Molecular Systems Design & Engineering最新文献

Antibiotics are currently the main strategy to treat bacterial infections, but they can cause antimicrobial resistance. Thus, it is urgent to solve this problem. The emergence of photothermal therapy provides a new opportunity for the prevention and control of bacterial infection. In recent years, photothermal agents have been widely used in infection control and wound healing due to their strong antibacterial properties and low drug resistance. Photothermal agents (PTAs) are nanomaterials themselves, or small molecules loaded in nanoparticles, and are the basic elements of PPT. In this review, we discuss the characteristics of wound dressings in skin wound healing, types and main functions of antibacterial photothermal therapy (PTA), and the fabrication and application of wound dressings. Finally, the current challenges and future development of PTAs as a photothermal antibacterial platform for wound healing are summarized and discussed.

Plastics are ubiquitous and essential to our society. Unfortunately, they contribute to environmental pollution due to their lack of degradation upon disposal. Here, we describe some model polymers that were used to demonstrate controlled degradation under environmental conditions (pH 7). The polymers were made from a 7 : 3 ratio of hydroquinone (HQA) and terephthalate (TPhA) alkyne derivatives with various amounts of polyethylene glycol (PEGAz) and acetal azides (AAz). Their structures were determined by ¹H NMR. The ratio of monomer units in the polymers was shown to be similar to the feed ratio. The polymers are amorphous with low glass transition temperatures (T_g). Furthermore, the polymer containing 1 : 1 ratio of PEG to acetal units was degraded in pH 5 and 7 buffer solutions over a 3 month period, whereas the polymer with only acetal group degraded at pH 5. Our results show that degradation can be controlled with different amounts of PEG and acetal groups.

Auxetic structures are unique with a negative Poisson's ratio. Unlike regular materials, they respond to external loading with simultaneous expansion or compression in all directions, rendering powerful properties advantageous in diverse applications from manufacturing to space engineering. The auxetic behaviors are determined by structural design and architecture. Such structures have been discovered in natural crystals and demonstrated synthetically with bulk materials. Recent development of DNA-based structures has pushed the unit cell size to the nanometer scale. DNA nanotechnology utilizes sequence complementarity between nucleotides. By combining sequence designs with programmable self-assembly, it is possible to construct complex structures with nanoscale accuracy and to perform dynamic reconfigurations. Herein, we report a novel design of auxetic nanostars with sliding behaviors using DNA origami. Our proposed structure, inspired by an Islamic pattern, demonstrates a unit cell with two distinct reconfigurations by programming directed sliding mechanisms. Compared to previous metamaterials, the DNA nanostars show an architecture with tunable auxetic properties for the first time. We envision that this strategy may form the basis of novel metastructures with adaptability and open new possibilities in bioengineering.

Human cytochrome c (hCyt c) contains a covalently attached heme group with six-coordination (Met/His) and plays vital biological functions, including electron transfer and peroxidase activity by structural alterations, as well as other functions by interactions with partners such as neuroglobin (Ngb). In this study, we designed and engineered an artificial disulfide bond in hCyt c via double mutations (A51C/G77C) which bridges the Ω-loops C and D. The formation of the intramolecular disulfide bond (Cys51–Cys77) was confirmed by mass spectrometry. The molecular modeling study showed that the disulfide bond did not alter the overall structure, and the local structure where Cys51 was located was well folded into an α-helix. Spectroscopic studies were also performed to probe the effects of the disulfide bond on the protein structure, which revealed that the heme coordination of Met80 was likely weakened. Consequently, the rate of ligand binding and the peroxidase activity were enhanced. Meanwhile, the interaction between hCyt c and Ngb was weakened, as suggested by titration studies. These observations indicate that the dynamic properties of Ω-loops C and D may favor the heme coordination and protein–protein interactions by conformational change, which supports the native functions of hCyt c.

In this study, the effects of the substituent and solvent on the photophysical properties of the designed ESIPT active as well as donor–acceptor structured unsymmetrical azine dyes L1–L5 (R1–5 = –H, –NH₂, –OCH₃, –CF₃ and –CN, respectively) were investigated at PBE0/6-31++G(d,p) and CAM-B3LYP/6-31++G(d,p) levels of theory in the gas phase and three solvent media. The structural parameters, relative energies, vibrational spectra, photophysical properties, potential energy curves, natural bond orbital (NBO) charges, charge transfer (CT) indices, electron density properties, and reduced density gradient (RDG) spikes were computed. The results of vibrational spectra, structural parameters and electron density analysis demonstrated that the O–H⋯N H-bonding interaction is strengthened in all dyes upon photoexcitation from the S₀ to S₁ state which can facilitate the ESIPT process. All dyes exhibited both enol and keto emissions, in good agreement with the reported experimental results. The largest Stokes shift for keto emissions in solvent media was observed in MeOH solvent and is in the order 143 nm (L5) > 138 (L4) > 133 (L1) > 120 (L3) > 115 (L2) at the PBE0/6-31++G(d,p) level of theory. Introducing electron-withdrawing groups can increase the absorption and emission wavelengths as well as the red shift in fluorescence emission of L4 and L5, but hinder the occurrence of the ESIPT process compared with L2 and L3. The results demonstrated that the substituent effect is more significant in changing the molecular optical properties than the solvent effect. Our designed ESIPT molecules can simultaneously show enol and keto emissions and thus can be regarded as candidates to design single-molecule white-light emission materials.

