Chromatin dynamics controls epigenetic domain formation.

In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, which are triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive-feedback (modification begets modification) mechanism.

Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding.

Macromolecular crowding influences protein mobility and stability . A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding.

Temperature Unmasks Allosteric Propensity in a Thermophilic Malate Dehydrogenase via Dewetting and Collapse.

In this work, we combine experiments and molecular simulations to unveil the hidden allosteric propensity of a thermophilic malate dehydrogenase protein (MDH). We provide evidence that, at its working temperature, the nonallosteric MDH takes a compact structure because of internal dewetting and reorganizes the active state toward functional conformations similar to its homologous allosteric LDHs. Moreover, a single-point mutation confers on the MDH a cooperative behavior that mimics an allosteric LDH.

Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion.

Internal subnanosecond timescale motions are key for the function of proteins, and are coupled to the surrounding solvent environment. These fast fluctuations guide protein conformational changes, yet their role for protein stability, and for unfolding, remains elusive. Here, in analogy with the Lindemann criterion for the melting of solids, we demonstrate a common scaling of structural fluctuations of lysozyme protein embedded in different environments as the thermal unfolding transition is approached.

Configurational Disorder of Water Hydrogen-Bond Network at the Protein Dynamical Transition.

We introduce a novel strategy to quantify the disorder of extended water-water hydrogen-bond (HB) networks sampled in particle-based computer simulations. The method relies on the conformational clustering of the HB connectivity states. We successfully applied it to unveil the fine relationship among the protein dynamical transition in hydrated powder, which marks the activation of protein flexibility at T ≈ 240 K, and the sudden increase in the configurational disorder of the water HB network enveloping the proteins.