ForcesElectrostatic InteractionspKa estimation (protonation state)PROPKAHydrogen BondingSlide 6Can the lone-pair on sulfur in Met and Cys act as an H-bond acceptor?p-p interactionsCation-p interactionsVDW interactionsHydrophobic EffectForces•inter-atomic interactions–electrostatic - Coulomb's law, dielectric constant–hydrogen-bonds–charge-dipole, dipole-dipole, dipole-quadrapole–polarizability–van der Waals, London dispersion (stickiness)–cation-pi (Arg/Lys to aromatic)–aromatic ring-stacking (Phe, Tyr, Trp, His)•hydrophobic effect – driving force•enthalpy balanced against entropy– G=H-TS– H adds contributions from 100s of interactions at ~1kcal/mol each–yet net stability of proteins is often G ~ 15 kcal/molElectrostatic Interactions•formal charges–Arg, Lys: +1–Asp, Glu: -1–His=0 or +1?•Coulomb’s law, range•dielectric constant–water: = 80–vacuum: = 1–protein interior: = 2-4? (due to dipoles)•solvent screening, ionic strength •salt bridges in proteins–strength: ~1kcal/mol (Horowitz et al., 1990) (desolvation effects)•(later: potential surface calculation, Poisson-Boltzmann equation)Warshel, Russell, and Churg (1984) -• without solvation effects, lone ionized groups would be highly unfavorable to bury in non-polar environments, and salt bridges would predominate folding with G=~-30kcal/mol• with “self-energy”, G=~1-4kcal/molpKa estimation (protonation state)•ionizable residues: Arg, Lys, Asp, Glu, His, Nterm, Cterm•Cys, Tyr can also get deprotonated•H++: solve Poisson-Boltzmann equation–protonation state depends on energy of charge presence in local electrostatic potential field–reflects neighboring charges, solvent accessibility–self-energy (Warshel et al., 1984)•Henderson-Hasselbach equation•interactions between sites•Monte Carlo search (Beroza et al 1991)•Onufriev, Case & Ullman (2001) – can do orthogontal transform to identify independently titrating pseudo-sites•conformational changes (Marilyn Gunner) – it helps if side-chains can re-orienttwo interacting sites withintrinsic pKa’s of 7.0 and 7.1PROPKA•empirical rules (Li, Robertson, Jensen, 2005)–pKa = model + adjustments–1. hydrogen-bonds–2. solvent exposure–3. nearby charges•iterative search: deprotonate side-chain with lowest pKa first, then determine effect on rest...•dipole-dipole interactions•donors and acceptors•Stickle et al. (1992), Baker and Hubbard (1994)•~1-5 kcal/mol (Pace)•distance, geometric dependence of strength–avg. distD-A = 2.9±0.1 Å–think of tetrahedral lone-pair orbitals on O•distribution in proteins:–backbone >C=O..H-N< (68.1%)–>C==O..side chain (10.9%)–>N-H..side chain (10.4%)–side chain--side chain hydrogen bonds (10.6%)Hydrogen BondingdistD-A•parameters for H-bond energy term in crystallographic refinement (Michael Chapman)•Cys often acts as a donor in H-bonds–Cys, Met rarely participate in H-bonds as acceptor–more often involved in VDW interactions (hydrophobic)•“Hydrogen bonds involving sulfur atoms in proteins”, Gregoret..(2004).–Met as acceptor, <25%–free Cys: donor ~72%, acceptor ~36%•Non-hydrogen bond interactions involving the methionine sulfur atom. Pal D, Chakrabarti P. (1998)–Out of a total of 1276 Met residues, •22% exhibit S O interaction (with an average distance 3.6A), ⋅⋅⋅•8% interact with an aromatic face (S-aromatic-atom dist. being 3.6A) •9% are in contact with an aromatic atom at the edge (3.7A).Can the lone-pair on sulfur in Met and Cys act as an H-bond acceptor? interactions•Misura, Morozov, Baker (2004)•anisotropy of side-chain interactions•geometry: preference for planar (face-on) interactions•strength?–FireDock uses: E=-1.5..-0.5 kcal/mol for contact dist 5.5-7.5Å Cation- interactions•Gallivan and Dougherty (1999)•3.6-3.8Å, face-on vs. edge-on •frequency: ~1 per 77 residues (1/2 as common as salt bridges)•strength: 0-6 kcal/mol? nicotinic acetylocholine receptorquadrupole momentVDW interactions•van der Waals forces: stickiness–~0.1kcal/mol per contact–induced polarization, London dispersion forces–typically modeled with 12-6 Lennard-Jones potential–1/r6 attractive, 1/r12 repulsive–minimum at around sum of VDW radiiHydrophobic Effect•Tanford, Kauzmann (1950s)•burial of hydrophobic residues to avoid disruption of solvent H-bond networks–collapse of hydrophobic core–similar to oil-water phase separation; micelle formation; cause of surface tension•solvent layer around crambin (0.88Å): clathrate cages (pentagonal rings)•balance with other forces–desolvation of backbone/side-chains–reduction in entropy–dependence on temperature,
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