INTRODUCTION

There are numerous ways in which protein can be necessary for our body. There are different ways in which any polypeptide can arrange to form functional structure for protein. Without this proper confirmation protein will not be able to attain its functional form. Disulfide bonds play a role in the stabilization of structure in some proteins. Hydrogen bonds and ionic interactions also contribute for stable structures.

PRIMARY STRUCTURE OF PROTEIN

Polymers of amino acid forming peptide bond connected to one another forming sequence of amino acids are referring to as primary structures of protein. Following is the example of the primary structure of protein. 

A series of amino acids joined by peptide bonds form a polypeptide chain, and each amino. A polypeptide chain has polarity because its ends are different, with an -amino group at one end and an -carboxyl group at the other. By convention, the amino end is taken to be the beginning of a polypeptide chain, and so the sequence of amino acids in a polypeptide chain is written starting with the aminoterminal residue. polypeptide chain consists of a regularly repeating part, called the main chain or backbone, Basic example of polypeptide of primary structure is :-

PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEIN

SECONDARY STRUCTURE OF PROTEIN

There are a few types of secondary structure that are particularly stable and occur widely in proteins. The most widely occurring are the α-helix and β conformations; another common type is the β turn.

  • ALPHA HELIX

Alpha helix is rigid rod like structure that forms when polypeptide chain can twist into helical forms. There are 3.6 amino acid residues per turn of the helix. And the distance between corresponding points per turn i.e., pitch is 0.54 nm. Each residue is separated by other by 0.15 nm distance. In single turn there are 13 atoms from first oxygen to last hydrogen. Hence alpha helix can also be referring to as 3.613 helix. Length of alpha helix is usually about 10-15 amino acid only. Alpha helix can be of two types right handed or left handed but right handed is more stable one. Helices can be formed from either d or l amino acid, but given helix can be entirely composed of same type of amino acids.

PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEIN
  • BETA PLEATED

In the β conformation, the polypeptide chain is forming into a zigzag fashion. Hydrogen bonds form between adjacent segments of polypeptide chain within the sheet. The individual segments that form a β sheet are usually nearby on the polypeptide chain but can also be quite distant from each other in the linear sequence of the polypeptide; they may even be in different polypeptide chains. The R groups of adjacent amino acids protrude from the zigzag structure in opposite directions, creating the alternating pattern. The distance between adjacent amino acid is 0.35nm. The adjacent polypeptide chains in a β sheet can be either parallel or antiparallel. In parallel sheet the adjacent strand runs in same direction however in antiparallel the adjacent strand run in opposite direction. Antiparallel are more stable than parallel because fully collinear hydrogen bond is formed.

PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEIN
  • TURNS

β turns are able to connect the ends of two adjacent segments of an antiparallel β sheet. The structure is a 180° turn involving four amino acid residues, with the carbonyl oxygen of the first residue forming a hydrogen bond with the amino-group hydrogen of the fourth. The peptide groups of the central two residues do not participate in any inter-residue hydrogen bonding. Gly and Pro residues often occur in β turns, the gly because  it is small and flexible, the proline because of presence of imino group . Beta  turns are commonly found in globular proteins, which have a compact folded structure.

PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEIN

TERTIARY STRUCTURE OF PROTEIN

The overall three-dimensional arrangement of all atoms in a protein is referred to as the protein’s tertiary structure. Amino acids that are far apart in the polypeptide sequence and are in different types of secondary structure may interact within the completely folded structure of a protein term as tertiary structure. The following types of covalent and non covalent interactions stabilize tertiary structures.

  1. Hydrophobic interaction major
  2. Electrostatic interaction [salt bridge]
  3. Hydrogen bond
  4. Van der waal force of interaction
  5. Covalent bond [intra chain disulphidebond]

QUATERNARY STRUCTURE OF PROTEIN

Some proteins contain two or more separate polypeptide chains, or subunits, which may be identical or different. The arrangement of these protein subunits in three-dimensional complexes constitutes quaternary structure. In considering these higher levels of structure, it is useful to designate two major groups into which many proteins can be classified: fibrous proteins, with polypeptide chains arranged in long strands or sheets, and globular proteins, with polypeptide chains folded into a spherical or globular shape. The two groups are structurally distinct. Fibrous proteins usually consist largely of a single type of secondary structure, and their tertiary structure is relatively simple. Globular proteins often contain several types of secondary structure. The two groups also differ functionally: the structures that provide support, shape, and external protection to vertebrates are made of fibrous proteins example collagen, whereas most enzymes and regulatory proteins are globular proteins example myoglobin.

PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEIN
STRUCTURE OF FIBROUS PROTEIN

PROTEIN FOLDING

Each type of protein has a particular three-dimensional structure, which is determined by the order of the amino acids in its polypeptide chain. The final folded structure, or conformation, adopted by any polypeptide chain is determined by energetic considerations: a protein generally folds into the shape in which its free energy (G) is minimized. The folding process is thus energetically favorable. Protein folding has been studied in the laboratory using highly purified proteins. A protein can be unfolded, or denatured, by treatment with solvents that disrupt the noncovalent interactions holding the folded chain together. This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape. Under the right conditions, when the denaturing solvent is removed, the protein often refolds spontaneously into its original conformation—a process called renaturation. The fact that a denatured protein can, on its own, refold into the correct conformation indicates that all the information necessary to specify the three-dimensional shape of a protein is contained in its amino acid sequence.

PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEIN

PROTEIN DEGRADATION

When protein loses its normal conformation it’s said to be denatured. It may be lost of native structure or breaking of covalent and non covalent bonds. Denature can be occur naturally or performed artificially through denaturing agent. Given below are some of main denaturing agents

  • Strong acids or base :- Change in pH results in prolongation or deprotonation of side group of amino acid which can alter the hydrogen bonding or salt bridge forming.
  • Organic solvents :- Intermolecular hydrogen bond can be formed by the reagents such as ethanol that can break or interrupt intramolecular hydrogen bond.
  • Detergent :- They are amphipathic molecules hence can disrupt hydrophobic interactions
  • Reducing agents :- It can reduces disulphide bond to sulfhydryl group can break intra or interchain disulphide bond.
  • Heavy metal ion :- Many heavy metals such as mercury or lead can affect protein structure by interrupting salt bridge by forming bond with negatively charge ion.
  • Heat :- Due to high molecular vibration at high temperature weak interaction such as hydrogen bond or van der waal interaction can be broken.

CONCLUSION

Protein is an unbranched polymer which has 4 level of organization. Folded and arrange properly for its proper structure and functional activity. Amino acids that are forming polypeptide already have signals for its proper organization. If not folded or arranged properly it can cause severe disease in our body that can have life threatening effects one such disease is Amyloid. In this disease various progressive disorders are included such as Alzheimer’s , the spongiform encephalopathy’s and type 2 diabetes.

REFERENCES 

  • Lehninger  principles of biochemistry seventh edition By  David L. Nelson and Michael M. Cox
  • Life sciences  fundamental and practices sixth edition, pathfinder publication By Pranav Kumar and Usha Mina
  • Essential cell biology (fourth edition) by ALBERTS, BRAY, HOPKIN, JOHNSON, LEWIS, RAFF, ROBERTS, WALTER

:- Article Written By Zahra Madraswala

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