Project description: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. By combining elastic incoherent neutron scattering and advanced molecular simulations, we show that, although different solvents modify the protein melting temperature, a unique dynamical regime is attained in proximity of thermal unfolding in all solvents that we tested. This solvation shell-independent dynamical regime arises from an equivalent sampling of the energy landscape at the respective melting temperatures. Thus, we propose that a threshold for the conformational entropy provided by structural fluctuations of proteins exists, beyond which thermal unfolding is triggered.
Project description:Prior in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) studies of electrochemical CO2 reduction catalyzed by Au, one of the most selective and active electrocatalysts to produce CO from CO2, suggest that the reaction proceeds solely on the top sites of the Au surface. This finding is worth updating with an improved spectroelectrochemical system where in situ IR measurements can be performed under real reaction conditions that yield high CO selectivity. Herein, we report the preparation of an Au-coated Si ATR crystal electrode with both high catalytic activity for CO2 reduction and strong surface enhancement of IR signals validated in the same spectroelectrochemical cell, which allows us to probe the adsorption and desorption behavior of bridge-bonded *CO species (*COB). We find that the Au surface restructures irreversibly to give an increased number of bridge sites for CO adsorption within the initial tens of seconds of CO2 reduction. By studying the potential-dependent desorption kinetics of *COB and quantifying the steady-state surface concentration of *COB under reaction conditions, we further show that *COB are active reaction intermediates for CO2 reduction to CO on this Au electrode. At medium overpotential, as high as 38% of the reaction occurs on the bridge sites.
Project description:Electrocatalytic reduction of CO2 to fuels and chemicals is one of the most attractive routes for CO2 utilization. Current catalysts suffer from low faradaic efficiency of a CO2-reduction product at high current density (or reaction rate). Here, we report that a sulfur-doped indium catalyst exhibits high faradaic efficiency of formate (>85%) in a broad range of current density (25-100?mA cm-2) for electrocatalytic CO2 reduction in aqueous media. The formation rate of formate reaches 1449??mol h-1 cm-2 with 93% faradaic efficiency, the highest value reported to date. Our studies suggest that sulfur accelerates CO2 reduction by a unique mechanism. Sulfur enhances the activation of water, forming hydrogen species that can readily react with CO2 to produce formate. The promoting effect of chalcogen modifiers can be extended to other metal catalysts. This work offers a simple and useful strategy for designing both active and selective electrocatalysts for CO2 reduction.
Project description:Nanoscale molecular clusters in cell membranes can serve as platforms to recruit membrane proteins for various biological functions. A central question is how these nanoclusters respond to physical contacts between cells. Using a statistical mechanics model and Monte Carlo simulations, we explore how the adhesion of cell membranes affects the stability and coalescence of clusters enriched in receptor proteins. Our results show that intercellular receptor-ligand binding and membrane shape fluctuations can lead to receptor aggregation within the adhering membranes even if large-scale clusters are thermodynamically unstable in nonadhering membranes.
Project description:2D metal-organic-framework (MOF) based composites have emerged as promising candidates for electrocatalysis due to their high structural flexibility and fully exposed active sites. Herein, a freestanding metal-organic layer (MOL) with a 2D kgd (kagome dual) lattice was constructed with abundant surface oxygenate groups serving as anchoring sites to immobilize diverse guests. Taking Bi as an example, tetragonal Bi2 O3 nanowires can be uniformly grown on MOLs after solvothermal treatment, the structural evolution of which was followed by ex situ electron microscopy. The as-prepared Bi2 O3 /MOL exhibits excellent CO2 electroreduction activity towards formate reaching a specific current of 2.3 A mgBi -1 and Faradaic efficiencies of over 85 % with a wide potential range from -0.87 to -1.17 V, far surpassing Bi2 O3 /UiO (a 3D Zr6 -oxo based MOF) and Bi2 O3 /AB (Acetylene Black). Such a post-synthetic modification strategy can be flexibly extended to develop versatile MOL composites, highlighting the superiority of optimizing MOL-based composites for electrocatalysis.
