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Protein structure and ramachandran plot
- 1. PROTEIN STRUCTURE AND RAMACHANDRAN PLOT -AMIT TIWARI 1
- 2. AMINO ACIDS Buildingblocks of proteins α-amino acid consists of a central carbon atom, called the α carbon, linked to an amino group, a carboxylic acid group a hydrogen atom, and a distinctive R group Twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity are commonly found in proteins 2
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- 4. PRIMARY STRUCTURE OFPROTEINS Sequence of the amino acid residue Short chain of amino acids linked by peptide bonds and having a defined sequence is called a peptide Longer chains are referred to as polypeptides Peptides generally contain fewer than 20–30 amino acid residues, whereas polypeptides contain as many as 4000 residues. biochemistry3rst.wordpress.com 4
- 5. SECONDARY STRUCTURE OFPROTEINS Consists of several repeating units namely alpha helix and beta pleated sheets Patterns are stabilized by hydrogen bonds phi angles and psi bond angles are equal in a polypeptide segment Alpha-helix is a rigid, rodlike structure that forms when a polypeptide chain twists into a right-handed helical conformation Zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats 5
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- 7. TERTIARY STRUCTURE OFPROTEINS Describes the global conformation of a protein Determined by ionic interactions between charged amino acid R-groups, by hydrophobic interactions and by hydrogen and van der Waals bonds Stabilised by S-S bonds between Cys residues Lacasamorett.com 7
- 8. QUATERNARY STRUCTURE OF PROTEINS Made up of multiple polypeptide chains Subunits may be the same (as in a homodimer) or different (as in a heterodimer) Stabilized by various interactions, including hydrogen-bonding, disulfide-bridges and salt bridges 8
- 9. RAMACHANDRAN ANGLES Twoangles define the conformation of a residue in a protein and are called the Ramachandran angles, ψ (psi) and φ (phi) ψ (psi) angle is formed between the α-carbon to the carbonyl group (at the C-terminus) of the amino acid residue can rotate and turn the whole plane of the amide group, which includes the carbonyl carbon, in a 360-degree range φ (phi) Angle is formed between the nitrogen (at the N-terminus) to the α-carbon of the amino acid residue can rotate and turn the whole plane of the other amide group, which includes the nitrogen, in a 360-degree range. 9
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- 11. RAMACHANDRAN PLOT Developedby Gopalasamudram Ramachandran, an Indian physicist, in 1963 Way to visualize dihedral angles ψ against φ of amino acid residues in protein structure Many combinations of angles in a polypeptide chain are forbidden because of steric collisions between atoms Two-dimensional plot shows the allowed and disfavored values of ψ and φ 11
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- 13. CONCLUSION Proline isoften found at the end of helices and functions as a helix disruptor. Glycine does not have a complex side chain, which allows high flexibility in the polypeptide chain as well as torsion angles. Many combinations of angles in a polypeptide chain are forbidden because of steric collisions between atoms Functionally relevant residues are more likely than others to have torsion angles that plot to the allowed but disfavored regions of a Ramachandran plot. 13
- 14. REFERENCES BOOKS REFERRED:- DonaldVoet, Judith G Voet, Biochemistry, 4th edition, Wiley, 2011 Engelbert Buxbaum, Fundamentals of Protein Structure and Function, Springer,2007 David.E.Metzler, Biochemistry- The chemical reactions of living cell, 2nd edition, Elsevier David.L.Nelson, Michael.M.Cox, Lehninger- Principles of Biochemistry, 4th edition, W.H.Freeman, 2005 WEBLINKS :- https://proteinstructures.com www.cryst.bbk.ac.uk https://swissmodel.expasy.org https://www.cgl.ucsf.edu 14
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