How Proteins are folded into 3D functional structure

1. S.Prasanth Kumar, Bioinformatician Proteomics The Mechanism of Protein Folding S.Prasanth Kumar Dept. of Bioinformatics Applied Botany Centre (ABC) Gujarat University, Ahmedabad, INDIA www.facebook.com/Prasanth Sivakumar FOLLOW ME ON ACCESS MY RESOURCES IN SLIDESHARE prasanthperceptron CONTACT ME [email_address]

2. Alignment scoring schemes Protein folding Physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure Folded proteins Hydrophobic core -> side chain packing stabilizes the folded state Charged or polar side chains occupies the solvent-exposed surface -> interact with surrounding water

3. Alignment scoring schemes Important driving force in the folding process: Minimize the number of hydrophobic side-chains exposed to solvent Formation of intramolecular hydrogen bonds Protein Stability: Protein folding Strength of hydrogen bonds depends on their environment H-bonds in a hydrophobic core contribute more than H-bonds exposed to the aqueous environment to the stability of the native state

4. Alignment scoring schemes Classical Models If folding is driven by local interactions, secondary structure formation precedes collapse

5. Alignment scoring schemes Classical Models If folding is driven by nonlocal interactions, collapsed rives concurrent secondary structure formation

6. Alignment scoring schemes Perturbed Model Energies of (HH, PP,HP) contacts are (-1, 0,0) Contacts (AA, BB, AB) have energies (-3, -3, -1) Native structures of HP models have hydrophobic cores, whereas the perturbed homopolymer model tend to separate into two sides with different monomer types hydrophobic polar

7. Alignment scoring schemes Sidechain Model Linear chain lattice model (LCM) to represent the main chain (A) A sidechain model (SCM) is created by attaching a single sidechain unit to each main-chain monomer To represent side-chain rotameric DOF, each sidechain unit has the freedom to occupy any one empty lattice site

8. Alignment scoring schemes Molecular Chaperons Specialized proteins called chaperones assist in the folding of other proteins

9. Alignment scoring schemes Molecular Chaperons A well studied example is the bacterial GroEL system, assists in the folding of globular proteins. In eukaryotic organisms chaperones are known as heat shock proteins (HSP) Most globular proteins are able to assume their native state unassisted Chaperone-assisted folding is required in the crowded intracellular environment to prevent aggregation Used to prevent misfolding and aggregation which may occur as a consequence of exposure to heat or other changes in the cellular environment

10. Alignment scoring schemes The molecular surface of the immunodominant heat-shock chaperonin-10 of mycobacterium leprae Molecular Chaperons

11. Alignment scoring schemes Transitioning to the Native State Establishment of regular secondary and supersecondary structures, particularly alpha helices and beta sheets, and afterwards tertiary structure Amino acid sequence Formation of quaternary structure usually involves the "assembly" or "coassembly" of subunits that have already folded The regular alpha helix and beta sheet structures fold rapidly because they are stabilized by intramolecular hydrogen bonds

12. Alignment scoring schemes Transitioning to the Native State Finally, energetically favorable native conformation,. Folding may involve covalent bonding in the form of (disulfide bridges) and/or the formation of metal clusters Pass through an intermediate "molten globule" state

13. Alignment scoring schemes Levinthal Paradox Total number of possible conformations of a polypeptide chain is large Takes an astronomical length of time to find correct structure by means of a systematic search of all conformational space Recent experimental and theoretical studies suggest no such apparent paradox Stochastic Approach Folding process does not involve a series of mandatory steps between specific partially folded states, but rather a stochastic search of the many conformations accessible to a polypeptide chain

14. Alignment scoring schemes Stochastic Search Conformational space accessible to the polypeptide chain is reduced as the native state is approached Inherent fluctuations in the conformation of an incompletely folded polypeptide chain enable even residues at very different positions in the amino acid sequence to come into contact with one other Attempt to find the lowest energy structure Sequences that have been selected during evolution to fold to globular structures, and requires only a very small number of all possible conformations needs be sampled during the search process

15. Alignment scoring schemes Stochastic Search Free energy (F) of the system = a function of the total number of contacts between residues (C) and the number of contacts that correspond to those of the most stable native structure(Q0)

16. Alignment scoring schemes Contact Order Correlation between the folding rates of small proteins and the “ contact order” of their structures Contact order = the average separation in the sequence between residues that are in contact with each other in the native Structure This correlation appears to be largely independent of other details of the protein folds, such as their size and secondary structure content (i.e. the helices and sheets that are seen in almost all native protein structures) Due to very different architectures of secondary structure

17. Alignment scoring schemes Energy Landscape

18. Alignment scoring schemes Fast Track “ fast track” in which the two domains fold simultaneously and produce an intermediate (alpha/beta) and finally converts into native state

19. Alignment scoring schemes Slow Track Folding from this intermediate involves either a transition over a higher barrier, or partial unfolding to enable the remainder of the folding to take place along a fast track “ slow track” - chain becomes trapped in a long-lived intermediate state with persistent structure only in the alpha domain

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