* 1 kcal/mol ~ 4 kJ/mol
* H-bond (O-H....N) is about 7 kcal/mol
* bond length is from H-donor to H-acceptor
* London forces, a special type of van der Waals attraction, is when two aromatics are on top of each other, induced dipoles
* charge-charge (electrostatic) strongest IN VACUUM F=kq1q2/r^2*e (Coulomb's Law) e = dielectric, in H2O, e ~ 80, interior of protein e ~ 2 (almost vacuum)
* dipole(mu) (permanent and induced), diff. in electronegativity, Molecules with no netchargebut with asymmetric distribution of charge (e.g. CO or H2O) –Polar (permanent dipole),
* peptide bond has dipole, eg H2O, vector toward q+, mu = qx q=charge, x=distance
* van der Waals (short range than charge-charge), very weak but plays important role in stability
* van der Waals (vdw) radii rv=R1+R2 H(1.2A), **C(1.7), N(1.5), O(1.4) (radii decrease because # protons increase but # orbitals stay the same)
* Lennard-Jones potential, e=(1/r)^12-(1/r)^6 balance between vdw attractions (1/r)^6 and repulsions (1/r)^12 http://en.wikipedia.org/wiki/Lennard-Jones_potential* hydrogen bonds, between H-bond donor (O or N) and H-bond acceptor (O or N), strong and specific non-convalent interaction, 2.6-3.5A H-bond length, 180 degrees, straight H-bond is strongest, found in secondary structure, alpha-helices, at 2.55A, the h-bond is very strong and there's a low barrier hydrogen bond (LBHB)
* water, unique because of H-bonds, sphere of hydration enables salt to dissolve, water can steal hydrogen bonds from alpha-helices, breaking it* hydrophobic interaction - lipids aggregate because it takes less energy to form a single cage than 2 separate water cages
Summary
* hydrophobic effect and van der Waal's forces
** weakest
** for stability of folded protein
** non-specific (doesn't matter what orientation is the water cage, as long as it helps minimize energy)
vs
* hydrogen bonding and electrostatic (charge-charge)
** strongest
** for single folded state formation, NOT stability of folded state
** highly specific
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