Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provi... more Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics.
The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigat... more The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigated at different pH values to compare with the native one. It was found that the limiting molecular area of the reduced lysozyme was not subphase pH dependent as the native lysozyme. To explain this result in terms of the conformation and orientation of the lysozyme Langmuir monolayer at various subphase pH values, we have used infrared reflection absorption spectroscopy. The interpretation of the results make plausible change of the conformation and orientation of the native lysozyme Langmuir monolayer with the subphase pH 3, 6, and 11.
Accumulation or aggregation of amyloidogenic proteins in the brain plays a central role in neurod... more Accumulation or aggregation of amyloidogenic proteins in the brain plays a central role in neurodegenerative diseases. The most common and highly growing form of dementia in the elderly population is Alzheimer's disease (AD) followed by Parkinson's disease (PD). The major proteins associated are amyloid beta (Abeta) and alpha-synuclein (alpha-syn) in AD and PD, respectively. These proteins are released or found
A compact, label-free sensor array for rapid detection of Escherichia coli (E. coli) using antimi... more A compact, label-free sensor array for rapid detection of Escherichia coli (E. coli) using antimicrobial peptide assisted impedimetric sensor platform.
Amyloid-fibril formation in human serum albumin (HSA) led to hydrogel formation in the presence o... more Amyloid-fibril formation in human serum albumin (HSA) led to hydrogel formation in the presence of clusters of bismuth ferrite (BiFeO 3 or BFO) nanoparticles (NPs). Factors responsible for hydrogel formation were size and phase of NPs.
ABSTRACTAn urgent need exist for developing handheld devices for rapid, sensitive, and specific d... more ABSTRACTAn urgent need exist for developing handheld devices for rapid, sensitive, and specific detection method for pathogens. Here we demonstrate a rapid detection method for Gram-positive and Gram-negative bacteria using an impedance sensor array functionalized with antimicrobial peptides (AMPs). This impedance sensor screens pathogens in real-time and has comparable sensitivity with current detection methods like polymerase chain reaction (PCR) and immunoassay. Functionalized electrodes in array selectively bind to the corresponding bacteria strains, resulting in variations in the impedance modulus. Impedance variation is used to detect incubated bacterial cell concentration with a resolution of 1 cell µL-1. The dynamic range of detection for both Gram-positive and Gram-negative bacteria is found to be 103-106cfu mL-1. Micropatterned electrodes modified with AMPs in an impedimetric array offer an excellent platform for rapid and selective detection of pathogens in contaminated w...
ABSTRACT Microfabricated cantilevers, similar to those used in Atomic Force Microscopy (AFM), are... more ABSTRACT Microfabricated cantilevers, similar to those used in Atomic Force Microscopy (AFM), are generating growing interest as a sensor platform for label-free detection of chemical and biological molecules [1–17]. Using recent advances in surface microfabrication, it is possible to design and fabricate cantilevers and cantilever arrays with extremely high sensitivity for mass or surface stress. These cantilevers are generally fabricated from silicon or silicon nitride by top-down micromachining methods and can be produced efficiently and affordably. Although the cantilevers have micrometer dimensions, their response are in nanometer-scale, which lends itself to their reference as nanomechanical transducers. The cantilever can be made in different shapes and sizes allowing for flexibility in the design, which renders the resulting cantilevers ideal candidates for the possible incorporation in microfluidic and miniaturized lab-on-a-chip devices. Generally, these cantilevers are operated in either the static deflection mode or the dynamic resonant mode. The basic principle for the static mode is that a chemical or physical event occurring at the functionalized surface of one side of the cantilever generates a surface stress difference (between the active functionalized and passive non-functionalized sides) that causes the cantilever to bend away from its resting position. Whereas in the resonant mode, a binding event occurring on the cantilever increases the overall mass thus decreasing the resonant frequency, which is similar to quartz crystal microbalances. In general, when a force is applied to the end of a free standing cantilever a vertical bending will result. As described by Hooke’s Law (\( (F=-k_{spring}\Delta z),\)), the bending or deflection (Δz) of the cantilever is directly proportional to the applied force F, and the cantilever spring constant k spring is the proportionality factor. The cantilever spring constant dictates the flexibility and sensitivity of the cantilever and is defined by its dimensions and material constants. For a rectangular-shaped cantilever, k spring, is given by [18] $$ k_{spring}\frac{Ewt^{3}}{4l^3}
