PROTEIN PHYSICS LECTURES 5-6 Elementary interactions: hydrophobic&electrostatic; SS and coordinate bonds
Hydrophobic effect Concentration of C 6 H 12 in H 2 O: 50 times less than in gas! WHY? H2OH2OH2OH2O
G int : “Free energy of interactions” G int : “Free energy of interactions” (“mean force potential”) (“mean force potential”) Chemical potential: Chemical potential: G (1) = G int - Tk B ln(V (1) ) G int + Tk B ln[C] EQUILIBRIUM for transition of molecule 1 from A to B: G A (1) = G B (1) chemical potentials in A and B are equal chemical potentials in A and B are equal G int A B = G int B – G int A G int A B = k B Tln([C inA ]/[C inB ]) ===================================================
Experiment: G int A B = k B T ln([C 1 in A ]/[C 1 in B ]) S int A B = -d( G int A B )/dT H int A B = G int A B +T S int A B C 6 H 12 [C] of C 6 H 12 in H 2 O: 50 times less than in gas; times less than in liquid C 6 H 12 T=298 0 K=25 0 C
-2/3 +1/3 Loss: S usual usual case case-2/3Loss: LARGE E rare rare case case H-bond: directed “hydrophobic bond”
High heat capacity d( H)/dT: Melting of “iceberg”
20-25 cal/mol per Å 2 of molecular accessible non-polar surface Octanol Water
______largeeffect _______ small small______ large large
Electrostatics in uniform media: potential 1 = q 1 / r Interaction of two charges: U = 1 q 2 = 2 q 1 = q 1 q 2 / r = 1 vacuum = 1 vacuum 3 protein 3 protein 80 water 80 water Protein/water interface In non-uniform media: = ? At atomic distances: = ?
Water => PROTEIN (ε 3) (ε 3) R Å U kcal/mol CHARGE inside PROTEIN: VERY BAD CHARGE inside insidePROTEIN Water => vacuum: U +100 kcal/mol
Non-uniform media: eff = ?
= q / 1 r
= (q / 1 )/r
Good estimate for non-uniform media – + – + –– + – + – – + – + –– + – + – eff ≈ 200 !! eff ≈40 = q / r eff in positions:
effective in non- uniformmedia
Large distance: Atomic distance: = 80 = ? = 80 = ? intermed. intermed. “vacuum”, ε ~ 1? “vacuum”, ε ~ 1? but absence but absence of intermed. of intermed. dipoles can dipoles can only increase only increase interaction… interaction…
At atomic distances in water: 1) =80 is not a bad approximation (much better than = 1 or 3 !!) (salt does not dissolve, if <50 at 3Å!) (salt does not dissolve, if <50 at 3Å!) 2) [H] 1/2 = [H] 1/2 = e - G el /RT at ~2.5Å! at ~2.5Å! G el = 2.5 ln(10) RT 6RT 3.5 kcal/mol at 2.5Å
Protein engineering experiments: (r) = pH 2.3RT eff (r)
Dipole interactions (e.g., H-bonds): (HO) -1/3 -H +1/3 ::::::(OH) -1/3 -H +1/3 Quadruple interactions Also: charge-dipole, dipole-quadruple, etc. Potentials: dipole ~ 1/ r 2 quadruple ~ 1/ r 3 dipole ~ 1/ r 2 quadruple ~ 1/ r 3
Electrostatic interactions also occur between charge (q) and non-charged body if its 2 differs from the media’s 1 : U ~ q [ 1/ 2 – 1/ 1 ] V (1/ r 4 ) at large r In water: repulsion of charges from non-polar molecules (since here 1 >> 2 ); in vacuum (where 1 < 2 ): just the opposite! in vacuum (where 1 < 2 ) : just the opposite! 22VV22VVV 11
Debye-Hückel screening of electrostatic by ions: U = [q 1 q 2 / r]exp(-r/D) ; in water: D = 3Å I -1/2 ; in water: D = 3Å I -1/2 ; Ionic strength I = ½ i C i (Z i ion ) 2. Usually: I 0.1 [mol/liter] ; D 8Å. Electrostatics is an example of a multi-body (charge1, charge2, media, ions) interaction
Electrostatics is T- dependent; U = (1/ )(q 1 q 2 /r) is free energy; TS = T (-dU/dT) = -T [d(1/ )/dT](q 1 q 2 /r) = = [dln( )/dlnT] U = [dln( )/dlnT] U in water: when T grows from 273 o to 293 o K (by 7%), decreases from 88 to 80 (by 10%): decreases from 88 to 80 (by 10%): TS ≈ -1.3 U; H -0.3 U In water the entropic term (-TS) is the main for electrostatics!
S-S bonds (Cys-Cys) exchange exchange S-S bond is not stable within a cell within a cell
Coordinate bonds (with Zn ++, Fe +++,…)
= q / r 1