Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1

Abstract

The Light-Oxygen-Voltage 2 (LOV2) domain of Avena Sativa phototropin 1 (AsLOV2) protein is one of the most studied domains in the field of designing photoswitches. This is due to the several unique features in the AsLOV2, such as the monomeric structure of the protein in both light and dark states and the relatively short transition time between the two states. Despite that, not many studies focus on the effect of the secondary structures on the drastic conformational change between the light and dark states. In this study, we focus on the role of A’α helix as a key player in the transition between both states using various computational tools as: 1.5 μs molecular dynamics simulations for each configuration, Markov state model, different machine learning techniques, and community analysis. The impact of the A’α helix was studied on the atomistic level by introducing two groups of mutations, helicity enhancing mutations (T406A and T407A) and helicity disrupting mutations (L408D and R410P), as well as on the overall secondary structure by using the community analysis. Maintaining the N-terminal hydrogen bond network was found to be essential for the transition between the two states. Via in-depth hydrogen bonding and contact analysis we were able to identify key residues (Thr407 and Arg410) involved in the functional conformational switch and their impact on the overall protein dynamics. Moreover, the community analysis highlighted the significant role of the β sheets in the overall protein allosteric process.

Keywords

• LOV domain
• Allostery
• AsLOV2
• Hydrogen bond network
• Machine learning