Microtubules’ bends, cryo-cool ribosomes, and wet proteins

Maxim Igaev, Lars V. Bock, Leonard Heinz, Helmut Grubmüller

In this talk we will survey some of the current challenges of the biomolecular simulations field, with a particular focus at large biomolecular systems, discussing three recent examples.

Microtubules provide both mechanical support and, via the kinetochore, mechanical forces to the cell. To this aim, the filaments can undergo growth/polymerisation and shrinking/depolymerisation phases, driven by GTP hydrolysis. Through non-equilibrium atomistic simulations of entire plus-end microtubule tips we show that the average nucleotide state of the plus-end MT tip determines the heights of energy barriers between tip conformations, such that the post-hydrolysis MT tip is exposed to higher activation energy barriers, which translates into its inability to elongate.

Much about the ultra-structure of microtubules – as well as of many other biomolecules and biomolecular complexes has been revealed by the recent resolution revolution in cryo electron microscopy. How much of the ambient temperature ensemble of biomolecules is preserved during shock freezing prior to image acquisition is, however, an unsolved question. In shock cooling atomistic simulations of fully solvated ribosomes at realistic time scales we observed, depending on cooling rates, a marked decrease of structural heterogeneity. Small barriers between the states (<10 kJ/mol) are overcome during cooling and do not contribute to the heterogeneity of the structural ensemble obtained by cryo-EM, whereas conformational states separated by barriers above 10 kJ/mol are expected to be trapped during plunge-freezing. Our results will allow one to quantify the heterogeneity of biologically relevant room-temperature ensembles from cryo-EM structures.

In these processes, as well as quite generally in protein folding and the thermodynamics of biomolecular stability, the solvent shell plays a pivotal role as, e.g., the effect of cold denaturation clearly demonstrates. We will present a new method to compute solvent enthalpies and entropies with spatial resolution and thus to quantify the underlying thermodynamic enthalpy/entropy tug-of-war. For the example protein crambin, we quantified the local effects on the solvent free-energy difference at each amino acid and identified strong dependencies of the local enthalpy and entropy on the protein curvature. Remarkably, more than half of the solvent entropy contribution arises from induced water correlations.