Project description:Existing elastic network models are typically parametrized at a given cutoff distance and often fail to properly predict the thermal fluctuation of many macromolecules that involve multiple characteristic length scales. We introduce a multiscale flexibility-rigidity index (mFRI) method to resolve this problem. The proposed mFRI utilizes two or three correlation kernels parametrized at different length scales to capture protein interactions at corresponding scales. It is about 20% more accurate than the Gaussian network model (GNM) in the B-factor prediction of a set of 364 proteins. Additionally, the present method is able to deliver accurate predictions for some large macromolecules on which GNM fails to produce accurate predictions. Finally, for a protein of N residues, mFRI is of linear scaling (O(N)) in computational complexity, in contrast to the order of O(N(3)) for GNM.
Project description:Despite recent tremendous progress in optical imaging and metrology1-6, there remains a substantial resolution gap between atomic-scale transmission electron microscopy and optical techniques. Is optical imaging and metrology of nanostructures exhibiting Brownian motion possible with such resolution, beyond thermal fluctuations? Here we report on an experiment in which the average position of a nanowire with a thermal oscillation amplitude of ∼150 pm is resolved in single-shot measurements with subatomic precision of 92 pm, using light at a wavelength of λ = 488 nm, providing an example of such sub-Brownian metrology with ∼λ/5,300 precision. To localize the nanowire, we employ a deep-learning analysis of the scattering of topologically structured light, which is highly sensitive to the nanowire's position. This non-invasive metrology with absolute errors down to a fraction of the typical size of an atom, opens a range of opportunities to study picometre-scale phenomena with light.
Project description:Metal-binding proteins (MBPs) play diverse and critical functions in all living systems and many human diseases are closely related to dysfunctional MBPs. Here we developed a chemoproteomic method named METAL-TPP for global discovery of MBPs in proteomes, which operates by extracting metals from MBPs with chelators and logging the resulting structural perturbation of MBPs with thermal proteome profiling. We applied METAL-TPP to the human proteomes and identified 2856 proteins with significant thermal shifts, including not only many known MBPs but also 75 proteins without previous annotation of metal-binding activity.
Project description:The fidelity of translation selection begins with the base pairing of codon-anticodon complex between the m-RNA and tRNAs. Binding of cognate and near-cognate tRNAs induces 30S subunit of the ribosome to wrap around the ternary complex, EF-Tu(GTP)aa-tRNA. We have proposed that large thermal fluctuations play a crucial role in the selection process. To test this conjecture, we have developed a theoretical technique to determine the probability that the ternary complex, as a result of large thermal fluctuations, forms contacts leading to stabilization of the GTPase activated state. We argue that the configurational searches for such processes are in the tail end of the probability distribution and show that the probability for this event is localized around the most likely configuration. Small variations in the repositioning of cognate relative to near-cognate complexes lead to rate enhancement of the cognate complex. The binding energies of over a dozen unique site-bound magnesium structural motifs are investigated and provide insights into the nature of interaction of divalent metal ions with the ribosome.
Project description:Although the interaction between light and motion in cavity optomechanical systems is inherently nonlinear, experimental demonstrations to date have allowed a linearized description in all except highly driven cases. Here, we demonstrate a nanoscale optomechanical system in which the interaction between light and motion is so large (single-photon cooperativity C0?103) that thermal motion induces optical frequency fluctuations larger than the intrinsic optical linewidth. The system thereby operates in a fully nonlinear regime, which pronouncedly impacts the optical response, displacement measurement and radiation pressure backaction. Specifically, we measure an apparent optical linewidth that is dominated by thermo-mechanically induced frequency fluctuations over a wide temperature range, and show that in this regime thermal displacement measurements cannot be described by conventional analytical models. We perform a proof-of-concept demonstration of exploiting the nonlinearity to conduct sensitive quadratic readout of nanomechanical displacement. Finally, we explore how backaction in this regime affects the mechanical fluctuation spectra.