Ppi

428 views

Published on

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
428
On SlideShare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
25
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Ppi

  1. 1. Atomic Structure of protein-protein interactions
  2. 2. Overview
  3. 3. The peptide bond(----ALA-HIS-GLY-ILE-LEU-PHE-TYR-LYSGLY---)n
  4. 4. CATH: Class Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). SCOP: Structural Classification of Proteins
  5. 5. Quaternary Structure Homodimers TetramersIcosahedral virus capsids Heterocomplex
  6. 6. Atomic resolution structures of biomolecules are stored at the Protein Data BankContains 60000 structures (mostly determined by X-ray crystallography and NMRAbout 3-5 new structures per day year
  7. 7. Application of Computational tools to solve specific biological problemsSpecific protein-protein interactions is a rule rather than exception and non- specific interactions can lead to several disease Protein-protein interactions in binary complexes:  What makes the specificity?  Discriminate specific and non-specific interfaces
  8. 8. Specific and non-spacific interactionsHomodimers HeterocomplexCrystal-packing interfaces of monomeric protein Is that pair a biological dimer? The non-covalent interactions that hold crystals together: are the same as in protein-protein complexes and oligomeric proteins BUT they are not subject to natural selection, thus, biologically non- specific.
  9. 9. The dataset and methodology Non-redundant dataset (taken from Protein Data Bank) • 70 Protein-protein complexes (Chakrabarti and Janin, 2002) • 120 Homodimers (Bahadur et al., 2003) • 183 Crystal packing interfaces of 145 monomeric proteins 2fold related interface =105 Non-2fold related interface=83 (Bahadur et al., 2004)Tools for the analysis• Structural features Solvent accessible surface are, Buried atoms, core-rim, atomic density• Physico-chemical properties Polar-non polar interactions, residue composition, hydration
  10. 10. Interface area definition Molecule A Molecule B Complex AB w w Interface area (B) = ASA(A) + ASA(B) – ASA(AB) (Lee & Richards, 1971) (‘Naccess’ by Hubbard SJ. 1992)Interface atoms and residues are all atoms and residues that lose ASA in the complex and contribute to B
  11. 11. Protein-protein interfaces Dimeric k-bungarotoxin (1kba) BSA = 1000 Å2 (Bahadur et al., 2004) Crystal dimer Pokeweed antiviral protein (1qci) BSA = 1000 Å2 (Bahadur et al., 2004)
  12. 12. Size of the protein-protein interfaces 70 No two-fold Interface Interface Ref. Crystal dimers area B 60 Homodimers Complexes (s.d.) 50 Homodimer 3880 Bahadur et Interfaces 40 al., (2003) (±2200) 30 20 Chakrabarti Complex 1910 & Janin, 10 (±760) (2002) 0 800 1000 1600 2400 3200 >3600 2 Interface area B (Å ) Crystal- 1510 Bahadur et. al., (2004) packing3% Homo +Complex 16% Crystal (±520) 30% Crystal 1200 Å2 > 2000 Å2 Standard size interface (Lo Conte et al, 1999) Interfaces formed in protein-protein complex are of ‘Standard size’ Homodimer interfaces are very large compared to crystal-packing interfaces
  13. 13. Non-polar interface area No two-fold 60 fnp*B = Interface area contributed by the C- Crystal dimers Homodimers Complexes containing groups only / Total interface area 40 Interfaces fnp* B (%) 20 Homodimer 65 Complex 58 Crystal-packing 58 0 >80 40 50 60 70 80 Non-polar fraction of the interface area (%) 0 Homo + 6% Crystal 0 Complex < 50 > 70Homodimers have hydrophobic interfaces compared to protein-protein complexes and crystal- packing interfaces.
  14. 14. Clustering of Interface atoms: single or multiple patch?…we cluster interface atoms by the averagelinkage method on a purely geometric basis. 1 3A threshold distance dM must be used in clustering. 4It is set to half the diameter of the interface; 5 2dM= 15 Å in a typical protein-protein complex, 22Å in homodimers. d13+d14+d15+d23+d24+d25 dM = 6(Chakrabarti & Janin, 2002)(Bahadur et. al., 2003)
  15. 15. Standard size single patch and multi-patch interfacesCytochrome c’(2ccy) B (Å2) #res #atoms Homodimers (70) 2740 74 280 Complex (46) 1560 47 170 95% of the crystal-packing interafces are of ‘single patch’Thrombin-ornithodorin(1toc) B (Å2) #res #atoms Homodimers (35) 4760 (0.67, 0.33) 126 486 Complex (18) 2510 (0.63, 0.37) 73 217 Multi-patch interfaces contains at least one large patch with ‘standard size’
