Virupakshi Soppina - Academia.edu (original) (raw)
Uploads
Papers by Virupakshi Soppina
Organic & Biomolecular Chemistry
Dinitrostyryl derivative as a probe for imaging and elucidating the viscosity of lipid droplets.
bioRxiv (Cold Spring Harbor Laboratory), Jun 10, 2023
KIF1A is involved in fast axonal transport of synaptic vesicle precursor, neurofilament, and dens... more KIF1A is involved in fast axonal transport of synaptic vesicle precursor, neurofilament, and densecore vesicle, essential for neuronal development and maintenance. Several point mutations in the KIF1A motor domain have been identified in patients with various motor neuron diseases. Recent studies have shown that these mutations affected the motor and cargo localization in cultured hippocampal and C.elegans neurons. However, a detailed analysis of these mutations on KIF1A motility, force generation, and cargo transport is largely unexplored. Here, we have analyzed the effect of 16 point mutations and showed that these mutations significantly decreased the motor velocity and landing rates compared to wild-type motors. Except for A255V, mutations V144F, V220I, and E233D mildly affected motor mechanical outputs. S58L, A202P, R216P, R216H, L249Q, T312M, and R316W mutants exhibited drastic impairments in the motility properties, force generation, and cargo transport. Notably, T46M, T99M, G102D, S215R, and E253K mutants showed strong microtubule binding, resulting in complete disruption of cargo transport. Our study provides the first comprehensive demonstration of KIF1A disease mutations at the molecular level. The observed changes in motility properties and cargo transport align with the severity of disease phenotype observed in KIF1A-associated neurological disorders)
New Journal of Chemistry
Trifluoromethyl-substituted fluorophores with naphthalene and julolidine groups were utilized ima... more Trifluoromethyl-substituted fluorophores with naphthalene and julolidine groups were utilized imaging and quantifying lipid droplets in COS-7 cells.
Journal of Photochemistry and Photobiology B: Biology
Organic & Biomolecular Chemistry
Sensing proteins and imaging sub-cellular organelles with N-sulfonyl pyridinium fluorophores.
Organic & Biomolecular Chemistry
ROS-mediated cross-talk between mitochondria and lysosomes can be visualized using rhodamine–phen... more ROS-mediated cross-talk between mitochondria and lysosomes can be visualized using rhodamine–phenothiazine conjugates.
Journal of Visualized Experiments
Biomedicines
Alcoholic liver disease (ALD) alters gut microbiota and tight junctions, causing bacterial compon... more Alcoholic liver disease (ALD) alters gut microbiota and tight junctions, causing bacterial components to enter the portal vein and induce oxidative stress-induced inflammation in the liver. Only corticosteroids and liver transplants are treatment options for severe alcoholic hepatitis. ALD’s pathophysiology is unknown. However, acetaldehyde’s toxic effects cause oxidative stress and intestinal permeability. This study investigates the influence of a synbiotic (a combination of aged garlic extract (AGE) and Lactobacillus rhamnosus MTCC1423) on colonic oxidative stress and inflammation in ALD male Wistar rats and Caco2 cells. MDA measurement by HPLC in CaCo2 cells, blood serum, and colon tissue demonstrated that synbiotic treatment in the ALD model reduces oxidative stress. Further, fecal high-throughput 16S rRNA gene sequencing revealed the microbiome’s shift towards Firmicutes in the synbiotic group compared to ethanol. In addition, DCFDA labeling and H/E staining demonstrate that t...
Frontiers in Cell and Developmental Biology
Journal of Visualized Experiments
Frontiers in Toxicology
Metal Organic Frameworks (MOFs) are extensively used for a wide range of applications due to thei... more Metal Organic Frameworks (MOFs) are extensively used for a wide range of applications due to their exceptionally high surface area. MOF particles are conventionally in micron size, but the nanosized MOFs show good transportation/mobility due to their small size, and when combined with the high surface area of MOFs, it makes MOF nanoparticles an ideal candidate to study for environmental remediation. Therefore, it is important to study the ecotoxicological impact of these MOFs. In this study, we developed rhodamine labelled nanoparticles of zinc imidazolate metal organic framework (ZIF-8 MOFs) as a means of in vivo tracing the MOF translocation in C. elegans. Rhodamine B isothiocyanate functionalized ZIF-8 MOFs nanoparticles (RBITC@ZIF-8 MOF nanoparticles; size 44 ± 7 nm) were fed to the worms naturally within a concentration range of 0.16–16.4 μg mg−1. Fluorescence was detected in the pharyngeal and gut lumen regions of the worms after 4 h of treatment, for exposure concentrations &...
