A5025334582- Antimicrobial Peptides and Activities
- Biochemical and Structural Characterization
- Protein Structure and Dynamics
- SARS-CoV-2 and COVID-19 Research
- Nicotinic Acetylcholine Receptors Study
- Computational Drug Discovery Methods
- Photoreceptor and optogenetics research
- vaccines and immunoinformatics approaches
- Chemical Synthesis and Analysis
- Supramolecular Self-Assembly in Materials
- Polydiacetylene-based materials and applications
- Receptor Mechanisms and Signaling
- Influenza Virus Research Studies
- Modular Robots and Swarm Intelligence
- Protein Hydrolysis and Bioactive Peptides
- Immunotherapy and Immune Responses
- Microbial Natural Products and Biosynthesis
- Advanced biosensing and bioanalysis techniques
- Antibiotic Resistance in Bacteria
- Innovative Microfluidic and Catalytic Techniques Innovation
- Photosynthetic Processes and Mechanisms
- Machine Learning in Materials Science
- Protein purification and stability
- Bacteriophages and microbial interactions
- Monoclonal and Polyclonal Antibodies Research
Concordia University
2021-2024
Concordia University
2023-2024
Los Alamos National Laboratory
2018-2021
University of Illinois Urbana-Champaign
2015-2021
Urbana University
2017
Swarthmore College
2009
Significance We developed antimicrobial polypeptides (AMPs) with unprecedented radial amphiphilicity. Unlike typical AMPs characterized by facial amphiphilicity or biomimetic polymers randomly distributed charged and hydrophobic groups, this class of is made up homo-polypeptides that feature a radially amphiphilic (RA) structure adopt stable α-helical conformation helical core exterior shell, which formed flexible side chains terminal charge group. The RA appear to offer several advantages...
Symmetrization of contacts in D614G SARS-CoV-2 Spike favors greater probability infection-capable conformation.
Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble biocompatible substrate. Nanoaggregate can be controlled tuning chemistry peptide composition, but the sequence-structure-function relations remain poorly characterized....
Current modularity-based community detection methods show decreased performance as relational networks become increasingly noisy. These also yield a large number of diverse structures solutions, which is problematic for applications that impose constraints on the acceptable solutions or in cases where user focused specific communities interest. To address both these problems, we develop semi-supervised spin-glass model enables current to incorporate background knowledge forms individual...
Summary The COVID-19 pandemic underwent a rapid transition with the emergence of SARS-CoV-2 variant that carried amino acid substitution D614G in Spike protein became globally prevalent. G-form is both more infectious vitro and associated increased viral loads infected people. To gain insight into mechanism underlying these distinctive characteristics, we employed multiple replicas microsecond all-atom simulations to probe molecular-level impact this on Spike’s closed open states. state...
Abstract Synthetic polypeptides have received increasing attention due to their ability form higher ordered structures similar proteins. The control over secondary structures, which enables dynamic conformational changes, is primarily accomplished by tuning the side-chain hydrophobic or ionic interactions. Herein we report a strategy modulate conformation of utilizing donor–acceptor interactions emanating from H-bonding ligands. Specifically, 1,2,3-triazole groups, when incorporated onto...
Efflux pump avoidance and inhibition are desired properties for the optimization of antibacterial activities against Gram-negative bacteria. However, molecular physicochemical interactions defining interface between compounds efflux pumps remain poorly understood. We identified that correlate with inhibition, predictive similar features in structurally diverse compounds, allow researchers to distinguish substrates, inhibitors, avoiders P. aeruginosa .
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, Spike RBD of SARS-CoV-2 binds human host cell receptor ACE2, enabling virus to enter cell. Both ACE2 are densely glycosylated, it unclear how distinctive glycan types modulate interaction ACE2. Detailed understanding these determinants key development therapeutic strategies....
Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication biocompatible electronics. Molecular-level understanding influence microscopic peptide chemistry on is vital rational design. In this study, we construct a coarse-grained model Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform...
The conformational states explored by polymers and proteins can be controlled environmental conditions (e.g., temperature, pressure, solvent) molecular chemistry weight side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from simulations, quantify changes landscape as a function of external chemistry, relate these modifications structure dynamics. In application n-eicosane chain, we...
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy combat this rational approaches expand search without relying on chemical intuition, avoid rediscovery of similar spaces. In work, we present proof concept an approach rationally identify "chemical vocabulary" related specific drug activity interest employing known rules. We focus pressing concern multidrug...
Understanding differences between search spaces for designing peptides to inhibit bacterial growth.
Coarse-grained molecular simulations reveal the influence of pH and flow on self-assembly DFAG-OPV3-GAFD optoelectronic peptides.
Self-assembling peptides containing aromatic groups are an attractive target for bioelectronic materials design because of their ease manufacture, biocompatibility, aqueous solubility, and chemical tunability. Microscopic understanding the properties that control assembly is a prerequisite rational design. In this work, we study family DXXX−Π–XXXD oligopeptides possessing π-conjugated core flanked by Asp-terminated tetrapeptide wings display pH-triggered into supramolecular aggregates. We...
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand structure and dynamics of this complex pathogen. spike glycoprotein is a significant target for immunogens as it means which virus enters human cells, while simultaneously sporting mutations responsible immune escape. These functional escape processes are regulated molecular-level interactions. Our study presents quantitative insights on domain residue contributions allosteric communication,...
Syk/Zap70 family kinases are essential for signaling via multichain immune-recognition receptors such as tetrameric (αβγ2) FcεRI. Syk activation is generally attributed to cis binding of its tandem SH2 domains dual phosphotyrosines within FcεRIγ-ITAMs (immunoreceptor tyrosine-based motifs). However, the mechanistic details docking on γ homodimers unresolved. Here, we estimate that multivalent interactions WT improve cis-oriented by three orders magnitude. We applied molecular dynamics (MD),...
Short, cysteine-rich peptides can exist in stable or metastable structural ensembles due to the number of possible patterns formation their disulfide bonds. One interesting subset this peptide group is conotoxins, which are produced by aquatic snails family Conidae. The μ antagonists and blockers voltage-gated sodium channel, a folding spectrum: on one end spectrum more hirudin-like folders, form bonds then reshuffle them, leading an ensemble kinetically trapped isomers, other BPTI-like...
Abstract COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, Spike RBD of SARS-CoV-2 binds human host cell receptor ACE2, enabling virus to enter cell. Both ACE2 are densely glycosylated, it unclear how distinctive glycan types modulate interaction ACE2. Detailed understanding these determinants key development therapeutic...
Abstract There is consensus among US Materials Science and Engineering departments (driven by discussions with government, academic, national lab stakeholders) that undergraduates require a deeper understanding of computational tools. The 2011 White House Genome Initiative to accelerate the development new materials asserts computer-aided design--and training next generation workforce in design--is vital competitiveness welfare. Skills modeling design are desirable employers hiring our...
Conotoxins are short, cysteine-rich peptides of great interest as novel therapeutic leads and concern lethal biological agents due to their high affinity specificity for various receptors involved in neuromuscular transmission. Currently, the approximately 6000 known conotoxin sequences, only about 3% have associated structural characterization, which a bottleneck rapid high-throughput screening (HTS) identification potential or threats. In this work, we combine graph-based approach with...
Antimicrobial peptides (AMPs) are of growing interest as potential candidates for antibiotics to which antimicrobial resistance increases slowly. In this article, we perform the first in silico study synthetic β sheet-forming AMP GL13K. Through atomistic simulations single and multipeptide systems under different charge conditions, able shine a light on short timescales early aggregation. We find that isolated peptide conformations primarily dictated by sequence rather than charge, whereas...