Synthetic fusion proteins of two or multiple domains using recombinant DNA technology are recently emerging in the field of protein engineering. The functional properties of the designed proteins were already enhanced and utilized for wide variety of biological and pharmaceutical applications [1]. However, there is no information about the super-molecular properties of two domain constructs of structurally and functionally different proteins. In order to understand the allostery at molecular level, we have performed all-atom explicit solvent molecular dynamics simulations in the isobaric-isothermal ensemble. We have selected the well characterized PDZ3 and SH3 domains of human zonula occludens (ZO-1) (3TSZ) along with other 5 artificial domains. Among other methods, we used IEM methodology to describe effect of second domain in the chimeric construct on the allostery of the first domain [2]. The influence of 5 artificial domains on the PDZ3 and SH3 were determined using a range of structural, dynamical and statistical analysis including residue fluctuation and inter-residue interaction energies in the solvent phase. Each amino acid contribution to the total intra-molecular stabilization energy of PDZ3 and SH3 were identified for all chimeras by means of direct and reverse combination approach. This allows us to describe artificial domains as modulators of dynamical and allosteric effect of the PDZ3 and SH3 domains.