Thermomechanical Response of a Representative Porin for Biomimetics

General Synergistic Hybrid Catalyst Synthesis Method Using a Natural Enzyme Scaffold-Confined Metal Nanocluster

Due to differences in the chemical properties or optimal reaction conditions of the catalysts, the challenge in the design of bio-chemical hybrid catalysts is that the bio-catalysts or chemical catalysts usually cannot maintain the initial catalytic performance. Herein, we report a general bio-chemical hybrid catalyst synthesis method using a natural enzyme scaffold-confined metal nanocluster. A redox-active enzyme is a nanoreactor that allows access to and reduces metal ions into metal nanoclusters in situ, resulting in the enzyme-confined metal nanocluster hybrid catalyst with a synergistic effect to boost catalytic performance. Specifically, bilirubin oxidase-Ir nanoclusters (BOD-Ir NCs) with catalytic properties for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are designed. The BOD-Ir NCs exhibit an approximately 2-fold ORR activity compared with pure BOD and a 4-fold OER activity compared with pure Ir NCs. BOD-Ir NCs exhibit stability for over 50,000 s, exceeding that of pure Ir NCs (22,000 s). The synergistic catalytic performance is attributed to the following: the mild preparation condition and matched sizes of BOD and the Ir NCs maintain the natural activity of BOD; the highly conductive Ir NCs improve the ORR activity of BOD; and the confining effect of BOD, which improves the stability and activity of the Ir NCs during the OER. In particular, BOD-Ir NCs exhibit a high half-wave potential of 0.97 V for the ORR and a low overpotential of 319 mV at 10 mA cm^-2 for the OER, surpassing most of reported catalysts under neutral conditions. Furthermore, laccase-Ir NCs and glucose oxidase-Pd NCs with synergistic catalytic performances are fabricated, proving the universality of this synthetic method. This facile strategy for designing synergistic hybrid catalysts is expected to be applied to more complex chemical transformations.

Temperature effect on the SARS-CoV-2: A molecular dynamics study of the spike homotrimeric glycoprotein

Rapid spread of SARS-CoV-2 virus have boosted the need of knowledge about inactivation mechanisms to minimize the impact of COVID-19 pandemic. Recent studies have shown that SARS-CoV-2 virus can be disabled by heating, the exposure time for total inactivation depending on the reached temperature (e.g. more than 45 min at 329 K or less than 5 min at 373 K. In spite of recent crystallographic structures, little is known about the molecular changes induced by the temperature. Here, we unravel the molecular basis of the effect of the temperature over the SARS-CoV-2 spike glycoprotein, which is a homotrimer with three identical monomers, by executing atomistic molecular dynamics (MD) simulations at 298, 310, 324, 338, 358 and 373 K. Furthermore, both the closed down and open up conformational states, which affect the accessibility of receptor binding domain, have been considered. Our results suggest that the spike homotrimer undergoes drastic changes in the topology of the hydrogen bonding interactions and important changes on the secondary structure of the receptor binding domain (RBD), while electrostatic interactions (i.e. salt bridges) are mainly preserved. The proposed inactivation mechanism has important implications for engineering new approaches to fight the SARS-CoV-2 coronavirus, as for example, cleaving or reorganizing the hydrogen bonds through chaotropic agents or nanoparticles with local surface resonant plasmon effect.

Tethering of the IgG1 Antibody to Amorphous Silica for Immunosensor Development: A Molecular Dynamics Study

A key factor for improving the sensitivity and performance of immunosensors based on mechanical-plasmonic methods is the orientation of the antibody proteins immobilized on the inorganic surface. Although experimental techniques fail to determine surface phenomena at the molecular level, modern simulations open the possibility for improving our understanding of protein-surface interactions. In this work, replica exchange molecular dynamics (REMD) simulations have been used to model the IgG1 protein tethered onto the amorphous silica surface by considering a united-atom model and a relatively large system (2500 nm² surface). Additional molecular dynamics (MD) simulations have been conducted to derive an atomistic model for the amorphous silica surface using the cristobalite crystal structure as a starting point and to examine the structure of the free IgG1 antibody in the solution for comparison when immobilized. Analyses of the trajectories obtained for the tethered IgG1, which was sampled considering 32 different temperatures, have been used to define the geometry of the protein with respect to the inorganic surface. The tilt angle of the protein with respect to the surface plane increases with temperature, the most populated values being 24, 66, and 87° at the lowest (250 K), room (298 K), and the highest (380 K) temperatures. This variation indicates that the importance of protein-surface interactions decreases with increasing temperature. The influence of the surface on the structure of the antibody is very significant in the constant region, which is directly involved in the tethering process, while it is relatively unimportant for the antigen-binding fragments, which are farthest from the surface. These results are expected to contribute to the development of improved mechanical-plasmonic sensor microarrays in the near future.

Biomimetic hybrid membranes: incorporation of transport proteins/peptides into polymer supports

Molecular sensing, water purification and desalination, drug delivery, and DNA sequencing are some striking applications of biomimetic hybrid membranes. These devices take advantage of biomolecules, which have gained excellence in their specificity and efficiency during billions of years, and of artificial materials that load the purified biological molecules and provide technological properties, such as robustness, scalability, and suitable nanofeatures to confine the biomolecules. Recent methodological advances allow more precise control of polymer membranes that support the biomacromolecules, and are expected to improve the design of the next generation of membranes as well as their applicability. In the first section of this review we explain the biological relevance of membranes, membrane proteins, and the classification used for the latter. After this, we critically analyse the different approaches employed for the production of highly selective hybrid membranes, focusing on novel materials made of self-assembled block copolymers and nanostructured polymers. Finally, a summary of the advantages and disadvantages of the different methodologies is presented and the main characteristics of biomimetic hybrid membranes are highlighted.

Ultrasensitive Microstring Resonators for Solid State Thermomechanical Analysis of Small and Large Molecules

Thermal analysis plays an important role in both industrial and fundamental research and is widely used to study thermal characteristics of a variety of materials. However, despite considerable effort using different techniques, research struggles to resolve the physicochemical nature of many thermal transitions such as amorphous relaxations or structural changes in proteins. To overcome the limitations in sensitivity of conventional techniques and to gain new insight into the thermal and mechanical properties of small- and large-molecule samples, we have developed an instrumental analysis technique using resonating low-stress silicon nitride microstrings. With a simple sample deposition method and postprocess data analysis, we are able to perform rapid thermal analysis of direct instrumental triplicate samples with only pico- to nanograms of material. Utilizing this method, we present the first measurement of amorphous alpha and beta relaxation, as well as liquid crystalline transitions and decomposition of small-molecule samples deposited onto a microstring resonator. Furthermore, sensitive measurements of the glass transition of polymers and yet unresolved thermal responses of proteins below their apparent denaturation temperature, which seem to include the true solid state glass transition of pure protein, are reported. Where applicable, thermal events detected with the setup were in good agreement with conventional techniques such as differential scanning calorimetry and dynamic mechanical analysis. The sensitive detection of even subtle thermal transitions highlights further possibilities and applications of resonating microstrings in instrumental physicochemical analysis.