During my postdoctoral research studies in the lab of Prof. Charles C. Richardson I have been investigating DNA replication in bacteriophage T7.
We have examined the effect of macromolecular crowding on the structure and function of the replisome of bacteriophage T7. Using small angle X-ray scattering (SAXS), biochemical assays, and NMR (in collaboration with Gerhard Wagner, HMS), we have demonstrated the impact of macromolecular crowding on DNA replication and related systems (Akabayov B. et al., Nature Communications, 2013; Akabayov SR et al., JACS 2013).
The SAXS based method I have developed (see Figure above) allows to probe the structure of weak protein-protein complexes and can be appliedusing other biological systems (one example is a collaborative study on translation initiation complexes Luna R. et al., Cell Reports 2012).
In other studies we have shown that substitution of pyrophosphate by pyrovanadate in a pyrophosphorolysis-like reaction by DNA polymerase may well constitute the first evidence that vanadium can substitute for phosphorous in biological processes (see Figure below, Akabayov B. et al., JBC, 2011).
X-ray absorption spectroscopy (XAFS) was employed to elucidate the role of zinc in the T7 encoded DNA primase (Akabayov B. et al. Biochemistry, 2009). I became intrigued by more mechanistically complex questions such as the biophysical basis for the processivity of T7 DNA polymerase. Using a variety of biophysical tools I have shown that the activation of T7 DNA polymerase upon binding to its processivity factor is accompanied by a conformational transition. The active conformation of the T7 DNA polymerase is necessary for better translocation on the DNA substrate (see Figure below, Akabayov B. et al., PNAS, 2010; Tran N. et al., JBC, 2012) and better utilization of dNTPs (Akabayov B. and Richardson CC., Powder Diffraction, 2011).
After my master studies at Bar-Ilan University, where I worked with cardiomyocytes in the area of cell physiology I became interested in the biophysics of biological molecules and I therefore moved to the Department of Structural Biology at the Weizmann Institute of Science. During my tenure at the WIS as a graduate student in the lab of Prof. Irit Sagi, I mastered a variety of structural biology, biophysical, and biochemical techniques. I applied X-ray absorption spectroscopy and small angle X-ray scattering as well as nucleic-acid/protein biochemistry to study the structure-function relationships of the E. coli RNA helicase DbpA. I also utilized optical tweezers for the study of RNA-protein interactions at the single molecule level.