Better tools to explain membrane protein dynamics
Protein dynamics is basically linked to protein function, aggregation and folding, and time-resolved spectroscopy is especially suited to reveal these dynamics. Protein dynamics also manifest themselves when a fast perturbation is applied. An example of this is when a laser pulse is applied to proteins with photocycles. Both in hydrogen/deuterium exchange (HDX) and in perturbation experiments the time-resolved response of the system is a multi-exponential relaxation process. The information to be characterised is the number, value and nature of the rate constants of the relaxation process, not the process itself. The NAGOYA2BCN project aimed to improve, develop and apply maximum entropy and Bayesian methods to analyse the multi-exponential data arising in the HDX of membrane proteins, and in the photocycles of membrane proteins. At the same time, it set out to use new experimental HDX approaches to obtain dynamics information of membrane proteins by infrared (IR) spectroscopy, and then apply them to at least three membrane protein systems: the melibiose transporter, bacteriorhodopsin, and a G-protein coupled receptor chimera. Results being reported reveal that the time-scale of protein fluctuations that can be monitored and characterised increases relevant to a longer time window covered in the HDX experiments. Although some obstacles were encountered in designing an experimental set-up for IR spectroscopy to improve the time-window of HDX experiments, the research team developed a simple approach changing the protein from a H2O medium to a 95% D2O medium in a few seconds. Achievements have also been noted during collaboration with Prof. Kandori in Nagoya, Japan, in Bayesian inference with Markov Chain Monte Carlo sampling. In other work, headway has been made in improving/developing various tools and software that facilitate the analysis of the HDX data and the bR photocycle. These improvements have been included in a visual program running in Matlab. The successes of the NAGOYA2BCN project offer unique and essential information to better grasp membrane protein dynamics.