Packing, Cavities

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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

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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)

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Molecular Surface (Connolly)
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Alpha-shape theory

• Voronoi methods
• Liang and Edelsbrunner
• pockets, pockets, depressions depends on width
  of opening

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Packing Density
from Richards (1977)
crambin (bluevdw, redinterstitial)
data on compressibility?
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• 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)
• P0.76 for hex-packed spheres
• P0.74 for protein interiors
• distribution of number/size of voids is more
  variable, like a liquid
• surface area scales linearly with volume, instead
  of A a V-2/3

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Clefts/Active Sites

• Liang Edelsbrunner, Woodward (1998)

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• Laskowski, Luscombe, Swindells, and Thornton
  (1996)

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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
  1.50.6 kcal/mol. This is additive.
• double-mutants?
• temperature-sensitive mutants?

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Side-chain contact profiles

• Sippl knowledge-based potentials
• Subramaniam PDFs
• dependence radial distance, sequence separation

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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)
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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 doesnt have to be
  perfect
• surface normals
• R Norel, SL Lin, HL Wolfson and R Nussinov

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• 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 1600400Å2

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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 DG
• charge correlations -0.1..0.1 (insignificant)
• electrostatic potential correlations 0.1..0.7
  (significant)

• steering and diffusion (Kozak et al., 1995)

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• Jones and Thornton Patch Analysis,
• PP-interface prediction

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Examples of P-P interactions

• b-lactamase/BLIP one of the tightest
• antibody-antigens (HYHel5)
• SH2/SH3 and tyrosine kinases
• PDZ domains
• calmodulin
• proteases, kinases (recognizecatalyze)

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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

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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 greencontact purpleconse
rved
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Crystal-lattice Contacts

• Carugo and Argos (1997)
• small 45lt100Å2, 8gt500Å2
• properties like rest of surface, so probably
  random
• induced changes (rms)?

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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, Da15º

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r-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

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• 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)