The surface defect dominated visible emission from one-dimensional multiferroic BiFeO 3 (BFO) nan... more The surface defect dominated visible emission from one-dimensional multiferroic BiFeO 3 (BFO) nanowires (NWs) is characterized by photoluminescence (PL) spectroscopy. The PL spectra of BFO NWs exhibit a weak near band emission (NBE) along with a strong defect-level emission (DLE). It is suggested that excess surface defects exist in BFO NWs which are responsible for strong visible green emission. Passivation of BFO NW surface with H 2 significantly improves the NBE emission while suppressing surface recombination. Such a surface enhanced emission promises many potential applications of BFO NWs not only in photonic devices such as LEDs but also in fluorescence-based chemical sensing.
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014
Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal... more Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal growth and development. The human fungal pathogen Aspergillus fumigatus expresses RodA hydrophobins that self-assemble on the outer conidial surface into tightly organized nanorods known as rodlets. AFM investigation of the conidial surface allows us to evidence that RodA hydrophobins self-assemble into rodlets through bilayers. Within bilayers, hydrophilic domains of hydrophobins point inward, thus making a hydrophilic core, while hydrophobic domains point outward. AFM measurements reveal that several rodlet bilayers are present on the conidial surface thus showing that proteins self-assemble into a complex three-dimensional multilayer system. The self-assembly of RodA hydrophobins into rodlets results from attractive interactions between stacked β-sheets, which conduct to a final linear cross-β spine structure. A Monte Carlo simulation shows that anisotropic interactions are the main driving forces leading the hydrophobins to self-assemble into parallel rodlets, which are further structured in nanodomains. Taken together, these findings allow us to propose a mechanism, which conducts RodA hydrophobins to a highly ordered rodlet structure. The mechanism of hydrophobin assembly into rodlets offers new prospects for the development of more efficient strategies leading to disruption of rodlet formation allowing a rapid detection of the fungus by the immune system.
Nanoparticle chemistry is emerging in the field of nanomedicine and nanodiagnostics. In recent ti... more Nanoparticle chemistry is emerging in the field of nanomedicine and nanodiagnostics. In recent times quantum dots have been considered as potential probes for bioimaging. These particles can be beneficial when it comes to study neurodegenerative diseases such as Alzheimer's disease. Amyloid beta (1-42) (A (1-42)) is a polypeptide that is the major constituent of the plaques in Alzheimer's disease patients. We have examined the surface and spectroscopic properties of A (1-42) mixed with or conjugated to dihydrolipoic acid-and poly(ethylene glycol)-capped CdSe/ZnS quantum dots. Surface pressure-area isotherms and in situ UV-vis absorption and fluorescence spectroscopy were used to characterize the A (1-42) mixed with or conjugated to quantum dots at the air-water interface. The capping of quantum dots played a role in surface chemistry as was determined by surface pressure-area isotherms and spectroscopic properties of the Langmuir monolayer.
Surface pressure and surface potential-area isotherms were used to characterize a lysozyme Langmu... more Surface pressure and surface potential-area isotherms were used to characterize a lysozyme Langmuir monolayer. The compression-decompression cycles and stability measurements showed a homogeneous and stable monolayer at the air-water interface. Salt concentration in the subphase and pH of the subphase were parameters controlling the homogeneity and stability of the Langmuir monolayer. In situ UV-vis and fluorescence spectroscopies were used to verify the homogeneity of the lysozyme monolayer and to identify the chromophore residues in the lysozyme. Optimal experimental conditions were determined to prepare a homogeneous and stable lysozyme Langmuir monolayer.
