Proteins and Peptides: Structure and Biologically Active Peptides

2. Proteins Dr. Ketki Assistant Professor Department of Biochemistry Heritage IMS, Varanasi

3. Lecture 1 • Content • Proteins & Peptides • Biologically active peptides • Bonds- covalent & non-covalent • Structure of proteins- levels • Primary Structure

4. Proteins • Proteins are polymers of amino acids, linked by peptide bonds. • Linear polymers extending from amino terminal to carboxy terminal. • Carbon, hydrogen, oxygen and nitrogen. Sulfur and phosphorus are minor elements.

5. Peptide bonds α-carboxyl group of one amino acid condenses with α-amino group of next amino acid to form peptide bond NH2-CH-COOH + NH2-CH-COOH R1 R2 NH2-CH-C N- CH-COOH R1 R2 O H

6. Dipeptide Two amino acids linked by a peptide linkage forms a dipeptide Ex. Alanyl-glycine Glycyl-cysteine

7. Tripeptide Three amino acids linked by 2 peptide bonds form a tripeptide glu-cys-glycine Ala-val-phe Conventionally amino terminal amino acid is written on the left…..last one containing free carboxyl group at the right

8. Peptides with few amino acids 4-10 are generally termed as Oligopeptides. Generally polymers containing10-50 amino acids are called Polypeptides. Polypeptides containing more than 50 amino acids are called Proteins.

9. Protein with 100 amino acids will have 20100 different kinds possible. We find thousands of different kinds proteins in the cells – with different amino acid composition and sequence. They differ in shape, property, function.

10. Biologically active peptides • They are Oligopeptides which are physiologically active • Ex: Glutathione,TRH,Vasopressin, Angiotensin I & II, Bradykinin, Enkephalin,Gramicidin S, Anserine, Carnosine, etc…

11. Glutathione It is a tripeptide consisting of glu, cys & gly Gamma glutamyl cysteinyl glycine. It is an important component of cellular antioxidant defense system. It participates as cofactor in many reactions. 2 molecules of GSH can donate a pair hydrogen to reduce a substrate

12. SH CH2 CH H N O C N H C O CH2 COO - CH2 CH2 H-C-NH3+ COO - Glutamyl cysteinyl glycine

13. H2O2 + 2 GSH 2H2O + GS-SG glutathione peroxidase GS-SG 2 GSH NADPH + H+ NADP+ Glutathione reductase

14. TRH PyroGlu-His-Prolinamide: is thyrotropin releasing hormone secreted by hypothalamus. It stimulates release of Thyroid stimulating hormone (TSH) from by anterior pituitary

15. Vasopressin ( antidiuretic hormone) CYFQNCPRG-NH2 ( 9 aa) Secreted by posterior pituitary gland. It regulates water excretion by kidney Enkephalin: Peptide found in brain. It inhibits sense of pain YGGFM (5 aa)

16. Angiotensin II& I a peptide with 8 & 10 aa respectively DRVYIHPF(angiotensin II /8 aa) It stimulates release of aldosterone from adrenal cortex. Bradykinin Vasodilator peptide RPPGFSPFR ( 9 aa)

17. Gramicidin S: Antibiotic produced by bacillus brevis Contains 10 amino acids Circular Contains D phenyl alanine

18. Carnosine: β-alanylhistidine Anserine: It is N-methyl carnosine These two peptides are found in muscle. They activate myosin ATPase activity. Both are capable of chelating copper and enhance copper uptake.

19. The complex structure of proteins is stabilised by two types of bonds:- 1. Covalent or strong bonds 2. Non-covalent or weak bonds

20. Covalent Bonds These bonds are relatively strong These include:- 1. Peptide bonds 2. Disulphide bonds

21. Peptide bonds The basic linkages between two consecutive amino acids. As they are formed between α-amino groups and α -carboxyl groups, they are known as peptide bonds. All amino acids present in a protein take part in the formation of peptide bonds.

23. Disulphide bonds Formed between two cysteine residues. The sulphydryl groups of the cysteine residues are linked together. It may be formed between two cysteine residues in the same polypeptide chain or in two different polypeptide chains.

