A5016314336- Microtubule and mitosis dynamics
- Protein Structure and Dynamics
- Machine Learning in Bioinformatics
- Cellular transport and secretion
- Bacteriophages and microbial interactions
- Photosynthetic Processes and Mechanisms
- Cellular Mechanics and Interactions
- Enzyme Structure and Function
- Microfluidic and Bio-sensing Technologies
- Gold and Silver Nanoparticles Synthesis and Applications
- Spectroscopy Techniques in Biomedical and Chemical Research
- Genomics and Chromatin Dynamics
- Computational Drug Discovery Methods
- Molecular spectroscopy and chirality
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Biosensors and Analytical Detection
- Extracellular vesicles in disease
- Receptor Mechanisms and Signaling
- Mass Spectrometry Techniques and Applications
- Axon Guidance and Neuronal Signaling
- Hereditary Neurological Disorders
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
University of Cincinnati
2022-2025
The current pandemic has shown that we need sensitive and deployable diagnostic technologies. Surface-enhanced Raman scattering (SERS) sensors can be an ideal solution for developing such advanced point-of-need (PON) tests. Homogeneous (reagentless) SERS work by directly responding to the target without any processing step, making them capable simple one-pot assays, but their limitation is achievable sensitivity, insufficient compared what needed sensing of viral biomarkers. Noncovalent DNA...
Several dozen mutations in the M87 isoform of spastin enzyme have been associated with mobility impairment hereditary spastic paraplegias. Some them impact structural determinants two functional conformations protein: spiral and ring. Here we investigate possible patterns between these disease-related residues aligned regions closely related protein katanin toward their role transition conformations, which is essential for both enzymes' function. By performing a variety molecular simulations...
Abstract Early diagnosis remains of pivotal importance in reducing patient morbidity and mortality cancer. To this end, liquid biopsy is emerging as a tool to perform broad cancer screenings. Small extracellular vesicles (sEVs), also called exosomes, found bodily fluids can serve important biomarkers these Our group has recently developed label-free electrokinetic microchip purify sEVs from blood. Herein, we demonstrate the feasibility integrate approach with surface-enhanced Raman...
The nanomachine from the ATPases associated with various cellular activities superfamily, called spastin, severs microtubules during processes. To characterize functionally important allostery in we employed methods evolutionary information, to graph-based networks, machine learning applied atomistic molecular dynamics simulations of spastin its monomeric and functional hexameric forms, presence or absence ligands. Feature selection, using approaches, for transitions between states...
The identification and characterization of the main conformations from a protein population are challenging inherently high-dimensional problem. Here, we evaluate performance Secondary sTructural Ensembles with machine LeArning (StELa) double-clustering method, which clusters structures based on relationship between φ ψ dihedral angles in backbone secondary structure protein, thus focusing local properties structures. classification states as vectors composed clusters' indices arising...
Essential cellular processes of microtubule disassembly and protein degradation, which span lengths from tens μm to nm, are mediated by specialized molecular machines with similar hexameric structure function. Our simulations at atomistic coarse-grained scales show that both the microtubule-severing spastin caseinolytic protease ClpY, accomplish spectacular unfolding their diverse substrates, a lattice dihydrofolate reductase (DHFR), taking advantage mechanical anisotropy in these proteins....
Severing proteins are nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily whose function is to remodel largest filaments, microtubules. The standard machines adopt hexameric ring structures for functional reasons, while being primarily monomeric in absence of nucleotide. Both major severing proteins, katanin and spastin, believed follow this trend. However, studies proposed that they populate lower-order oligomers presence cofactors, which...
Microtubules (MTs), a cellular structure element, exhibit dynamic instability and can switch stochastically from growth to shortening; but the factors that trigger these processes at molecular level are not understood. We developed 3D Microtubule Assembly Disassembly DYnamics (MADDY) model, based upon bead-per-monomer representation of αβ-tubulin dimers forming an MT lattice, stabilized by lateral longitudinal interactions between tubulin subunits. The model was parameterized against...
Abstract Essential cellular processes of microtubule disassembly and protein degradation, which span lengths from tens μ m to nm, are mediated by specialized molecular machines with similar hexameric structure function. Our simulations at atomistic coarse-grained scales show that both the severing spastin caseinolytic protease ClpY, accomplish spectacular unfolding their diverse substrates, a lattice dihydrofolate reductase (DHFR), taking advantage mechanical anisotropy in these proteins. By...
Several dozen mutations in the large human spastin enzyme assembly have been associated with mobility impairment hereditary spastic paraplegias. Some of them impact structural determinants two functional conformations protein, spiral and ring. Here we investigate possible effect on transition between conformations, which is essential for enzymatic function. By performing a variety molecular simulations (including metadynamics) closely related protein katanin, suggest that about one fourth...
Abstract Severing proteins are nanomachines from the AAA+ (ATPases associated with various cellular activities) superfamily whose function is to remodel largest filaments, microtubules. The standard machines adopt hexameric ring structures for functional reasons, while being primarily monomeric in absence of nucleotide. Both major severing proteins, katanin and spastin, believed follow this trend. However, studies proposed that they populate lower-order oligomers presence co-factors, which...
Abstract The identification and characterization of the main conformations from a protein population is challenging, inherently high-dimensional problem. We introduce Secondary sTructural Ensembles with machine LeArning (StELa) double clustering method, which clusters structures based on underlying Ramachandran plot. Our approach takes advantage relationship between phi psi dihedral angles in backbone secondary structure protein. classification states as vectors composed clusters’ indices...