Improving the interaction of Myc‐interfering peptides with Myc using molecular dynamics simulations

Previously, a Myc‐interfering peptide (Mip) was identified for the targeted inactivation of the Myc:Max complex by the combination of rational design and an in vivo protein‐fragment complementation assay. In the subsequent work presented here, molecular dynamics simulations and free energy calculations based on the molecular mechanics GBSA method were performed to define the contribution of the different amino acids in the Myc:Mip coiled coil domain, and compared to wild‐type Myc:Max. For further optimization of the Myc interference, point mutations were introduced into Mip and analyzed, from which two showed much higher binding affinities in the computational studies in good agreement with the experiment. These mutants with very high potential for inactivation of Myc can now be used as starting point for further optimizations based on the computational as well as experimental protocols presented here. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.     

Determination of the dissociation constants for recombinant c-Myc, Max, and DNA complexes: the inhibitory effect of linoleic acid on the DNA-binding step

c-Myc, the protein product of protooncogene c-myc, functions in cell proliferation, differentiation, and neoplastic disease. In this study, recombinant c-Myc and Max proteins, encompassing DNA binding (basic region) and dimerization (helix-loop-helix/leucine zipper) domain of human origin, were expressed in bacteria as Myc87 and Max85. Myc87 was purified under denatured conditions and was renatured again. The dissociation constant for the protein dimers and for dimer/DNA complexes were not detectable by isothermal titration calorimetry because of the low degree of solubility of Myc87 and Max85. Therefore, we set up equations which were used to determine the dissociation constants from the proportion of protein-DNA complexes. The dimer dissociation constants in TBS were 5.90(+/-0.54)x10(-7)M for Max85/Max85 homodimer, 6.85(+/-0.25)x10(-3)M for Myc87/Myc87 homodimer, and 2.55(+/-0.29)x10(-8)M for Myc87/Max85 heterodimer, and the DNA-binding dissociation constants in TBS were 1.33(+/-0.21)x10(-9)M for Max85/Max85/DNA, 2.27(+/-0.08)x10(-12)M for Myc87/Myc87/DNA, and 4.43(+/-0.37)x10(-10)M for Myc87/Max85/DNA. In addition, we revealed that linoleic acid which is known as an inhibitor for the formation of Max/Max/DNA complex reduced the affinity of Max homodimer for DNA. This result indicates that linoleic acid may bind to the DNA-binding region of Max homodimer.