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Suraj Prakash Sharma | Ekta Chotia

PROTEIN STRUCTURE
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4.2.1.2.   Amino acids affecting a-helical structure

1. A prolyl reisdue has its a-N atom in a rigid ring system and cannot participate in a-helical structure . Proline is called as helix breaker and creates a sharp bend in the helix.
2. A long repeat  of aspartyl and/or glutamyl residues can destabilize a-helical structure because the negatively-charged side chains repel one another (electrostatic repulsion), and the forces of repulsion are greater than those of hydrogen bonding.
3. A long sequence  of isoleucyl residues disrupts  helix formation, because of steric hindrance imposed by their bulky R groups.
4. Glycine, with a small hydrogen atom as a R group, is another destabilizer. The lack of a side chain on glycine allows for a great degree of rotation about the amino acid’s a-carbon. Thus conformations other than a helical bond angles are possible for glycine  which destabilize the helix.

4.2.2.     $\beta$sheet :

$\beta$ sheet are formed by hydrogen bonding, between the alpha carboxylic (CO) group of amino acid with the alpha amino group (–NH) is adjacent amino acid. It exist in antiparallel and parallel form. Antiparallel $\beta$ sheet are more stable. $\beta$ Sheets are common structural motifs in proteins. In globular proteins, they consist of from two to as many as twenty two polypeptide strands. In $\beta$-sheet hydrogen bonds are more or less one. In antiparallel $\beta$-sheet hydrogen bonds are more than one and in parallel it is less than one. Parallel and antiparallel $\beta$-sheets are connected by loops.

The energetically preferred dihedral angles $\phi$, $\varphi$ are –135° and 135° respectively for $\beta$ sheet. However the $\phi$ and $\varphi$ angles are –140° and 135° for antiparallel $\beta$ Sheet and - 120° and 115° for parallel $\beta$ sheet.

Globular proteins consist of an average, ~31% a helix and ~28% b sheet. The remaining polypeptide segments of protein are said to have a coil or loop conformation.

Silk fibroin is one example of a protein that has the antiparallel pleated sheet structure. It is a member of a class of fibrillar proteins called $\alpha$-keratin.

4.2.3.     Turns :

Turns are secondary structure. They are reversal in nature i.e. they reverse the direction of polypeptide chain. In turn three amino acids participate. Turn is stabilized by hydrogen bonding between the CO of residue ‘n’ and the NH of residue n + 3. Proline amino acid usually present in turn at position number two.

Only helix can form turn, proline amino acid is sometimes known as “helix breakers”. Because they disrupts the regularity of the a helical backbone conformation.

Types of turn

Basically turn are of two types designated as I and II. Type I turn contain all residues in position n  to n + 3. In type I turn proline is present at position number two and the 3rd position is acquired by any amino acid..

Type II turn contain proline at similar position to type I turn, but the third amino acid in type II turn is Glycine.

• Turn helps to form secondary structure and provide stability to protein, maintain its structure.
• Some aromatic amino acids that participate in $\alpha$ helix formation are tryptophan, tyrosine and phenylalanine. The Methionine, Glutamate, Leucine and alanine also has strong tendency to form a helix.  Amino acids that form b sheet includes valine, isoleucine, and proline. Among these amino acids, methionine has the highest tendency to form a helix and valine has highest tendency to form $\beta$ sheet. Minimum seven amino acids are required to form $\alpha$ helix and six amino acids are require to form $\beta$ sheet.

4.3.         Super secondary structure

They are also called as motif, it is a folding pattern involving two or more elements of secondary structure. Motif provides function to domain. They are of different types simplest among them with specific function consists of two alpha-helices joined by a loop region.

Examples of motif are :

4.3.1.     DNA binding motif :–

A motif specific for calcium bending and is present in paravalbumin, calmodulin, troponin c, and the proteins that bind calcium and thereby regulate cellular activities.

4.4.         Tertiary structure of protein -

Tertiary structure of protein is a three dimensional structure of protein. Tertiary structure is formed during protein folding. Protein folding involves the interaction of diverse R group (side chain) of amino acids. Various forces are involve in formation of tertiary structure.

1.            Hydrogen bonding

2.            Disulphide bond

3.            Electrostatic or Ionic bond

4.            Hydrophobic bonding

The protein can be classified broadly based upon the tertiary structure.

(A)          Globular proteins have a core of hydrophobic amino acid residue and a water exposed, polar, charged hydrophilic residue on surface. This arrangement makes protein soluble in water and stable in conformation. The disulphide bond  increase the stability of protein. The protein folding process in achieved with help of chaperons

4.4.1.     Importance of tertiary structure

Protein specific function depends on tertiary structure. If this is disrupted, the protein is said to be denatured and show loss its activity. eg : Denature enzymes loss its catalytic power with denatured antibodies can no longer bind with antigen. A mutation in the DNA may alter the amino acid in protein which resulted into improper folding. Misfolding protein fail to perform its function.

4.4.2.     Some of examples includes :

Cystic fibrosis is caused because of failure of the mutant CFTR protein to its target place in plasma membrane.

Diabetes is caused by improper folding of mutant versions of : V2 the vasopressin (ADH) receptor and aquaporin.

Hypercholesterolemia is caused by failure of mutant low density lipoprotein receptors to reach the plasma membrane.

Osteogenesis imperfecta is caused by failure of mutant type one collagen molecules to assemble correctly.

Mutant protein form inclusion bodies that is aggregation of insoluble protein caused by nonfunctional deposits.

4.5.         Quaternary structure :

Quaternary structure is formed by more than one polypeptide. A protein with multiple polypeptide chains is multimeric in nature . Multimeric protein  exhibit quaternary structure.

One       Subunit          Monomer

Two       Subunit          Dimer

Three    Subunit          Trimer

Four       Subunit         Tetramer

More than four–Multimers Changes in conformation within individual subunits can cause change in quaternary structure.

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