A5086167440- Protein Structure and Dynamics
- Bacterial Genetics and Biotechnology
- Lipid Membrane Structure and Behavior
- Bacteriophages and microbial interactions
- Particle accelerators and beam dynamics
- Spectroscopy and Quantum Chemical Studies
- Antimicrobial Peptides and Activities
- Antibiotic Resistance in Bacteria
- Enzyme Structure and Function
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Electrostatic Discharge in Electronics
- Mass Spectrometry Techniques and Applications
- Immune Response and Inflammation
- Nanopore and Nanochannel Transport Studies
- Influenza Virus Research Studies
- Escherichia coli research studies
- Cellular transport and secretion
- Nicotinic Acetylcholine Receptors Study
- Biochemical and Structural Characterization
- Genomics and Phylogenetic Studies
- Atomic and Molecular Physics
- Streptococcal Infections and Treatments
- Yersinia bacterium, plague, ectoparasites research
- RNA Research and Splicing
University of Southampton
2015-2025
Defence Science and Technology Laboratory
2015-2025
University of Bristol
2004-2012
Cornell University
2004
Bacterial membranes are complex organelles composed of a variety lipid types. The differences in their composition key factor determining relative permeabilities. success antibacterial agents depends upon interaction with bacterial membranes, yet little is known about the molecular-level interactions within different species. To address this, we have performed molecular dynamics simulations two membranes: outer membrane E. coli and cell S. aureus . We retained chemical complexity by...
Abstract Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make scattered various locations and formats for data-driven machine learning using overlay databank To demonstrate practical relevance such approach, present NMRlipids Databank—a community-driven, open-for-all database featuring programmatic...
Molecular dynamics simulations provide a route to studying the of lipid bilayers at atomistic or near resolution. Over past 10 years so, molecular have become an established part biophysicist's tool kit for study model biological membranes. As simulation time scales move from tens hundreds nanoseconds and beyond, it is timely re-evaluate accuracy models. We describe comparative analysis five freely available force fields that are commonly used bilayers. focus our on...
Antimicrobial peptides are small, cationic proteins that can induce lysis of bacterial cells through interaction with their membranes. Different mechanisms for cell have been proposed, but these models tend to neglect the role chemical composition membrane, which differs between species and be heterogeneous even within a single cell. Moreover, envelope Gram-negative bacteria such as E. coli contains two membranes differing compositions. To this end, we report first molecular dynamics...
For molecular dynamics simulations of biological membrane systems to live up the potential providing accurate atomic level detail into properties and functions, it is essential that force fields used model such are as possible. One property often assess field accuracy carbon-hydrogen (or carbon-deuterium) order parameters lipid tails, which can be accurately measured using experimental NMR techniques. There a variety analysis tools available calculate these from computational work correctly...
OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite wealth reported structural and biophysical studies, structure-function relationships this remain unclear. For example, it still debated whether functions as pore, precise molecular role plays attachment to peptidoglycan periplasm unknown. The absence consensus view partly due lack complete structure full-length protein. To address issue, we performed molecular-dynamics simulations model dimer...
Phosphatidylserine (PS) is a negatively charged lipid type commonly found in eukaryotic membranes, where it interacts with proteins via nonspecific electrostatic interactions as well specific binding. Moreover, the presence of calcium ions, PS lipids can induce membrane fusion and phase separation. Molecular details these phenomena remain poorly understood, partly because accurate models to interpret experimental data have not been available. Here we gather set previously published NMR C–H...
Interest in lipid interactions with proteins and other biomolecules is emerging not only fundamental biochemistry but also the field of nanobiotechnology where lipids are commonly used, for example, carriers mRNA vaccines. The outward-facing components cellular membranes nanoparticles, headgroups, regulate membrane approaching substances, such as proteins, drugs, RNA, or viruses. Because headgroup conformational ensembles have been experimentally determined physiologically relevant...
Membrane properties are determined in part by lipid composition, and cholesterol plays a large role determining these properties. Cellular membranes show diverse range of compositions, the effects which include alterations to cellular biomechanics, raft formation, membrane fusion, signaling pathways, metabolism, pharmaceutical therapeutic efficacy, disease onset. In addition, an important non-cellular membranes, with its concentration skin matrix being implicated several diseases....
Antimicrobial peptides (AMPs) are a potential solution to the increasing threat of antibiotic resistance, but successful design active nontoxic AMPs requires understanding their mechanism action. Molecular dynamics (MD) simulations can provide atomic-level information regarding how interact with cell membrane. Here, we have used MD study two linear analogs battacin, naturally occurring cyclic, lipidated, nonribosomal AMP. Like these against Gram-negative multidrug resistant and Gram-positive...
Cellular membrane lipid composition is implicated in diseases and major biological functions cells, but membranes are difficult to study experimentally due their intrinsic disorder complex phase behaviour. Molecular dynamics (MD) simulations have been useful understanding systems, they require significant computational resources often suffer inaccuracies model parameters. Applications of data-driven machine learning methods, currently revolutionising many fields, limited systems the lack...
Understanding the molecular basis for protein denaturation by urea and guanidinium chloride (GdmCl) should accommodate observation that, on a molar basis, GdmCl is generally 2−2.5-fold more effective as denaturant than urea. Previous studies [Smith, J. S., Scholtz, M. (1996) Biochemistry 35, 7292−7297] have suggested that effects of stability alanine-based helical peptides can be separated into salt effects, since adding equimolar NaCl to enhanced urea-induced unfolding an extent was close...
The bacterial cell envelope is composed of a mixture different lipids and proteins, making it an inherently complex organelle. interactions between integral membrane proteins are crucial for their respective spatial localization within cells. We have employed microsecond timescale coarse-grained molecular dynamics simulations vesicles varying sizes with range protein lipid compositions, used novel approaches to measure both local global system dynamics, the latter based on spherical...
Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due their intrinsic disorder complex phase behaviour. Molecular dynamics (MD) simulations have been useful understanding systems, they require significant computational resources often suffer from inaccuracies model parameters. Applications of data-driven machine learning methods, currently revolutionising many fields, remain limited use...