Probing thermal activation of functional modes in proteins

Contribution of different modes to the overall protein internal motion is determined in the optimal working temperature regime of the protein.

The life of a protein is one of constant wiggling and reshuffling, i.e.  fluctuating and transitioning from one conformational substate to another. Untangling the correlated protein motions and targeting those that are functionally relevant represents a fundamental challenge.

We have recently successfully coupled Neutron Spin Echo spectroscopy to Molecular Dynamics simulations and theoretical modelling to individuate long-range functional modes. In the experiment, the protein is heated over a temperature range that includes the optimal working temperature, and the correlated protein motions in the nanometer and nanosecond regime are characterized in terms of their diffusion coefficients. Subsequently, molecular simulations and theoretical modelling are used to probe the contributions of different protein regions to the experimental signal. The functional modes are individuated as those activated in the optimal working temperature regime and being relevant in the functional context of the protein  (i.e. proximity to the active site, conservation...).

When the methodology was applied to a non-allosteric eukaryotic Lactate Dehydrogenase in its apo state, we discovered that the temperature increase results in a conformational change equivalent to that achieved as an effect of allosteric activators in allosteric bacterial LDHs, reflecting the richness of evolutionary pathways leading to the same functional configuration.

Enjoy our work here .