A5061717074- Lipid Membrane Structure and Behavior
- Protein Structure and Dynamics
- Biomedical and Engineering Education
- Bacteriophages and microbial interactions
- Genetics, Bioinformatics, and Biomedical Research
- HIV Research and Treatment
- Research Data Management Practices
- Scientific Computing and Data Management
- Radiomics and Machine Learning in Medical Imaging
- RNA Interference and Gene Delivery
- RNA and protein synthesis mechanisms
- Spectroscopy and Quantum Chemical Studies
- Interdisciplinary Research and Collaboration
- Influenza Virus Research Studies
- Bacterial Genetics and Biotechnology
- Nanopore and Nanochannel Transport Studies
- Monoclonal and Polyclonal Antibodies Research
- Enzyme Structure and Function
- Computational Physics and Python Applications
- Receptor Mechanisms and Signaling
- Fibroblast Growth Factor Research
- Ion channel regulation and function
- Machine Learning in Materials Science
- Glycosylation and Glycoproteins Research
- Mosquito-borne diseases and control
Los Alamos National Laboratory
2017-2024
University of Oxford
2013-2018
Centre Hospitalier de Fougères
2015
Oxfam
2014
Dalhousie University
2008-2013
Indian Institute of Technology Guwahati
2010
MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories individual protein structures. MD simulations biological molecules have become an important tool to elucidate the relationship between structure physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output in their own formats so that development new trajectory algorithms confined...
The influenza virus is surrounded by an envelope composed of a lipid bilayer and integral membrane proteins. Understanding the structural dynamics provides biophysical insights into aspects viral function, such as wide-ranging survival times virion in different environments. We have combined experimental data from X-ray crystallography, nuclear magnetic resonance spectroscopy, cryo-electron microscopy, lipidomics to build model intact A virion. This basis microsecond-scale coarse-grained...
Cell membranes are crowded and complex environments. To investigate the effect of protein-lipid interactions on dynamic organization in mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing >100 copies an inwardly rectifying potassium (Kir) channel which forms specific with regulatory lipid phosphatidylinositol 4,5-bisphosphate (PIP2). The tendency protein molecules to cluster has organizing membrane into compartments. At same time, diversity...
Abstract The spatiotemporal organisation of membranes is often characterised by the formation large protein clusters. In Escherichia coli , outer membrane (OMP) clustering leads to OMP islands, which underpins turnover and drives across cell envelope. Modelling how islands form in order understand their origin behaviour has been confounded inherent difficulties simulating numbers OMPs over meaningful timescales. Here, we overcome these problems training a mesoscale model incorporating...
Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic structural properties of biological membranes. Molecular dynamics (MD) simulations provide valuable tool for studying models, complementing experimental approaches. It is now possible to simulate large systems, such as simplified models bacterial viral envelope Consequently, there pressing need develop tools visualize quantify these immense which typically comprise millions particles. To...
G-protein coupled receptors (GPCRs) comprise a large family of membrane proteins with rich functional diversity. Signaling through the apelin receptor (AR or APJ) influences cardiovascular system, central nervous system and glucose regulation. Pathophysiological involvement has been shown in atherosclerosis, cancer, human immunodeficiency virus-1 (HIV-1) infection obesity. Here, we present high-resolution nuclear magnetic resonance (NMR) spectroscopy-based structure N-terminus first...
The appeal of multiscale modeling approaches is predicated on the promise combinatorial synergy. However, this can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider molecular dynamics (MD) simulations that combine accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations sampling speed reductive, coarse-grained (CG) representations. AA-to-CG conversions relatively straightforward because deterministic...
The Na<sup>+</sup>/H<sup>+</sup> exchanger isoform 1 (NHE1) is an integral membrane protein that regulates intracellular pH by removing one H<sup>+</sup> in exchange for extracellular Na<sup>+</sup>. It has a large N-terminal domain of 12 transmembrane segments and C-terminal regulatory domain. We characterized the cysteine accessibility amino acids putative segment IX (residues 339–363). Each residue was mutated to functional cysteineless NHE1 protein. Of 25 mutated, 5 were inactive or...
The cytoskeleton underlying cell membranes may influence the dynamic organization of proteins and lipids within bilayer by immobilizing certain transmembrane (TM) forming corrals membrane. Here, we present coarse-grained resolution simulations a biologically realistic membrane model asymmetrically organized TM proteins. We determine effects cytoskeletal immobilization selected using long time scale molecular dynamics simulations. By introducing compartments with varying degrees restraints...
Enveloped viruses are enclosed by a lipid membrane inside of which all the components necessary for virus life cycle; viral proteins, genome and metabolites. Viral envelopes bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived host cell during replication. Thus, composition bilayer depends on complex constitution lipids host-cell’s organelle(s) where assembly and/or budding particle occurs. Here, molecular dynamics (MD) simulations authentic, asymmetric...
Receptor tyrosine kinases are single-pass membrane proteins that form dimers within the membrane. The interactions of their transmembrane domains (TMDs) play a key role in dimerization and signaling. Fibroblast growth factor receptor 3 (FGFR3) is interest as G380R mutation its TMD underlying cause ~99% cases achondroplasia, most common human dwarfism. structural consequences this remain uncertain: shifts position relative to lipid bilayer but does not alter association free energy. We have...
Rhomboid proteases are integral membrane serine that catalyze peptide bond hydrolysis in biological membranes. Little is currently known about the interaction of enzyme and substrate. Coarse-grained molecular dynamics simulations hydrated lipid bilayers employed herein to study E. coli rhomboid protease GlpG (ecGlpG) with transmembrane domain (TMD) substrate Spitz. Spitz does not associate ecGlpG exclusively at putative gate near TMD 5. Instead, there six prominent stable sites, including...
Enveloped viruses, such as SARS-CoV-2, infect cells via fusion of their envelope with the host membrane. By employing molecular simulations to characterize viral envelopes, researchers can gain insights into key determinants infection. Here, Frontera supercomputer is leveraged for large-scale modeling and analysis authentic whose lipid compositions are complex realistic. Visual Molecular Dynamics (VMD) support MPI employed, overcoming previous computational limitations enabling investigation...
A mathematical expression for the outage probability of a selection combining diversity receiver with an arbitrary number input branches is presented exponentially correlated K fading channels. Numerical and simulation results are plotted effect correlation, parameter on performance studied. Results suggest that correlation coefficient less than 0.5 may be used in practice.