25. Non-covalent Bonds These bonds are much weaker than the covalent bonds. But they also contribute to the stability of the structure of proteins. The main non-covalent bonds in proteins are:- 1. Hydrogen bonds 2. Electrostatic bonds 3. Hydrophobic bonds 4. Van der waals forces

26. Hydrogen bonds These weak bonds are formed between two peptide linkages which may be present in the same polypeptide chain or in two different polypeptide chains. In hydrogen bonds, the hydrogen atom of the N–H group participating in a peptide bond is shared between nitrogen and oxygen atoms.

27. The nitrogen atom involved in this sharing belongs to one peptide bond, and the oxygen atom belongs to another peptide bond.

28. Electrostatic bonds Electrostatic bonds or salt bonds are formed between two oppositely charged groups. Between anionic polar side chains [Ex: glutamate,aspartate ] And cationic polar side chains [Ex: lysine,histidine,arginine]

29. Hydrophobic bonds The side chains of non-polar amino acids attract each other because of their hydrophobic nature. However, this is only a physical attraction and no chemical bonds are really formed.

30. Van derwaals forces • Weak forces of attraction between groups and amino acid side chains, both polar & nonpolar

31. Structure of proteins Proteins are linear polymers of amino acids. They have highly organized 3-dimensional structure unique to each of the proteins. Structure of proteins can be explained at 4 levels. Primary, secondary, tertiary and quaternary structures

32. Primary structure • The linear sequence of amino acids along the polypeptide chain. • Amino acids are linked by peptide bond. • Is unique to each protein. Ex: 1)Gly-Ala-Val 2) Gly –Val-Ala • It is dictated by the gene that codes for the protein

33. Primary structure…. • It dictates other levels of structure and its function. • Proteins from different organisms performing similar function have similar sequence. Myoglobin, hemoglobin, cytochrome c from different organisms have conserved primary structure.

34. Characteristics of peptide bond (Co-N) • Partial double bond character. • Rigid and planar • Trans configuration • Distance is 1.32 A. , midway between single bond(1.49 A.) and double bond (1.27 A.) • Uncharged but polar

35. No freedom of rotation around the peptide bond • -C=O and N-H groups are capable of forming hydrogen bond.

36. The backbone of peptide chain: by α carbon( Cα ) , αcabronyl carbon( Co ) , α amino nitrogen( N ). • Side chains project out from backbone • Co-N bond length= 0.132 nm • Freedom of rotation around Cα-N & Cα- Co • Angle around Cα-N= phi angle (ᴓ) • Angle around Cα- Co = psi angle (ᴪ)

37. These angles of rotation are k/a Ramchandran angles, it determines special orientation of peptide chain

39. Ramchandran Plot • Study of combination of phi and psi angles which allow and disallow the stable confirmation by the graphical representation is called Ramchandran Plot. • Discovered by G.N. Ramchandran.

41. Free rotation possible around N-Cα and Cα-C bonds

42. R1 H H O O C C NC NC C N H O H R2 H 0.36 nm

43. H N C C N C H O 0.147 0.132 α α 0.153

44. Numbering of amino acids in protein • The peptide has a free amino group at one end and a free carboxyl group at the other. • The former is known as the amino end (N-terminal end)/left side and • the latter as the carboxy end (C-terminal end)/right side.

45. Branched /circular protein • Polypeptides are linear chain • Branching point produced by interchain/intrachain disulfide bonds • Pseudopeptide ( peptide bond formed by carboxyl group,other than that present in alpha position) Ex: • Circular protein: Ex;

46. Insulin primary structure GIVEQCCTSICSLYQLENYCN FVNQHLCGSHLVEALYLVCGERGFFYTPKT 719 6 11 20

47. Insulin • β-cells of islets of Langerhans. • It has A chain(21 aa,glycine chain),B chain(30 aa,phenylalanine chain) & C-peptide(35 aa) • Bovine insulin differs from human in 3 amino acids in A chain, A8,9,10 ala,ser,val and in B chain ,B30 is ala • Porcine insulin differs in 1 amino acid, B30 Ala

48. C-Peptide A-chain B-chain

49. Human insulin

50. 1 1 A-chain -S- 6 -S–S- 7 -S- 11 19 -S S- 20 21 B-chain 30