A meanfield approach to the thermodynamics of a protein-solvent system with application to the oligomerization of the tumor suppressor p53.
The thermodynamic stability and oligomerization status of the tumor suppressor p53 tetramerization domain have been studied experimentally and theoretically. A series of hydrophilic mutations at Met-340 and Leu-344 of human p53 were designed to disrupt the hydrophobic dimer-dimer interface of the tetrameric oligomerization domain of p53 (residues 325-355). Meanfield calculations of the free energy of the solvated mutants as a function of interdimer distance were compared with experimental data on the thermal stability and oligomeric state (tetramer, dimer, or equilibrium mixture of both) of each mutant. The calculations predicted a decreasing stability and oligomeric state for the following amino acids at residue 340: Met (tetramer) > Ser Asp, His, Gln, > Glu, Lys (dimer), whereas the experimental results showed the following order: Met (tetramer) > Ser > Gln > His, Lys > Asp, Glu (dimers). For residue 344, the calculated trend was Leu (tetramer) > Ala > Arg, Gln, Lys (dimer), and the experimental trend was Leu (tetramer) > Ala, Arg, Gln, Lys (dimer). The discrepancy for the lysine side chain at residue 340 is attributed to the dual nature of lysine, both hydrophobic and charged. The incorrect prediction of stability of the mutant with Asp at residue 340 is attributed to the fact that within the meanfield approach, we use the wild-type backbone configuration for all mutants, but low melting temperatures suggest a softening of the alpha-helices at the dimer-dimer interface. Overall, this initial application of meanfield theory toward a protein-solvent system is encouraging for the application of the theoretical model to more complex systems.
Noolandi
J
J
Xerox Research Centre, Canada, 2660 Speakman Drive, Mississauga, ON, Canada, L5K 1L2. jnooland@parc.xerox.com
Davison
T S
TS
Volkel
A R
AR
Nie
X
X
Kay
C
C
Arrowsmith
C H
CH
D019943:Amino Acid Substitution; D019281:Dimerization; D006801:Humans; D007930:Leucine; D046911:Macromolecular Substances; D008715:Methionine; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry; D012997:Solvents; D013816:Thermodynamics; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry*
D046911:Macromolecular Substances; D011506:Proteins; D011994:Recombinant Proteins; D012997:Solvents; D016159:Tumor Suppressor Protein p53; D008715:Methionine; D007930:Leucine