Organic & Biomolecular Chemistry
The tuning of lutidines for selective sub-cellular localization in the mitochondria and endoplasm... more The tuning of lutidines for selective sub-cellular localization in the mitochondria and endoplasmic reticulum.
Journal of Alloys and Compounds, 2021
This study focuses on the development of a highly defective, non-stoichiometric and amorphous TiO... more This study focuses on the development of a highly defective, non-stoichiometric and amorphous TiOx as an efficient anti-viral surface coating. This amorphous phase is found to be significantly more effective against the baculovirus as compared to the conventionally used anatase modification. Moreover, the coating is found to be highly transparent in the entire visible-near infrared range. Radio frequency (RF) magnetron sputtering, one of the industrial scale techniques is used here to synthesize this film at room temperature. Furthermore, this film is found to be non-cytotoxic, durable, chemically stable and has strong adhesiveness with that of the substrate. Being cost-effective and environment friendly, this anti-viral surface coating holds huge promises of commercialization.
BMC Biology
Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical... more Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood. Results We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B >...
BMC Biology
Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical... more Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood. Results We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B >...
Cell Biochemistry and Biophysics, 2022
We use two-state ratchet models containing single and coupled Brownian motors to understand the r... more We use two-state ratchet models containing single and coupled Brownian motors to understand the role of motor-microtubule binding, ATPase reaction rate and dimerisation on the translational velocities of Kinesin motors. We use model parameters derived from the experimental measurements on KIF1A, KIF13A, KIF13B, and KIF16B motors to compute velocities in μm/s. We observe that both the models show the same trend in velocities (KIF1A > KIF13A > KIF13B > KIF16B) as the experimental results. However, the models significantly underpredict the velocities when compared with the experiments. The predictions of the coupled-motor model are closer to the experiments than those of the single-motor model. Our results indicate that the variation of ATPase reaction rate governs the trend in velocities for the above four motors. The variation of motor-microtubule binding affinity and the coupling strength between the motor domains may only have a secondary effect. More rigorous models that incorporate the power-stroke mechanism are necessary for better quantitative compliance with the experiments.
Organic & Biomolecular Chemistry
Dinitrostyryl derivative as a probe for imaging and elucidating the viscosity of lipid droplets.
bioRxiv (Cold Spring Harbor Laboratory), Jun 10, 2023
KIF1A is involved in fast axonal transport of synaptic vesicle precursor, neurofilament, and dens... more KIF1A is involved in fast axonal transport of synaptic vesicle precursor, neurofilament, and densecore vesicle, essential for neuronal development and maintenance. Several point mutations in the KIF1A motor domain have been identified in patients with various motor neuron diseases. Recent studies have shown that these mutations affected the motor and cargo localization in cultured hippocampal and C.elegans neurons. However, a detailed analysis of these mutations on KIF1A motility, force generation, and cargo transport is largely unexplored. Here, we have analyzed the effect of 16 point mutations and showed that these mutations significantly decreased the motor velocity and landing rates compared to wild-type motors. Except for A255V, mutations V144F, V220I, and E233D mildly affected motor mechanical outputs. S58L, A202P, R216P, R216H, L249Q, T312M, and R316W mutants exhibited drastic impairments in the motility properties, force generation, and cargo transport. Notably, T46M, T99M, G102D, S215R, and E253K mutants showed strong microtubule binding, resulting in complete disruption of cargo transport. Our study provides the first comprehensive demonstration of KIF1A disease mutations at the molecular level. The observed changes in motility properties and cargo transport align with the severity of disease phenotype observed in KIF1A-associated neurological disorders)
New Journal of Chemistry
Trifluoromethyl-substituted fluorophores with naphthalene and julolidine groups were utilized ima... more Trifluoromethyl-substituted fluorophores with naphthalene and julolidine groups were utilized imaging and quantifying lipid droplets in COS-7 cells.
Journal of Photochemistry and Photobiology B: Biology
Organic & Biomolecular Chemistry
Sensing proteins and imaging sub-cellular organelles with N-sulfonyl pyridinium fluorophores.
Organic & Biomolecular Chemistry
ROS-mediated cross-talk between mitochondria and lysosomes can be visualized using rhodamine–phen... more ROS-mediated cross-talk between mitochondria and lysosomes can be visualized using rhodamine–phenothiazine conjugates.
