Speaker
Description
uL22 is one of the universally present ribosomal proteins. Its β-hairpin loop protrudes from the ribosome surface into the exit tunnel. In this work, I have performed all-atom simulations of this isolated uL22 fragment dissolved in water using two different simulation techniques (unbiased molecular dynamics and Hamiltonian Replica Exchange) and 3 force fields. The goal was to examine the behaviour of this fragment, particularly its secondary structure formation tendencies.
I have compared the simulation results with experimental XRD-obtained structure of the fragment when present in the ribosome. I also predicted NMR shifts using the CamShift algorithm and compared them with experimentally measured shifts in order to determine which force field describes the behaviour of the loop most accurately.
