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Physical forces that stabilise the native structure of proteins

Physical forces that stabilise the native structure of proteins. Inter-University DEA/DES Bioinformatics 2000-2001 Shoshana J. Wodak, SCMBB-ULB. What determines the stability of the Native state of proteins??. Features of the native state :. -well defined 3D structure, -melting t,

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Physical forces that stabilise the native structure of proteins

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  1. Physical forces that stabilise the native structure of proteins Inter-University DEA/DES Bioinformatics 2000-2001 Shoshana J. Wodak, SCMBB-ULB

  2. What determines the stability of the Native state of proteins?? Features of the native state: -well defined 3D structure, -melting t, -Isoelectric point (PI) -Some characterised molecular function

  3. Denatured state (D) Native state (N) C C N N N C C N N C Stability of the native state is defined as the difference in free energy between the native and denatured states

  4. The various physical contributions to the stability of the native state Different physical forces, which sometimes counteract and compensate one another, contribute to the stability of the native state of proteins. Somewhat artificially, one can group them into the following main contributions: -Hydrophobic effect -Electrostatic interactions between charged and polar groups -van der Waals interactions -Conformational (chain) entropy

  5. The hydrophobic effect H H H H H H H H H H H H H H H H H H - H + H H H H H H + H H H H - H H H H H H H H H H H Polar solute Non-polar solute The dissolution of a non-polar solute in water is unfavourable The dissolution of a non-polar solute in water is unfavourable

  6. The hydrophobic effect Non-polar solutes prefer to interact with each other than with water, because this reduced the contact surface of the solute with the solvent. For a polypeptide, this means that hydrophobic sidechains such as Val, Ile, Leu,Phe, would tend to be buried in the protein interior. N D

  7. The hydrophobic effect The free energy gain from burying a hydrophobic group is proportional to the surface area buried Calculating the surface area in contact with solvent (Lee & Richards, 1971)

  8. The hydrophobic effect DGtransfer DGtransfer= -g ASA g = 25 cal/Å2 ASA(Å2) Linear relation between the solvent accessible surface area and the transfer free energy of amino acids (Chothia, 1972)

  9. Van del Waals interactions

  10. The Ramachandran map Dipeptide unit

  11. The Ramachandran map (further details)

  12. Electrostatic interactions Coulomb’s law Electrostatic energy of interaction, between charged and polar groups Electric field (vector) Electrostatic potential Electrostatic potential (scalar), computed using a continuum model to represent the surrounding water displayed on molecular surface

  13. Electrostatic interactions Coulomb’s law: rij qj qi D is the dielectric constant of the medium (here Water). It is a macroscopic property of the medium. It results from two main physical properties: 1-Polarisation: dynamic reorientation of the dipoles of the mobile solvent around the charge - +

  14. Electrostatic interactions The second origin of the dielectric constant D is: 2- Electronic Polarisability: The distorsion of the electronic cloud of the atom or molecule due to the presence of other dipoles

  15. Electrostatic interactions Electrostatic interactions are not only formed between charges But also between neutral (uncharged) polar atoms. These are The interactions between dipoles Example of a dipole: the dipole of the peptide group: d- Ca Ca O O C N C N Ca H Ca H d+ The dipole moment: m= Z. d Z= excess charge d= excess charge separation m= 3.5 Debye (units for measuring dipoles) 1 Debye = 10-18 esu.cm

  16. Hydrogen bonds: a special case of electrostatic interactions H-bond geometry A-H + B a is close to 180º (180 ±30º) d depends on the donor-acceptor pair N-H--O 2.55 - 3.04 Å O-H--N 2.62 - 2.93 Å O-H--O 2.65 - 2.93 Å

  17. Native state (N) Denatured state C C N N N C C N C N N C Size of cavity in solvent~6500Å2 Average size of cavity in solvent :20,500Å2 DS chain: significantly decreased, due to the well defined conformation DS chain: large, due to the large number of different conformations Non-bonded interactions: intra-molecular Non-bonded interactions: inter-molecular Compact structure Non compact structure

  18. Contributions to the stabilisation free energy of a soluble monomeric protein of 100 residues Native state (N) Denatured state (D) DGN/D= DGh + DGc + DGnb DGh = ~25 cal/mol/Å2 x (20,500 - 6,500)Å2 ~ -350 kcal/mol (if denatured chain completely extended) (if denatured chain partially folded) ~ 0.8 x-350 = -280 kcal/mol DGc = ~2.5-3.5 kcal/mol/residue x 100 residues ~ +300 kcal/mol DGnb= very small overall ~-5-10kcal/mol DGN/D= ~ -10-15 kcal/mol

  19. Protein folding Energy landscape is funnel shaped D T* DE DGa N DGa’ D 2 state system DG N DG is usually small, it is around ~12±5 kcal/mol DE, is much larger, can be as large as ~100 kcal/mol

  20. Specificity of intermolecular interactions Protein 2 Protein 1 protein-ligand protein-protein protein-DNA

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