1. Packing, Cavities atomic radii, contact- distance profiles cavities P-P interactions crystal contacts solvent channels de-stabilizing mutations in core (TS mutants?) entropy effects on surface

2. Surface Calculations Lee & Richards - solvent accessible surface –expanded atom spheres, reentrant surfaces typical water probe radius: 1.4A computation: grid points vs. tangents (algebraic/analytic)

3. Molecular Surface (Connolly)

4. Alpha-shape theory Voronoi methods Liang and Edelsbrunner pockets, pockets, depressions – depends on width of opening

5. Packing Density from Richards (1977) crambin (blue=vdw, red=interstitial) data on compressibility?

6. Jie Liang and Ken A. Dill (BiophysJ, 2001). Are Proteins Well-Packed? 636 proteins; 1.4A probe radius proteins are dense (like solids), yet atoms are arranged like liquids (without voids) P=0.76 for hex-packed spheres P=0.74 for protein interiors distribution of number/size of voids is more variable, like a liquid surface area scales linearly with volume, instead of A  V -2/3

7. Clefts/Active Sites Liang Edelsbrunner, Woodward (1998)

9. Laskowski, Luscombe, Swindells, and Thornton (1996)

10. De-stabilizing mutations in core cavities, tolerance, re-packing Serrano L., Kellis J., Cann P., Matouschek A. & Fersht A. (1992) In barnase, 15 mutants were constructed in which a hydrophobic interaction was deleted strong correlation between the degree of destabilization (which ranges from 0.60 to 4.71 kcal/mol) and the number of methylene groups deleted average free energy decrease for removal of a completely buried methylene group was found to be 1.5±0.6 kcal/mol. This is additive. double-mutants? temperature-sensitive mutants?

11. Side-chain contact profiles Sippl – knowledge-based potentials Subramaniam – PDF’s dependence: radial distance, sequence separation

12. Protein-protein interactions flat and hydrophobic? Janin Jones and Thornton (1996), PNAS – data on flatness, H- bonds which is predominant: H- bonds vs. salt-bridges vs. hydrophobic interactions? (homodimers)

13. Complementarity of P-P interfaces shape complementarity –measure “gaps” or voids –cavities at interfaces (Hubbard and Argos, 1994) more common than in core suggests complementarity doesn’t have to be perfect –surface normals: R Norel, SL Lin, HL Wolfson and R Nussinov

14. LoConte, Chothia, and Janin (1999), JMB. –The average interface has approximately the same non-polar character as the protein surface as a whole, and carries somewhat fewer charged groups. –However, some interfaces are significantly more polar and others more non-polar than the average. –1/3 of interface atoms becomes completely buried; packing density is similar to core (like organic solids) –in high-res structures, remainder of space is filled in by water molecules (making H-bonds) –size for “typical” interfaces: 1600±400Å 2

15. Electrostatic Complementarity McCoy et al. (1997) –defined two correlation coefficients between surfaces (summed over contacts): charge complementarity (ion pairs), and electrostatic potentials –depends on assignment of partial charges, solvation... –examine effect on  G –charge correlations: -0.1..+0.1 (insignificant) –electrostatic potential correlations: 0.1..0.7 (significant) steering and diffusion (Kozak et al., 1995)

16. Jones and Thornton – Patch Analysis, PP-interface prediction

17. Examples of P-P interactions  -lactamase/BLIP – one of the tightest antibody-antigens (HYHel5) SH2/SH3 and tyrosine kinases PDZ domains calmodulin proteases, kinases (recognize+catalyze)

18. beta-sheet extension arylamine N-acetyltransferase (nat) –acetylates isoniazid in M.smegmatis –pdb: 1W6F –active in solution as both monomer and dimer –lower surface area, but many H-bonds

19. PPI Trivia obligate vs. transient complexes - affinity differences between antigen-antibody, protease-inhibitor, and rest of complexes induced conformational changes allostery evolutionary conservation at interfaces (Caffrey et al. 2004), correlated mutations? mutational hot spots, evolutionary trace (Lichtarge) why are homodimers so common? (Lukatsky et al, 2007) succinyl-CoA synthetase green=contact purple=conserved

20. Crystal-lattice Contacts Carugo and Argos (1997) small: 45% 500Å 2 properties like rest of surface, so probably random induced changes (rms)?

21. Protein-Protein Docking FTDOCK - Gabb, Jackson, and Sternberg (1997) –use Fourier transform to evaluate shape correlation function –correlation function includes shape and electrostatic complementarity of surfaces –try 6912 rotations,  =15º

22.  =-15 grid nodes within 1.8A of protein atom are “inside” Multidock (Jackson, Gabb, Sternberg, 1998) –what about induced fit? alternative side-chain rotamers? domain rotations? –need refinement to do scoring of complexes, increase sensitivity to recognize correct interaction –add term for solvation energy (soft-sphere Langevin interactions between solvent grid points and surface side-chains) –sample different rotamers –Betts & Sternberg (1999) – induced fit at interfaces side-chain and backbone movements

23. GRAMM (Vakser) –low resolution protein docking –maybe removing details will help... –search 6D space for maximal surface overlap (20º rotations) –intermolecular overlap function –evaluated on a coarse 7Å grid PatchDock, FireDock (Nussinov & Wolfson)