Combining ancestral reconstruction with folding-landscape simulations to engineer heterologous protein expression

Obligate symbionts exhibit high evolutionary rates and extensive sequence divergence. Here, we use the thioredoxin from Candidatus Photodesmus katoptron, an uncultured symbiont of flashlight fish, to explore evolutionary and engineering aspects of protein folding in heterologous hosts. The symbiont protein is a standard thioredoxin in terms of 3D-structure, stability and redox activity. However, its refolding in vitro is very slow and its expression in E. coli leads to insoluble protein. By contrast, resurrected Precambrian thioredoxins express efficiently in E. coli, plausibly reflecting an ancient adaptation to unassisted folding. We have used a statistical-mechanical model of the folding landscape to guide back-to-ancestor engineering of the symbiont protein. Remarkably, we find that the efficiency of heterologous expression correlates with the in vitro refolding rate and that the ancestral expression efficiency can be achieved with only 1-2 back-to-ancestor replacements. These results demonstrate a sequence-engineering approach to rescue inefficient heterologous expression, a major biotechnological bottleneck.

Interplay Between Receptor-Ligand Binding and Lipid Domain Formation Depends on the Mobility of Ligands in Cell-Substrate Adhesion

Cell-cell adhesion and the adhesion of cells to extracellular matrix are mediated by the specific binding of receptors on the cell membrane to their cognate ligands on the opposing surface. The adhesion receptors can exhibit affinity for nanoscale lipid clusters that form in the cell membrane. Experimental studies of such adhesion systems often involve a cell adhering either to a solid surface with immobile ligands or a supported lipid bilayer with mobile ligands. A central question in these cell-substrate adhesions is how the mobility of the ligands physically affects their binding to the adhesion receptors and thereby the behavior of the nanoscale lipid clusters associated with the receptors. Using a statistical mechanical model and Monte Carlo simulations for the adhesion of cells to substrates with ligands, we find that, for mobile ligands, binding to adhesion receptors can promote the formation of mesoscale lipid domains, which in turn enhances the receptor-ligand binding. However, in the case of immobile ligands, the receptor-ligand binding and the tendency for the nanoscale lipid clusters to further coalesce depend on the distribution of the ligands on the substrate. Our findings help to explain why different adhesion experiments for identifying the interplay between receptor-ligand binding and heterogeneities in cell membranes led to contradictory results.

Red-Edge Excitation Shift Spectroscopy (REES): Application to Hidden Bound States of Ligands in Protein–Ligand Complexes

Ligand-protein binding is responsible for the vast majority of bio-molecular functions. Most experimental techniques examine the most populated ligand-bound state. The determination of less populated, intermediate, and transient bound states is experimentally challenging. However, hidden bound states are also important because these can strongly influence ligand binding and unbinding processes. Here, we explored the use of a classical optical spectroscopic technique, red-edge excitation shift spectroscopy (REES) to determine the number, population, and energetics associated with ligand-bound states in protein–ligand complexes. We describe a statistical mechanical model of a two-level fluorescent ligand located amongst a finite number of discrete protein microstates. We relate the progressive emission red shift with red-edge excitation to thermodynamic parameters underlying the protein–ligand free energy landscape and to photo-physical parameters relating to the fluorescent ligand. We applied the theoretical model to published red-edge excitation shift data from small molecule inhibitor–kinase complexes. The derived thermodynamic parameters allowed dissection of the energetic contribution of intermediate bound states to inhibitor–kinase interactions.

Statistical Mechanical Model of Gas Adsorption in a Metal-Organic Framework Harboring a Rotaxane Molecular Shuttle

Metal-organic frameworks (MOFs) are modular and tunable nano-porous materials with applications in gas storage, separations, and sensing. Flexible/dynamic components that respond to adsorbed gas can give MOFs unique or enhanced adsorption properties. Here, we explore the adsorption properties that could be imparted to a MOF by a rotaxane molecular shuttle (RMS) in its pores. In the unit cell of an RMS-MOF, a macrocyclic wheel is mechanically interlocked with a strut of the MOF scaffold. The wheel shuttles between stations on the strut that are also gas adsorption sites. At a level of abstraction similar to the seminal Langmuir adsorption model, we pose and analyze a simple statistical mechanical model of gas adsorption in an RMS-MOF that accounts for (i) wheel/gas competition for sites on the strut and (ii) gas-induced changes in the configurational entropy of the shuttling wheel. We determine how the amount of gas adsorbed, position of the wheel, and differential energy of adsorption depend on temperature, pressure, and the interactions of the gas/wheel with the stations. Our model reveals that, compared to a rigid, Langmuir material, the chemistry of the RMS-MOF can be tuned to render gas adsorption more or less temperature-sensitive and to release more or less heat upon adsorption. The model also uncovers a non-monotonic relationship between the temperature and the position of the wheel if gas out-competes the wheel for its preferable station.

Statistical Mechanical Model of Gas Adsorption in a Metal-Organic Framework Harboring a Rotaxane Molecular Shuttle

Metal-organic frameworks (MOFs) are modular and tunable nano-porous materials with applications in gas storage, separations, and sensing. Flexible/dynamic components that respond to adsorbed gas can give MOFs unique or enhanced adsorption properties. Here, we explore the adsorption properties that could be imparted to a MOF by a rotaxane molecular shuttle (RMS) in its pores. In the unit cell of an RMS-MOF, a macrocyclic wheel is mechanically interlocked with a strut of the MOF scaffold. The wheel shuttles between stations on the strut that are also gas adsorption sites. At a level of abstraction similar to the seminal Langmuir adsorption model, we pose and analyze a simple statistical mechanical model of gas adsorption in an RMS-MOF that accounts for (i) wheel/gas competition for sites on the strut and (ii) gas-induced changes in the configurational entropy of the shuttling wheel. We determine how the amount of gas adsorbed, position of the wheel, and differential energy of adsorption depend on temperature, pressure, and the interactions of the gas/wheel with the stations. Our model reveals that, compared to a rigid, Langmuir material, the chemistry of the RMS-MOF can be tuned to render gas adsorption more or less temperature-sensitive and to release more or less heat upon adsorption. The model also uncovers a non-monotonic relationship between the temperature and the position of the wheel if gas out-competes the wheel for its preferable station.

Stochastic Thermodynamics Analysis of Ultrafast AgAu Nanoshell Dynamics in the Nonlinear Response Regime

The understanding of relaxation dynamics of metallic nanoshells is important for a range of nanotechnological applications. In this work, we present a combined experimental-theoretical study of the relaxation dynamics of AgAu nanoshells. This was investigated using ultrafast pump-probe experiments resonant with the surface plasmon of the nanoshells, as well as via atomistic molecular dynamics simulations of relaxation and temperature-jump (DT-jump) processes. Both techniques were then discussed and complemented using a non-equilibrium statistical mechanical model. Data collected at low energies were consistent with our previously reported work and allowed the characterization of intrinsic electron-phonon coupling times (EPCT) and of the overall relaxation dynamics in terms of a two-temperature model. Data at intermediate and higher energies, in turn, showed a nonlinear dependence of EPCT as a function of the pump power, faster relaxation being observed at higher pump energies. In the limit of small DT-jumps, relaxation based on a two-temperature model is recovered, whereas in the limit of large DT-jumps, the relaxation becomes faster with increasing temperature change. The results reported here give insight on the ultrafast dynamics of AgAu nanoshells and might also be applied to other metallic systems, paving the way to the better understanding of relaxation dynamics of nanoparticles in general.<br>