Hard carbon is one of the most promising anode materials for sodium-ion batteries (SIBs). Biomass-derived hard carbon is deemed to be a good choice because of its superior material properties, abundance source, and cost advantages. This work used Physalis alkekengi L.'s husks as precursors to prepare a series of hard carbon materials via a pyrolysis method. It was found that the carbonization temperature is closely linked to the lattice characteristics of PLH-derived hard carbon. Higher temperatures promote the degree of graphitization of the lattice, which produces a smaller carbon interlayer spacing. The optimal sample demonstrated a high electrochemical performance and good reaction kinetics. It maintained a capacity of 291.6 mA h g⁻¹ after 100 cycles at 0.1 A g⁻¹ and delivered an average capacity of 61.9 mA h g⁻¹ at a high rate of 2.0 A g⁻¹. Furthermore, a full cell assembled using the optimal sample as an anode and Na₃V₂(PO₄)₃ as a cathode gave a high reversible capacity of 161.9 mA h g⁻¹ at 0.1 A g⁻¹ after 100 cycles.

The binding of the receptor binding domain (RBD) of spike protein to the human ACE2 receptor is the primary step in the SARS-CoV-2 infection process. Spike protein has been an important therapeutic target. Emerging variants of SARS-CoV-2 have been imposing a significant challenge. Variants, especially with mutations on the RBD of spike protein, provide enhanced affinity towards the hACE2 receptor compared to the wild-type. Despite the development of many therapeutics, their efficacy towards the variants remains poor. In the present study, we used a fragment replacement approach to probe the fragment's space for analog design. We screened various fragments based on the geometric requirements to fit within the specified local environments of the RBD–ACE2 complex. Among all the screened analogs, two showed a better binding affinity with the RBD–ACE2 complex of the P.1 variant. Our all-atom simulations and free-energy calculations revealed a stable interaction of analogs with the interface residues of the RBD–ACE2 complex. The binding of analogs influenced the interactions of the key residues and led to structural interference in the complex. Essential dynamics analysis revealed that both analogs induce a change in the dynamic motion throughout the complex. The designed analogs may modulate the dynamics of the RBD–ACE2 complex formation and can be used as one of the lead molecules to interfere with the initial infection process of COVID-19 infections.

While the rise of superbugs and new resistance mechanisms continues decreasing the effectiveness of classical antibiotics, antimicrobial peptides (AMPs) are emerging as a new class of antimicrobials. Still, several drawbacks limit their transition to the clinic, including high production cost, haemolytic activity and possible inactivation by proteases. Here, we give an overview of the most recent work on short AMPs, which are currently a minority in the AMP databases, and of the main AMP design rules, describing their application for short sequences. We also summarize the techniques that can serve to investigate the key steps of the antimicrobial action and that can aid in the engineering of a tuned AMP interaction with bacterial barriers. Particular emphasis is given to the relationship between peptide sequence features and interfacial behaviour, highlighting the role of AMPs self-assembly in the interaction with membranes and their antimicrobial activity.

A mixed-ligand metal–organic framework (MOF) material composed of both amine- and hydroxyl-bearing linkers, KSU-1, was reacted with a variety of isocyanates. The hydroxyl groups reacted to a greater extent than the amines, in conflict with the previously observed relative nucleophilicities of these functionalities in the same MOF. When immobilized individually in monofunctional MOFs, the amine-functionalized linker was more reactive than the hydroxyl linker, indicating that the reactivity reversal observed in KSU-1 is due to the groups' mutual confinement within the MOF.

Chondroitin is a natural occurring glycosaminoglycan with applications as a nutraceutical and pharmaceutical ingredient and can be extracted from animal tissues. Microbial chondroitin-like polysaccharides emerged as a safer and more sustainable alternative source. However, chondroitin titers using either natural or recombinant microorganisms are still far from meeting the increasing demand. The use of genome-scale models and computational predictions can assist the design of microbial cell factories with possible improved titers of these value-added compounds. Genome-scale models have been herein used for the first time to predict genetic modifications in Escherichia coli engineered strains that would potentially lead to improved chondroitin production. Additionally, using synthetic biology approaches, a pathway for producing chondroitin has been designed and engineered in E. coli. Afterwards, the most promising mutants identified based on bioinformatics predictions were constructed and evaluated for chondroitin production in flask fermentation. This resulted in the production of 118 mg L⁻¹ of extracellular chondroitin by overexpressing both superoxide dismutase (sodA) and a lytic murein transglycosylase (mltB). Then, batch and fed-batch fermentations at the bioreactor scale were also evaluated, in which the mutant overexpressing mltB led to an extracellular chondroitin production of 427 mg L⁻¹ and 535 mg L⁻¹, respectively. The computational approach herein described identified several potential novel targets for improved chondroitin biosynthesis, which may ultimately lead to a more efficient production of this glycosaminoglycan.