Broad-spectrum biosensing technologies examine sensor signals using biomarkers, such as proteins,... more Broad-spectrum biosensing technologies examine sensor signals using biomarkers, such as proteins, DNA, antibodies, specific cells, and macromolecules, based on direct- or indirect-conformational changes. Here, we have investigated the pH-dependent conformational isomerization of human serum albumin (HSA) using microcantilevers as a sensing platform. Native and denatured proteins were immobilized on cantilever surfaces to understand the effect of pH on conformational changes of the protein with respect to the coupling ligand. Our results show that protonation and deprotonation of amino acid residues on proteins play a significant role in generating charge-induced cantilever deflection. Surface plasmon resonance (SPR) was employed as a complementary technique to validate the results.
The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigat... more The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigated at different pH values to compare with the native one. It was found that the limiting molecular area of the reduced lysozyme was not subphase pH dependent as the native lysozyme. To explain this result in terms of the conformation and orientation of the lysozyme Langmuir monolayer at various subphase pH values, we have used infrared reflection absorption spectroscopy. The interpretation of the results make plausible change of the conformation and orientation of the native lysozyme Langmuir monolayer with the subphase pH 3, 6, and 11.
Lipid rafts being rich in cholesterol and sphingolipids are considered to provide ordered lipid e... more Lipid rafts being rich in cholesterol and sphingolipids are considered to provide ordered lipid environment in the neuronal membranes, where it is hypothesized that the cleavage of amyloid precursor protein (APP) to A (1-40) and A (1-42) takes place. It is highly likely that the interaction of lipid raft components like cholesterol, sphingomylein or GM1 leads to nucleation of A and results in aggregation or accumulation of amyloid plaques. One has investigated surface pressure-area isotherms of the lipid raft and A (1-40) Langmuir monolayer. The compression-decompression cycles and the stability of the lipid raft Langmuir monolayer are crucial parameters for the investigation of interaction of A (1-40) with the lipid raft Langmuir monolayer. It was revealed that GM1 provides instability to the lipid raft Langmuir monolayer. Adsorption of A (1-40) onto the lipid raft Langmuir monolayer containing neutral (POPC) or negatively charged phospholipid (DPPG) was examined. The adsorption isotherms revealed that the concentration of cholesterol was important for adsorption of A (1-40) onto the lipid raft Langmuir monolayer containing POPC whereas for the lipid raft Langmuir monolayer containing DPPG:cholesterol or GM1 did not play any role. In situ UV-vis absorption spectroscopy supported the interpretation of results for the adsorption isotherms.
Amyloid beta (1-40) and (1-42) peptides are the major constituents of hallmark senile plaques fou... more Amyloid beta (1-40) and (1-42) peptides are the major constituents of hallmark senile plaques found in Alzheimer's disease (AD) patients. Study of aggregation of Abeta (1-40) and (1-42) peptides and the truncated Abeta fragments could lead towards the mechanism of AD. Langmuir monolayer approach is one of the excellent methods to investigate the mechanism and origin of AD. Particularly, to study the steps involved in the formation and assembly of beta-sheet structures leading to formation of amyloid fibrils. Surface pressure- and surface potential-area isotherms provide information regarding the nature of short-range and long-range interactions between the molecules especially the lipids and the Abeta peptides. Spectroscopic methods like IRRAS, PM-IRRAS, FTIR-ATR, and GIXD at the air-water interface provide insight into the structural characterization, and orientation of the molecules in the Langmuir monolayer.
Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provi... more Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics.
