Molecular Dynamics Study for Streptavidin Mutant With/Without Biotin Analog

Abstract

The streptavidin (SA) is a tetrameric protein with four identical subunits. Each subunit has a biotin-binding pocket. The biotin-SA system is known to have a strongest noncovalent biological interaction, and has been widely used as not only a molecular detection tool in many biotechnological applications but also medical applications such as pre-targeting system. One of pre-targeting approach to cancer radioimmunotherapy uses an antibody-streptavidin conjugate that is first localized to the tumor. The excess reagent is then cleared from blood and the biotinylated radiation carriers are administered. So far, many trials for the clinical application have not been successful due to mainly two problems, the immunogenicity of a bacterium-derived SA and the endogenous BTN species. Recently, a pre-targeting system, which overcomes such the two problems, has been developed by kawato et al. In the system, the SA is modified to decrease the immunogenicity, and the SA mutant binds to an artificial biotin analog while abolishing affinity for natural biocytin. Here, we have performed a series of long molecular dynamics simulations for the SA or its mutants with/without biotin analog systems developed by kawato et al. to investigate the effect of mutations on the structural change, dynamics and the thermodynamic properties of the system. We also have calculated free energy of the systems using MPCAFEE method to evaluate binding affinity of artificial biotin analogs with SA mutants. We found that the mutations in the biotin-binding pocket affect not only the interaction with surrounding residues and with biotin analog, but also the tetramerization of the SA mutants.