Journal of Visualized Experiments
Biomedicines
Alcoholic liver disease (ALD) alters gut microbiota and tight junctions, causing bacterial compon... more Alcoholic liver disease (ALD) alters gut microbiota and tight junctions, causing bacterial components to enter the portal vein and induce oxidative stress-induced inflammation in the liver. Only corticosteroids and liver transplants are treatment options for severe alcoholic hepatitis. ALD’s pathophysiology is unknown. However, acetaldehyde’s toxic effects cause oxidative stress and intestinal permeability. This study investigates the influence of a synbiotic (a combination of aged garlic extract (AGE) and Lactobacillus rhamnosus MTCC1423) on colonic oxidative stress and inflammation in ALD male Wistar rats and Caco2 cells. MDA measurement by HPLC in CaCo2 cells, blood serum, and colon tissue demonstrated that synbiotic treatment in the ALD model reduces oxidative stress. Further, fecal high-throughput 16S rRNA gene sequencing revealed the microbiome’s shift towards Firmicutes in the synbiotic group compared to ethanol. In addition, DCFDA labeling and H/E staining demonstrate that t...
Frontiers in Cell and Developmental Biology
Journal of Visualized Experiments
Frontiers in Toxicology
Metal Organic Frameworks (MOFs) are extensively used for a wide range of applications due to thei... more Metal Organic Frameworks (MOFs) are extensively used for a wide range of applications due to their exceptionally high surface area. MOF particles are conventionally in micron size, but the nanosized MOFs show good transportation/mobility due to their small size, and when combined with the high surface area of MOFs, it makes MOF nanoparticles an ideal candidate to study for environmental remediation. Therefore, it is important to study the ecotoxicological impact of these MOFs. In this study, we developed rhodamine labelled nanoparticles of zinc imidazolate metal organic framework (ZIF-8 MOFs) as a means of in vivo tracing the MOF translocation in C. elegans. Rhodamine B isothiocyanate functionalized ZIF-8 MOFs nanoparticles (RBITC@ZIF-8 MOF nanoparticles; size 44 ± 7 nm) were fed to the worms naturally within a concentration range of 0.16–16.4 μg mg−1. Fluorescence was detected in the pharyngeal and gut lumen regions of the worms after 4 h of treatment, for exposure concentrations &...
Organic & Biomolecular Chemistry
The tuning of lutidines for selective sub-cellular localization in the mitochondria and endoplasm... more The tuning of lutidines for selective sub-cellular localization in the mitochondria and endoplasmic reticulum.
Journal of Alloys and Compounds, 2021
This study focuses on the development of a highly defective, non-stoichiometric and amorphous TiO... more This study focuses on the development of a highly defective, non-stoichiometric and amorphous TiOx as an efficient anti-viral surface coating. This amorphous phase is found to be significantly more effective against the baculovirus as compared to the conventionally used anatase modification. Moreover, the coating is found to be highly transparent in the entire visible-near infrared range. Radio frequency (RF) magnetron sputtering, one of the industrial scale techniques is used here to synthesize this film at room temperature. Furthermore, this film is found to be non-cytotoxic, durable, chemically stable and has strong adhesiveness with that of the substrate. Being cost-effective and environment friendly, this anti-viral surface coating holds huge promises of commercialization.
BMC Biology
Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical... more Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood. Results We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B >...
BMC Biology
Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical... more Background Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood. Results We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B >...
Cell Biochemistry and Biophysics, 2022
We use two-state ratchet models containing single and coupled Brownian motors to understand the r... more We use two-state ratchet models containing single and coupled Brownian motors to understand the role of motor-microtubule binding, ATPase reaction rate and dimerisation on the translational velocities of Kinesin motors. We use model parameters derived from the experimental measurements on KIF1A, KIF13A, KIF13B, and KIF16B motors to compute velocities in μm/s. We observe that both the models show the same trend in velocities (KIF1A > KIF13A > KIF13B > KIF16B) as the experimental results. However, the models significantly underpredict the velocities when compared with the experiments. The predictions of the coupled-motor model are closer to the experiments than those of the single-motor model. Our results indicate that the variation of ATPase reaction rate governs the trend in velocities for the above four motors. The variation of motor-microtubule binding affinity and the coupling strength between the motor domains may only have a secondary effect. More rigorous models that incorporate the power-stroke mechanism are necessary for better quantitative compliance with the experiments.