A5090398452- Bacterial Genetics and Biotechnology
- Antibiotic Resistance in Bacteria
- Protein Structure and Dynamics
- Bacteriophages and microbial interactions
- Glycosylation and Glycoproteins Research
- Nanopore and Nanochannel Transport Studies
- Microfluidic and Bio-sensing Technologies
- Advanced biosensing and bioanalysis techniques
- Lipid Membrane Structure and Behavior
- Particle accelerators and beam dynamics
- Antimicrobial Peptides and Activities
- DNA and Nucleic Acid Chemistry
- Vibrio bacteria research studies
- Carbohydrate Chemistry and Synthesis
- Molecular Sensors and Ion Detection
- Genomics and Phylogenetic Studies
- Metabolism and Genetic Disorders
- Antimicrobial Resistance in Staphylococcus
University of Oxford
2025
University of Southampton
2018-2024
Hydrogen mass repartitioning (HMR) that permits time steps of all-atom molecular dynamics simulation up to 4 fs by increasing the hydrogen atoms has been used in protein and phospholipid bilayers simulations improve conformational sampling. Molecular input generation via CHARMM-GUI now supports HMR for diverse programs. In addition, considering ambiguous pH at bacterial outer membrane surface, different protonation states, either −2e or −1e, phosphate groups lipopolysaccharides (LPS) are...
Sugars are ubiquitous in biology; they occur all kingdoms of life. Despite their prevalence, have often been somewhat neglected studies structure-dynamics-function relationships macromolecules to which attached, with the exception nucleic acids. This is largely due inherent difficulties not only studying conformational dynamics sugars using experimental methods but indeed also resolving static structures. Molecular (MD) simulations offer a route prediction ensembles and time-dependent...
Sugars are ubiquitous in biology; they occur all kingdoms of life. Despite their prevalence have often been somewhat neglected studies structure-dynamics-function relationships macromolecules to which attached, with the exception nucleic acids. This is largely due inherent difficulties studying not only conformational dynamics sugars using experimental methods, but indeed also resolving static structures. Molecular Dynamics (MD) simulations offer a route prediction ensembles and...
The maintenance of lipid asymmetry (Mla) system in gram-negative bacteria transfers phospholipids between the outer and inner membrane to maintain asymmetry. Misplaced are extracted from leaflet by MlaA, transferred periplasmic transporter MlaC, shuttled membrane. We set out investigate transfer MlaA MlaC using native mass spectrometry, with aim determining preferences whether preselected lipids for MlaC. First, we characterized that copurified overexpressed phosphatidylglycerol (PG),...
The accurate sequencing of DNA using nanopores requires control over the speed translocation through pores and also conformation. Our studies show that ssDNA translocates hourglass-shaped with hydrophobic constriction regions when an electric field is applied. provides a barrier to thereby slows down movement pore compared without constriction. We moves these in extended conformation therefore does not form undesirable secondary structures may affect accuracy partial current blockages for sequencing.
The cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the interior from external environment. Two membranes encapsulate aqueous periplasm, which contains wall. Little known about mechanisms via antimicrobial peptides move through periplasm outer membrane to their site action, inner membrane. We utilize all-atom molecular dynamics study two peptides, polymyxins B1 and E, within models E. coli different extents. In simple chemical environment, both...
Abstract The periplasm of Gram-negative bacteria is a highly crowded environment comprised many different molecular species. Antibacterial agents that causes lysis by their action against the inner membrane must cross to arrive at target membrane. Very little currently known about route through periplasm, and interactions they experience. To this end, here atomistic dynamics simulations are used study path taken antibiotic polymyxin B1 number models which with proteins osmolytes extents....