protein

Occurrence

Proteins are of importance in all biological systems, playing a wide variety of structural and functional roles. They form the primary organic basis of structures such as hair, tendons, muscle, skin, and cartilage. All of the enzymes, the catalysts in biochemical transformations, are protein in nature. Many hormones, such as insulin and growth hormone, are proteins. The substances responsible for oxygen and electron transport (hemoglobin and the cytochromes, respectively) are conjugated proteins that contain a metalloporphyrin as the prosthetic group. Chromosomes are highly complex nucleoproteins, that is, proteins conjugated with nucleic acid. Viruses are also nucleoprotein in nature. Of the more than 200 amino acids that have been discovered either in the free state or in small peptides, only 20 amino acids are present in mammalian

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Specificity

The linear arrangement of the amino acid residues in a protein is termed its sequence (primary structure). The sequence in which the different amino acids are linked in any given protein is highly specific and characteristic for that particular protein.

This specificity of sequence is one of the most remarkable aspects of protein chemistry. The number of possible permutations of sequence in even so small a protein as insulin, of molecular weight 5732 and with 51 amino acid residues, is astronomic: 1051 permutations. Yet it has been established that the pancreatic cell of a given species has only one of these possible sequences. The elucidation of the mechanism conferring such a high degree of specificity on the biosynthetic reactions by which proteins are built up from free amino acids has been one of the key problems of modern biochemistry. See Molecular biology

Proteins are not stretched polymers; rather, the polypeptide backbone of the molecule can fold in several ways by means of hydrogen bonds between the carbonyl oxygen and the amide nitrogen. The folding of each protein is determined by its particular sequence of amino acids. The long polypeptide chains of proteins, particularly those of the fibrous proteins, are held together in a rather well-defined configuration. The backbone is coiled in a regular fashion, forming an extended helix. As a result of this coiling, peptide bonds separated from one another by several amino acid residues are brought into close spatial approximation. The stability of the helical configuration can be attributed to hydrogen bonds between these peptide bonds.

In addition to hydrogen bonds, there are electrostatic interactions, such as those between COO^- and NH₃⁺ groups of the side chains, and van der Waals forces, that is, hydrophobic interactions, which help to determine the configuration of the polypeptide chain. The term secondary structure is used to refer to all those structural features of the polypeptide chain determined by noncovalent bonding interactions.

In addition to the α-helical sections of proteins, there are segments that contain β-structures in which there are hydrogen bonds between two polypeptide chains that run in parallel or antiparallel fashion.

The tertiary structure (third level of folding) of a protein comes about through various interactions between different parts of the molecule. Disulfide bridges formed between cysteine residues at different locations in the molecule can stabilize parts of a three-dimensional structure by introducing a primary valence bond as a cross-link. Hydrogen bonds between different segments of the protein, hydrophobic bonds between nonpolar side chains of amino acids such a phenylalanine and leucine, and salt bridges such as those between positively charged lysyl side chains and negatively charged aspartyl side chains all contribute to the individual tertiary structure of a protein.

Finally, for those proteins that contain more than one polypeptide chain per molecule, there is usually a high degree of interaction between each subunit, for example, between the α- and β-polypeptide chains of hemoglobin. This feature of the protein structure is termed its quarternary structure.

Properties

The properties of proteins are determined in part by their amino acid composition. As macromolecules that contain many side chains that can be protonated and unprotonated depending upon the pH of the medium, proteins are excellent buffers. The fact that the pH of blood varies only very slightly in spite of the numerous metabolic processes in which it participates is due to the very large buffering capacity of the blood proteins.

Biosynthesis

The processes by which proteins are synthesized biologically have become one of the central themes of molecular biology. The sequence of amino acid residues in a protein is controlled by the sequence of the DNA as expressed in messenger RNA at ribosomes. See Deoxyribonucleic acid (DNA), Ribonucleic acid (RNA), Ribosomes

Degradation

As with many other macromolecular components of the organism, most body proteins are in a dynamic state of synthesis and degradation (proteolysis). During proteolysis, the peptide bond that links the amino acids to each other is hydrolyzed, and free amino acids are released. The process is carried out by a diverse group of enzymes called proteases. During proteolysis, the energy invested in generation of the proteins is released. See Enzyme

Distinct proteolytic mechanisms serve different physiological requirements. Proteins can be divided into extracellular and intracellular, and the two groups are degraded by two distinct mechanisms. Extracellular proteins such as the plasma immunoglobulins and albumin are degraded in a process known as receptor-mediated endocytosis. Ubiquitin-mediated proteolysis of a variety of cellular proteins plays an important role in many basic cellular processes such as the regulation of cell cycle and division, differentiation, and development; DNA repair; regulation of the immune and inflammatory responses; and biogenesis of organelles.

Molecular chaperones

Molecular chaperones are specialized cellular proteins that bind nonnative forms of other proteins and assist them to reach a functional conformation. The role of chaperone proteins under conditions of stress, such as heat shock, is to protect proteins by binding to misfolded conformations when they are just starting to form, preventing aggregation; then, following return of normal conditions, they allow refolding to occur. Chaperones also play essential roles in folding under normal conditions, providing kinetic assistance to the folding process, and thus improving the overall rate and extent of productive folding.

Protein engineering

The amino acid sequences, sizes, and three-dimensional conformations of protein molecules can be manipulated by protein engineering, in which the basic techniques of genetic engineering are used to alter the genes that encode proteins. These manipulations are used to generate proteins with novel activities or properties for specific applications, to discover structure-function relationships, and to generate biologically active minimalist proteins (containing only those sequences necessary for biological activity) that are smaller than their naturally occurring counterparts.

Many subtle variations in a particular protein can be generated by making amino acid replacements at specific positions in the polypeptide sequence. For example, at any specific position an amino acid can be replaced by another to generate a mutant protein that may have different characteristics by virtue of the single replaced amino acid. Amino acids can also be deleted from a protein sequence, either individually or in groups. These proteins are referred to as deletion mutants. Deletion mutants may or may not be missing one or more functions or properties of the full, naturally occurring protein. Moreover, part or all of a protein sequence can be joined or fused to that of another protein. The resulting protein is called a hybrid or fusion protein, which generally has characteristics that combine those of each of the joined partners.