12/6/12. Dr. Sanjeeva Srivastava IIT Bombay. Primary Structure. Secondary Structure. Tertiary Structure. Quaternary Structure.

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1 Dr. anjeeva rivastava Primary tructure econdary tructure Tertiary tructure Quaternary tructure Amino acid residues α Helix Polypeptide chain Assembled subunits 2 1

2 Amino acid sequence determines 3-D structure Protein folding Thermodynamics of protein folding Molecular chaperone for protein folding Protein misfolding; diseases 3 4 2

3 5 Anfinsen s experiment Denaturation Refolding 6 3

4 Ribonuclease A Urea, guanidine Hl - denaturants β-mercaptoethanol - breaks disulfide bonds 7 E R Q E T A A A K F H M D 1 20 K +H3N A N A T 30 Y K M 80 M Q N I T Q Q D T M Y Y R 70 R T N E Q N K G T K L 90 G Y N A T V P V A D F H V P V Y P N K N G N D 110 E K R A O O Q Y 100 A K T Q K P Q V T A H I V 60 Y N K I 40 V A N 4 disulfide bonds T F V H E A D V L

5 O NH2 + l H2N Urea NH2 H2N Guanidium hloride NH2 Effectively disrupts non-covalent bonds of proteins 9 HO H2 H2 ß-mercaptoethanol H leavage of disulfide bonds Large excess converts disulfides to sulfhydryls HO H2 H2 H H HO H2 H2 OH H H2 H2 10 5

6 8 M urea and β-mercaptoethanol treatment - converted native protein to fully reduced, randomly coiled polypeptide denatured - lacked enzymatic activity M Urea & ß- mercaptoethanol 95 H H 12 4 H H Native Ribonuclease Denatured reduced Ribonuclease 12 6

7

8 crambled Ribonuclease Trace of ß- mercaptoethanol 124 crambled wrong pairings, Native Ribonuclease Trace amount of b-mercaptoethanol catalyzed rearrangement of disulfide pairing 65 Urea and β-mercaptoethanol removed by dialysis Denatured ribonuclease regained activity Enzyme refolded into active form ulfhydryl groups became oxidized by air 16 8

9 Horwich et al Amino acid sequence determines 3D structure 18 9

10 Binding site Protein folding Unfolded Protein Folded Protein Polar amino acid side chains tend to gather on outside of the protein Non-polar amino acid side chains are buried inside 19 Amino Acid Abbreviation ymbol Hydrophobicity/ harge Aspar&c acid Asp D Nega&ve Glutamic acid Glu E Nega&ve Arginine Arg R Posi&ve Lysine Lys K Posi&ve His&dine His H Posi&ve Asparagine Asn N uncharged polar Glutamine Gln Q uncharged polar erine er uncharged polar Threonine Thr T uncharged polar Tyrosine Tyr Y uncharged polar ysteine ys non- polar Glycine Gly G non- polar Isoleucine Ile I non- polar Leucine Leu L non- polar Methionine Met M non- polar Phenylalanine Phe F non- polar Proline Pro P non- polar Tryptophan Trp W non- polar Valine Val V non- polar Alanine Ala A non- polar 20 10

11 Overall increase in an entropy drives the folding process Folded conformation in aqueous environment 21 Protein denaturation by chemical and heat Expose to high concentration of Urea Remove Urea Purified Protein islolated from cells Denatured Protein Original conformation of protein re-forms 22 11

12 100 Protein unfolded 0 Denaturant A sharp transition from native (folded) to denatured (unfolded) form Protein unfolded 50 0 Denaturant 24 12

13 Many unstable conformations One stable conformation 25 Folding is a cooperative process In general, any protein adopts only one conformation Or, few very closely related characteristic functional conformations native state 26 13

14 27 Amino acid sequence dictates protein structure knowledge-based and Ab initio from the beginning prediction to predict protein structure 28 14

15 29 Hydrophobic amino acids are driven to associatehydrophobic collapse Thus, overall increase in an entropy drives the folding process 30 15

16 Molten globule state

17 Molten globule state

18

19 Protein folds into a single, energetically favorable conformation, specified by its amino acid sequence A protein may fold into alternative 3D structure due to mutations, inappropriate covalent modifications 37 Newly ynthesized Protein Protein aggregate orrectly folded without help orrectly folded with help of molecular chaperone Incompletely folded forms digested by proteasome Increasing Time 38 19

20 Accumulation of misfolded protein or proteolytic fragments results into few degenerative diseases haracterized by presence of insoluble protein plaques in organs such as brain and liver 39 axis Fibril 40 20

21 Anfinsen experiment Protein folding Thermodynamics of protein folding Molecular chaperons Protein mis-folding and diseases 41 Horwich A. Protein aggregation in disease: a role for folding intermediates forming specific multimeric interactions. Volume 110, Issue 9 (November 1, 2002). J lin Invest. 2002;110(9): doi: /ji Harold A. cheraga. Protein structure and function, from a colloidal to a molecular view. arlsberg Research ommunications. January 1984, Volume 49, Issue 1, pp Berg J., Tmyoczko J. & tryer L., Biochemitry fifth ed., W. H. Freeman & company, IBN: Nelson D. & ox M.,Lehninger, Principles of Biochemistry fourth ed., W. H. Freeman and company. IBN: X. reighton T. E., Protein folding first ed., W. H. Freeman and company, IBN: X. Voet D. & Voet J., Biochemistry fourth ed., Wiley, IBN: X. 21

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