Marzinek JK
Mechanisms of allostery at the viral surface through the eyes of molecular simulation
The outermost surface layer of any virus is formed by either a capsid shell or envelope. Such layers have traditionally been thought of as immovable structures, but it is becoming apparent that they cannot be viewed exclusively as static architectures protecting the viral genome.
ReadImpact on S. aureus and E. coli Membranes of Treatment with Chlorhexidine and Alcohol Solutions: Insights from Molecular Simulations and Nuclear Magnetic Resonance
Membranes form the first line of defence of bacteria against potentially harmful molecules in the surrounding environment. Understanding the protective properties of these membranes represents an important step towards development of targeted anti-bacterial agents such as sanitizers
ReadNature-inspired synthetic oligourea foldamer channels allow water transport with high salt rejection
Biomimetic membranes incorporating artificial water channels (AWCs) are being developed for industrial water purification. Designing AWCs to achieve high water permeation with salt rejection is a challenge. We designed and synthesized oligourea foldamers, which form predictable helical structures that can be used to create biomimetic porin-like architectures. Two of these foldamers (H2OC1 and H2OC2) allow superior water permeability and almost total salt rejection across lipid membranes. Solid-state NMR, cryo-EM, and molecular dynamics analyses suggest proper insertion of foldamers into lipid vesicles. The H2OC1 crystal structure shows hydrophilic pores of diameters 4.8 and 6.4 Å. The oligourea helices pack together by hydrophobic and salt bridge interactions to build two channel-like assemblies. Besides their proteolytic stability and microbial resistance, the sequence of foldamers can be tailored to regulate selectivity. The ease of designing, synthesizing, and purifying oligourea foldamers is an added advantage. Our findings can help to develop novel AWCs for water purification applications.
ReadAntibacterial and Anti-Inflammatory Effects of Apolipoprotein E
Keywords: apolipoprotein E; antimicrobial peptides; Gram-negative bacteria; host defense; innate immunity; aggregation
ReadUncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein
The COVID-19 pandemic has prompted a rapid response in vaccine and drug development. Herein, we modeled a complete membrane-embedded SARS-CoV-2 spike glycoprotein and used molecular dynamics simulations with benzene probes designed to enhance discovery of cryptic pockets.
ReadMotional clustering in supra-τ c conformational exchange influences NOE cross-relaxation rate
Biomolecular spin relaxation processes, such as the NOE, are commonly modeled by rotational -tumbling combined with fast motions on the sub- timescale. Motions on the supra- timescale, in contrast, are considered to be completely decorrelated to the molecular tumbling and therefore invisible.
ReadManipulating turn residues on de novo designed β-hairpin peptides for selectivity against drug-resistant bacteria
Synthetic β-hairpin antimicrobial peptides (AMPs) offer a useful source for the development of novel antimicrobial agents. β-hairpin peptides generally consist of two side strands bridged by a reverse turn. In literature, most studies focused on the modifications of the side strands to manipulate the stability and activity of β-hairpin peptides, and much less is known about the impact of the turn region.
ReadThe nanotube express: Delivering a stapled peptide to the cell surface
Hypothesis Carbon nanotubes (CNTs) represent a novel platform for cellular delivery of therapeutic peptides. Chemically-functionalized CNTs may enhance peptide uptake by improving their membrane targeting properties.
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