Free Energy of Transfer for Protein Burial

Crystal structures of 37 proteins were examined

amino acid surface amino acid buried

f = (Nb/Nb)/(Ns/Ns) where

Nb = frequency of amino acid burial in the protein interior

Ns = frequency of occupancy on the protein surface by the same amino acid

Nb;Ns : sum of amino acids buried; on surface

burialG = -RTln f

Criterion used for surface/burial: accessable surface area ASAASA = surface area of aminoacid in the protein

area of aminoacid in the extended tripeptide glyNHRCHCOgly

where R = amino acid side chain in questionMiller, S.; Janin,J.; Lesk, A. M. Chothia. J. Mol. Biol 1987. 196, 641.

Side Chain Hydrophobicity

Solubility of R-CHCONH2 in water octanol |

NHCOCH where R = amino acid side chain K = solubility in 1-octanol solubility in waterwoG = -RTln K

Fauchere, L.; Pliska, V. Eur J.Med. Chem.-Chim. Ther. 1983, 18, 369.

Free Energy of Tranfer For Residue Burial (burialG) and Hydrophobicity (woG) at 300 K.

R woG burialG kJ mol-1

alanine -CH3 -1.8 -0.8asparagine -CH2CONH2 3.4 2.9aspartic acid -CH2CO2H 4.4 3cysteine -CH2SH -5.6 -2.8glutamine -CH2CH2CONH2 1.3 3.1glutamic acid -CH2CH2CO2H 3.6 4.6histidine -CH2(C3H3N2) -0.8 -0.2isoleucine -C(CH3)CH2CH3 -10.3 -3.1leucine -CH2CH(CH3)2 -9.7 -2.7lysine -(CH2)4NH2 5.6 8.4methionine -CH2CH2SCH3 -7 -3phenylalanine -CH2C6H5 -10.2 -2.8serine -CH2OH 0.2 1.4threonine -CH(CH3)OH -1.5 1.1tryptophane -CH2(C8H6N) -12.8 -1.9tyrosine -CH2(C6H4OH) -5.5 0.9valine -CH(CH3)2 -6.9 -2.6

transferG (Water to Octanol), kJ mol-1

-4 -2 0 2 4 6 8 10

tranf

erG (P

rote

in B

uria

l), k

J mol-1

-15

-10

-5

0

5

10

15

r2: 0.7716m: 1.560b: -3.655

Why is there scatter in the plot of woG vs burialG ?

Consider an aminoacid in the exterior of a protein and compare it to an aminoacid in the interior. Then consider the same aminoacid in water and in octanol.

Is there anyway to correct for loss of side chain mobility on the interior of the protein?

Contributions to Entropy Accompanying Melting

Sfus = Strans + Srot + Svib + Selec; Srot = Srigid body rot + Sconf

During melting, let’s assume that Svib + Selec are not significantly affected.

For an ideal gas at 298 K:Strans = 37.0 + 3/2Rln(M/40); Srigid body rot = 11.5 + R/2ln(Im

3/e) + Rln(n)

where: M = molecular weight; Im3 = product of the three moments of inertia

about the center of gravity of the molecule; e = external symmetry number; n = number of optical isomers.

Since translation and rigid body molecular rotation vary as the logarithm of molecular weight and moment of inertia, respectively, their contribution to the total entropy change would be similar for a related group of compounds.

If the contribution of an amino acid side chain (R) to the entropy of fusion is compared to that of a standard (CH3), then

Sfus(R) – Sfus(CH3) = Strans + Srigid body rot + Sconf

and if: Strans(R) Strans(CH3); Srigid body rot(R) Srigid body rot(CH3);

then: Sfus(R) – Sfus(CH3) Sconf or Sconf(R)

where Sconf(R) is the entropy change as a result of the gain or loss of conformational flexibility relative to methyl.

R tpceS TS woG woG burialG -TS

alanine -CH3 17.6 0 -1.8 -1.8 -0.8asparagine -CH2CONH2 35 5.1 3.4 8.7 2.9aspartic acid -CH2CO2H 37.3 5.8 4.4 10.2 3cysteine -CH2SH 30.1 3.7 -5.6 -1.9 -2.8glutamine-CH2CH2CONH2 42.1 7.2 1.3 8.5 3.1glutamic acid -CH2CH2CO2H 44.3 7.9 3.6 11.5 4.6histidine -CH2(C3H3N2) 32.2 6.0 -0.8 5.2 -0.2isoleucine -CH(CH3)CH2CH3 25.9 2.4 -10.3 -7.9 -3.1leucine -CH2CH(CH3)2 25.9 2.4 -9.7 -7.3 -2.7lysine -(CH2)4NH2 76.2 17.3 5.6 22.9 8.4methionine -CH2CH2SCH3 33.9 4.4 -7 -2.6 -3phenylalanine -CH2C6H5 34.5 5.0 -10.2 -5.2 -2.8serine -CH2OH 23.6 1.8 0.2 2 1.4threonine -CH(CH3)OH 24.2 2.0 -1.5 0.5 1.1tryptophane -CH2(C8H6N) 43.5 7.6 -12.8 -5.2 -1.9tyrosine -CH2(C6H4OH) 39.9 6.6 -5.5 1.1 0.9valine -CH(CH3)2 18.8 0.4 -6.9 -6.5 -2.6

tranferG (Water to Octanol) - TtpceS, kJ mol-1

-4 -2 0 2 4 6 8 10

trans

ferG

(Pro

tein

Bur

ial),

kJ m

ol-1

-10

-5

0

5

10

15

20

25

r2: 9209m: 2.445b: 1.181

“Protein side chain conformational entropy derived from fusion data - comparison with other empirical scales” Sternberg, M. J. E.; Chickos, J. S. Protein Engineering 1994, 7, 149 - 155.