Biology subjects

Mugnai, M.

Publications and source records attributed to Mugnai, M..

3 recordsLinked to original sources

bioRxiv2025

Droplet growth, Ostwald's rule, and emergence of order in Fused in Sarcoma

The low complexity domain of Fused in Sarcoma (FUS-LC consisting of 214 residues) undergoes phase separation, resulting in a dense liquid-like phase that forms early and slowly matures to reach ordered gel-like state on long time scales. Upon maturation, core-1, comprising of the 57 residues (39-95) in the N-terminus become structured, resulting in the formation of a non-polymorphic fibril. The truncated FUS-LC-C (residues 110-214) construct forms a fibril in which core-2 (residues 112-150) adopts a {beta}-sheet structure. Using coarse-grained monomer SOP-IDP model simulations of FUS-LC, we predict that residues 155-190 in the C-terminal (core-3) form rapidly, followed by core-2, and finally core-1. The time scale of formation of the cores and their stabilities are inversely correlated, as anticipated by the Ostwalds rule of stages. Unbiased multichain simulations show that the chemical potentials in the two phases are equal and the calculated densities of the dense and dilute phases are in agreement with experiments. The dense phase, which forms by a nucleation mechanism, coarsens over time by a process that is reminiscent of Ostwald ripening. AlphaFold predictions of the core-3 structure and the simulations show that {beta}-strand emerges in the core-3 region early during the droplet formation, and drives the initiation of FUS-LC assembly. The techniques introduced here are general and could be used to probe assembly of other IDPs such as TDP-43, which shares many features with FUS-LC.

biophysics↗

bioRxiv2022

Reduction of RBD Binding Affinity to Glycosylated ACE2 is Entropic in Origin

The spike protein in the virus SARS-CoV-2 (the causative agent of COVID-19) recognizes the host cell by binding to the peptidase domain (PD) of the extracellular enzyme Angiotensin-converting Enzyme 2 (ACE2). A variety of carbohydrates could be attached to the six asparagines in the PD, resulting in a heterogeneous population of ACE2 glycoforms. Experiments have shown that the binding affinity of glycosylated and deglycosylated ACE2 to the virus is virtually identical. In most cases, the reduction in glycan size correlates with stronger binding, which suggests that volume exclusion, and hence entropic forces, determine the binding affinity. Here, we quantitatively test the entropy-based hypothesis by developing a lattice model for the complex between ACE2 and the SARS-CoV-2 spike protein Receptor-binding Domain (RBD). Glycans are treated as branched polymers with only volume exclusion, which we justify using all atom molecular dynamics simulations in explicit water. We show that the experimentally measured changes in the ACE2-RBD dissociation constants for a variety of engineered ACE2 glycoforms are well accounted for by our theory, thus affirming that ACE2 glycans have only a weak, entropic effect on RBD binding.

biophysics↗

bioRxiv2021

Information flow, Gating, and Energetics in dimeric molecular motors

Molecular motors belonging to the kinesin and myosin super family hydrolyze ATP by cycling through a sequence of chemical states. These cytoplasmic motors are dimers made up of two linked identical monomeric globular proteins. Fueled by the free energy generated by ATP hydrolysis, the motors walk on polar tracks (microtubule or filamentous actin) processively, which means that only one head detaches and executes a mechanical step while the other stays bound to the track. Thus, the one motor head must regulate chemical state of the other, referred to as "gating", a concept that is not fully understood. Inspired by experiments, showing that only a fraction of the energy from ATP hydrolysis is used to advance the kinesin motors against load, we demonstrate that additional energy is used for coordinating the chemical cycles of the two heads in the dimer - a feature that characterizes gating. To this end, we develop a general framework based on information theory and stochastic thermodynamics, and establish that gating could be quantified in terms of information flow between the motor heads. Applications of the theory to kinesin-1 and Myosin V show that information flow occurs, with positive cooperativity, at external resistive loads that are less than a critical value, Fc. When force exceeds Fc, effective information flow ceases. Interestingly, Fc, which is independent of the input energy generated through ATP hydrolysis, coincides with force at which the probability of backward steps starts to increase. Our findings suggest that transport efficiency is optimal only at forces less than Fc, which implies that these motors must operate at low loads under in vivo conditions.

biophysics↗