  16. 16. Evaluating packing density of the interfaceHomodimer interface Crystal-packing interface 1qci, Antiviral1kba, Kappa- protien complex-bungarotoxin ed with adenine Ai Local density index Global density index count the number ni of interface atoms Calculate the principal moments of inertia Na2, within D = 12 Å of interface atom Ai Nb2, Nc2 of the set of interface atoms; the inertia ellipsoid has half-axes a>b> c average ni over all interface atoms the area at the equator is A=πab LD = Σ (ni) / N GD = N/A B(Å2) LD GD 1kba 998 34 0.95 1qci 994 14 0.31 Specific interfaces are well packed compared to non-specific interfaces
  17. 17. Buried atoms at the interface No two-fold Partially buried 50 Crystal dimers Homodimers w interface atoms Complexes 40 Interfaces 30 20 10 Fully buried 0 interface atoms >50 10 20 30 40 50 Fraction of fully buried interface atoms (%) 87% Crystal- 71% Homodimer + Number of fully buried interface atoms fbu= Total number of interface packing Protein-protein complex fbu<30% fbu>30% atomsSpecific interfaces: 34-36% of the interface atoms are fully buried Non-specific interfaces: this fraction is only 21%
  18. 18. Dissecting the interface: Core and Rim A Core residue: with at least one fully buried atom Rim residue: Contain accessible atoms only d allCI2 inhibitor bound to Bsubtilisin (2sni) Enolase (1ebh) d72% (B) in core 74% (B) in B core B A Core (B%) Homodimers 77 Complexes 72 ‘Core’ region is absent in crystal-packing interfaces
  19. 19. Amino acid composition of the specific interfaces The amino acid composition of the interface core and rim D E K SNumberwisefi = number of core (rim) residues of type i / T FYWM total number of core (rim) residues IL GAreawisef0i = interface area contributed by core (rim) residues of type i / total core (rim) interface area Core: aromatic and hydrophobic residues are abundant at the Rim: polar and charged residues
  20. 20. Composition of interface relative to surface Euclidean distance (Δf) between amino acid compositions of the interface and rest of the protein surface: (∆f)2 = 1/19 ∑ i=1 to 20 (ki – k0i)2 ki = composition of amino acid residues at interface k0i = composition of amino acid residues at surface 1.6 Monomers Interface Surface 2.1 0.5 Homodimers Interface Surface 3.4 Homodimer: interface differs from the protein surfaceCrystal-packing: Difference is negligible
  21. 21. Residue Propensity (RP) scoreRP = Σ ni * Pi , ni number of residues in the interface No two-foldPropensity of a residue to be 50 Crystal dimersat homodimer interface 40 Homodimers ComplexesPi = ln (ki/k0i) Interfaces 30ki = composition of amino acid 20residues at interface 10k0i = composition of amino acidresidues at surface 0 <-6 -4.5 -1.5 1.5 4.5 >6 Residue Propensity Score (RP) Residue propensity Only 5% 5% Crystal score (RP) Homo+Complex Homodimer 4.3 (±4.9) Complex 0.9 (±2.3) Crystal-packing -1.1 (±2.7) < -3 >3 Specific interfaces have +ve RP and non-specific interfaces have –ve RP score
  22. 22. Identifying homodimers and crystal dimers 50 Use a combination of parameters 40 Fraction of fully buried atoms (fbu)Fraction of buried atoms (%) Non-polar interface area (fnp*B) 30 U Residue Propensity score (RP) 20 Classification fnp*B (Å2) fbu (%) RP 10 Monomer ≤ 800 or ≤ 2000 and ≤ 20 M D Homodimer ≥ 2000 or 0 0 1000 2000 3000 4000 ≥ 800 and ≥ 30 Non-polar interface area ( Å2 ) Undecided 800-2000 and 20-30 < 1.5 (M) ≥1.5 (D) Monomer 95% Homodimer 93%
  23. 23. Structural rule of specificity  Minimum size: specific protein-protein interfaces have B ≥ 800 Å2 Most crystal packing interfaces are below that size, which may be the minimum for a biologically relevant macromolecular interaction.  Standard-size (1200-2000 Å2) interfaces make stable, specific and fully functional interactions  . Specificity is expressed in the following features: • close-packed interface atoms • a high fraction of buried atomsA combination of parameters, non-polar interface area, fraction of fullyburied interface atoms and residue propensity score discriminates thespecific interfaces from the non-specific ones with a 95% success rate.
  24. 24. ProFace: http://www.boseinst.ernet.in/resources/bioinfo/stag.html

×