In order to understand the structure and functions of proteins it is important to revise the basics of protein structure and function. Proteins are working molecules of a cell that carry out the ‘program’ of activities encoded onto them by genes. The ‘program’ which is nothing but the cell function, requires the coordinated effort of many different types of protein which work in synchronous with each other to provide the desired effect. [1]

Classification of Proteins:
Proteins are classified into several broad classes based on the functional role played by them within the body.
• Structural proteins- which provide structural rigidity to the cell.
• Transport proteins- those which control the flow of materials across the body and cellular membranes e.g. albumin and AFP.
• Regulatory proteins- they act as sensors and switches to control protein activity and gene function.
• Signaling proteins- including cell-surface receptors and other proteins that transmit external signals to the cell interior.
• Motor proteins- they are those which cause motion.
• Enzymes- specialized proteins which are capable of catalyzing an incredible range of intracellular and extracellular chemical reactions.

Hierarchical Structure of Proteins:
Although proteins are constructed by polymerization of only 20 different amino acids into linear chains, proteins carry out an incredible array of diverse tasks. Only whena protein is in its correct three dimensional structure, or conformation is it able to function efficiently. A key concept in understanding how proteins work is thatfunction is derived from three dimensional structure, and the three dimensional structure is in turn specified by the amino
acid sequence. The structure of proteins can be considered at four levels of organization starting with their monomeric building blocks, the amino acids as shown in Fig. 1

Fig. 1 The linear sequence of amino acids (primary structure) folds into helices or sheets (secondary structure) which pack into a globular or fibrous domain (tertiary structure). Some individual proteins selfassociate
into complexes (quaternary structure) that can consist of tens to hundreds of subunits (supramolecular assemblies)

THE PRIMARY STRUCTURE:
It is the linear arrangement of the amino acid sequences present in the protein. It is nothing but the formation of a peptide bond combining the carboxylic acid moiety of one amino acid with an amino moiety of another amino acid. Thus one end of the protein has a free (unlinked) amino group (the Nterminus) and the other end has a free
carboxyl group (the C-terminus). The sequence of a protein chain is conventionally written with its N-terminal
amino acid on the left and its C-terminal amino acid on the right. A short chain of amino acids (20-50 amino acid residues) linked by peptide bonds and having a definite sequence is called a peptide, while longer chains are referred to as polypeptides or proteins (up to 4000 amino acid residues). Fig.3 shows the primary structure of a set of amino acids and the formation of the peptide bonds between them.

Fig.3 Peptide bonds (yellow) link the amide nitrogen atom (blue) of one amino acid(aa) with the carbonyl carbon atom (gray) of an adjacent one in the linear polymers known as peptides or polypeptides depending on
their lengths.

THE SECONDARY STRUCTURE:
They are the core elements of protein architecture. The various spatial arrangements resulting from the folding of
localized parts of a polypeptide chain are referred to as the secondary structures. When stabilizing hydrogen bonds are formed between residues, parts of the backbone fold into one or more well defined periodic structures such as the alpha helix, the beta sheet also called the beta pleated sheet, and a set of turns (See Fig.4).

Fig.4 Shows the Alpha Helix which is above with the red backbone, and the beta pleated sheet below with the blue backbone.

THE TERTIARY STRUCTURE:
The overall folding of the polypeptide chain yields its tertiary structure. The tertiary structure refers to the overall conformation of a polypeptide chain-that is the three dimensional arrangement of all its amino acid residues. The tertiary structure is primarily stabilized by hydrophobic interactions between the non-polar side chains, by hydrogen bonds between the polar side chains and by peptide bonds. These stabilizing forces hold elements of the
secondary structure- alpha helices, beta strands, turns and random coils- compactly together. Since the stabilizing forces are weak the tertiary structure of a protein is not rigidly fixed, but it undergoes continual and minute fluctuation. This variation in structure has important consequences in the function and regulation of proteins.
There are two important substructures within the tertiary structure which are of interest to study:
1. Motifs: They are particular combinations of secondary structures. In some cases, motifs are signatures for a specific function. E.g. of motifs are - the helix-loop-helix which is a calcium binding motif found in more than hundred
calcium binding proteins.
- zinc-finger motif: it is an alpha helix and two beta strands held together by a zinc ion. This type of a motif is most commonly found in proteins that bind to DNA or RNA such as steroid hormone receptors.
- coiled coil: two or more alpha-helices orient themselves around each other in a coiled coil manner.

Fig. 5 gives a visual idea of how each of these motifs looks.

Fig. 5 shows various kinds of motifs commonly found in proteins. (a) two helices connected with a helix-loop-helix motif commonly found in calcium-binding and DNA-binding regulatory proteins. (b) The zinc-finger motif which is present in many DNA-binding proteins that help regulate transcription. (c) the parallel two stranded coiled-coil motif characterized by two alpha-helices wound one around the other and is stabilized by interactions between hydrophobic side chains.

2. Domains: A domain is a compactly folded region of a polypeptide.

Often a domain is characterized by some interesting structural feature, such as, an unusual abundance of a particular amino acid (e.g. a proline rich domain), sequences common to many proteins (e.g. the Epidermal Growth Factor domain) or a particular secondarystructure domain (e.g. the zinc finger domain).

Domains are sometimes defined in functional terms on the basis of observations that an activity of a protein is localized to a particular region along the length of the protein (e.g. DNA binding domain).
Experiment: Functional domains are often identified experimentally by whittling down a protein to its smallest active fragments with the aid of proteases, enzymes that cleave the polypeptide backbone- and then checking individual fragments for particular activity.

Alternatively, the DNA, encoding a particular protein, can be subjected to mutagenesis so that segments of the
protein’s backbone are removed or changed. The activity of the truncated or altered protein product synthesized from the mutated gene is then monitored and serves as a source of insight about which part of the protein is critical to its function.

THE QUARTENARY STRUCTURE
Multimeric proteins consist of two or more polypeptides or subunits. Quaternary structure of a protein describes the number (stoichiometry) and relative positions of the subunits in the multimeric proteins (e.g. Haemoglobin is a tetramer consisting of two alpha and two beta subunits as can be seen in Fig.6) [1]

Fig. 6 shows the quaternary structure of haemoglobin which is a tetramer of two alpha and two beta subunits.

References -

• Harvey Lodish [et al.]: Protein Structure and Function. In: Molecular Cell Biology (5th ed.). New York, W. H. Freeman and Company, 2003, p.59.
  

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