepsin or trypsin. Peptones: intermediate products of protein digestion. Same properties as proteases except that they cannot be salted out; of smaller molecular weight those proteases. Peptides: intermediate products of protein digestion. Two or more amino acids joined by a peptide linkage; hydrolyzed to individual amino acids.

Classification by protein functions

Proteins are responsible for many different functions in the living cell. It is possible to classify proteins on the basis of their functions. Very often, proteins can carry few functions and such proteins can be placed into different groups, but despite this, it is possible to assign main group for each protein.

Enzymes - proteins that catalyze chemical and biochemical reactions within living cell and outside. This group of proteins probably is the biggest and most important group of the proteins. Enzymes are responsible for all metabolic reactions in the living cells. Well known and very interesting examples are: DNA- and RNA-polymerases, dehydrogenases etc.

Hormones - proteins that are responsible for the regulation of many processes in organisms. Hormones are usually quite small and can be classifies as peptides. Most known protein hormones are: insulin, grows factor, lipotropin, prolactin etc. Many protein hormones are predecessor of peptide hormones, such as endorfine, enkephalin etc. It is possible to increase this group of proteins by adding of all protein venoms.

Transport proteins - These proteins are transporting or store some other chemical compounds and ions. Some of them are well known: cytochrome C - electron transport; haemoglobin and myoglobin - oxygen transport; albumin - fatty acid transport in the blood stream etc. It is possible to classify trance membrane protein channels as a transport protein as well.

Immunoglobulin or Antibodies - proteins that involved into immune response of the organism to neutralize large foreign molecules, which can be a part of an infection. Sometimes antibodies can act as enzymes. Sometimes this group of proteins is considered as a bigger group of protective proteins with adding such proteins as lymphocyte antigen-recognizing receptors, antivirals agents such as interferon, tumor necrosis factor (TNF). Probably the clotting of blood proteins, such as fibrin and thrombin should be classified as protective proteins as well.

Structural proteins - These proteins are maintaining structures of other biological components, like cells and tissues. Collagen, elastin, -keratin, sklerotin, fibroin - these proteins are involved into formation of the whole organism body. Bacterial proteoglycans and virus coating proteins also belongs to this group of proteins. Currently we do not know about other functions of these proteins.

Motor proteins. These proteins can convert chemical energy into mechanical energy. Actin and myosin are responsible for muscular motion. Sometimes it is difficult to make a strict separation between structural and motion proteins.

Receptors These proteins are responsible for signal detection and translation into other type of signal. Sometimes these proteins are active only in complex with low molecular weight compounds. Very well known member of this protein family id rhodopsin - light detecting protein. Many receptors are transmembrane proteins.

Signalling proteins - This group of proteins is involved into signalling translation process. Usually they significantly change conformation in presence of some signalling molecules. These proteins can act as

enzymes. Other proteins, usually small, can interact with receptors. Classical example of this group of proteins is GTPases.

Storage proteins. These proteins contain energy, which can be released during metabolism processes in the organism. Egg ovalbumin and milk casein are such proteins. Almost all proteins can be digested and used as a source of energy and building material by other organisms.

Classification of proteins by location in the living cell

Protein classification can be based on their appearance in the living cell. According to this, it is possible to classify all proteins into four main groups.

Membrane or transmembrane proteins - these proteins are located within cell membrane lipid bi-layer. These proteins can be completely or partially burred in membrane. Internal proteins - these proteins are located within living cell and all functions are related with intercellular needs. External or secret proteins - these proteins are functions outside the cell they produced. Such type of proteins is more common for multicells organisms. Virus proteins - These proteins are present only in virus organism, usually as a coat for viral particle.

Classification of proteins by posttranslational modification

After protein translation some of them are subjected to posttranslational modification. This modification can be related with many different aspects of changes. Again this classification split all proteins into overlapped groups.

Native proteins - these proteins are not changed after translation. Glico-proteins - these proteins are modified by covalent binding with linear or branched oligosaccharides. Cleaved proteins - the polypeptide chain of these proteins are cleaved into two or more pieces. Proteins with disulphide bonds. In these proteins pair of cysteins are linked between each other by S-S or disulphide bond (disulphide bridge) Protein complexes. Some proteins produce protein complexes of homo- and hetero- nature. Chemically modified proteins - in these proteins some residues are chemically modified by covalent bonding with other chemical compounds. Prions - these proteins are folded wrongly during translation, or change their configuration straight after translation.

Protein structure organisation (primary, secondary, ternary and quaternary)

The structural organisation of protein can be divided into four different levels.

Primary structure or protein sequence. The protein sequence, or amino acid sequence in polypeptide chain defines the protein primary structure. DNA (or RNA in viruses) codes the primary protein structure and this is comprehensive information for the protein structure and functions.

Secondary structure. One of the main conformational parameter of the amino acid structure is the value of the PHI and PSI angles. These angles completely define the conformation of the polypeptide chain. With some special values for these angles the main chain can adopt specially classified conformations, like alpha-helix or beta-strand. The other main feature of the protein secondary structure is the local stabilisation by hydrogen bonds. These conformations are classifies as a protein secondary structure.

Ternary structure, protein 3D structure or protein folding. Ternary structure or protein fold completely define the structural organization of the protein molecule in 3d.

Quaternary structure. The interaction between several protein molecules forms protein complexes, with their structure defined as a quaternary structure.