Invited to present by Himanshu Khandelia
Abstract
For hundreds of years, humans were excited by birds and their ability to fly across the globe to more favorable grounds for each season. What started with observing an African spear lodged inside a stork in Europe has evolved to studying a putative magnetic-sensitive protein inside the birds’ retinae, Cryptochrome 4. The protein has been shown to be magnetosensitive upon blue-light activation, and it might allow the birds to see Earth’s magnetic field. But how does the protein react to its light activation on the molecular level?
Through the talk, we will explore the initial activation of the protein and the following conformational changes in the protein structure. We will introduce a first similarity measure to compare two whole molecular dynamics trajectories. We will then explore the reaction of the protein if it is turned off again without any intermediate steps and explore the behavior using the Python package SiMBols. Finally, we will consider the entire time scales of intermediate states and look at more than 700 microseconds of coarse-grained molecular dynamics simulations of the cryptochrome 4 protein to eventually describe the complete cycle from the ground state to its activation and back to the ground state through steps of reoxidization.