The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigat... more The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigated at different pH values to compare with the native one. It was found that the limiting molecular area of the reduced lysozyme was not subphase pH dependent as the native lysozyme. To explain this result in terms of the conformation and orientation of the lysozyme Langmuir monolayer at various subphase pH values, we have used infrared reflection absorption spectroscopy. The interpretation of the results make plausible change of the conformation and orientation of the native lysozyme Langmuir monolayer with the subphase pH 3, 6, and 11.
Accumulation or aggregation of amyloidogenic proteins in the brain plays a central role in neurod... more Accumulation or aggregation of amyloidogenic proteins in the brain plays a central role in neurodegenerative diseases. The most common and highly growing form of dementia in the elderly population is Alzheimer's disease (AD) followed by Parkinson's disease (PD). The major proteins associated are amyloid beta (Abeta) and alpha-synuclein (alpha-syn) in AD and PD, respectively. These proteins are released or found
A compact, label-free sensor array for rapid detection of Escherichia coli (E. coli) using antimi... more A compact, label-free sensor array for rapid detection of Escherichia coli (E. coli) using antimicrobial peptide assisted impedimetric sensor platform.
Amyloid-fibril formation in human serum albumin (HSA) led to hydrogel formation in the presence o... more Amyloid-fibril formation in human serum albumin (HSA) led to hydrogel formation in the presence of clusters of bismuth ferrite (BiFeO 3 or BFO) nanoparticles (NPs). Factors responsible for hydrogel formation were size and phase of NPs.
ABSTRACTAn urgent need exist for developing handheld devices for rapid, sensitive, and specific d... more ABSTRACTAn urgent need exist for developing handheld devices for rapid, sensitive, and specific detection method for pathogens. Here we demonstrate a rapid detection method for Gram-positive and Gram-negative bacteria using an impedance sensor array functionalized with antimicrobial peptides (AMPs). This impedance sensor screens pathogens in real-time and has comparable sensitivity with current detection methods like polymerase chain reaction (PCR) and immunoassay. Functionalized electrodes in array selectively bind to the corresponding bacteria strains, resulting in variations in the impedance modulus. Impedance variation is used to detect incubated bacterial cell concentration with a resolution of 1 cell µL-1. The dynamic range of detection for both Gram-positive and Gram-negative bacteria is found to be 103-106cfu mL-1. Micropatterned electrodes modified with AMPs in an impedimetric array offer an excellent platform for rapid and selective detection of pathogens in contaminated w...
ABSTRACT Microfabricated cantilevers, similar to those used in Atomic Force Microscopy (AFM), are... more ABSTRACT Microfabricated cantilevers, similar to those used in Atomic Force Microscopy (AFM), are generating growing interest as a sensor platform for label-free detection of chemical and biological molecules [1–17]. Using recent advances in surface microfabrication, it is possible to design and fabricate cantilevers and cantilever arrays with extremely high sensitivity for mass or surface stress. These cantilevers are generally fabricated from silicon or silicon nitride by top-down micromachining methods and can be produced efficiently and affordably. Although the cantilevers have micrometer dimensions, their response are in nanometer-scale, which lends itself to their reference as nanomechanical transducers. The cantilever can be made in different shapes and sizes allowing for flexibility in the design, which renders the resulting cantilevers ideal candidates for the possible incorporation in microfluidic and miniaturized lab-on-a-chip devices. Generally, these cantilevers are operated in either the static deflection mode or the dynamic resonant mode. The basic principle for the static mode is that a chemical or physical event occurring at the functionalized surface of one side of the cantilever generates a surface stress difference (between the active functionalized and passive non-functionalized sides) that causes the cantilever to bend away from its resting position. Whereas in the resonant mode, a binding event occurring on the cantilever increases the overall mass thus decreasing the resonant frequency, which is similar to quartz crystal microbalances. In general, when a force is applied to the end of a free standing cantilever a vertical bending will result. As described by Hooke’s Law (\( (F=-k_{spring}\Delta z),\)), the bending or deflection (Δz) of the cantilever is directly proportional to the applied force F, and the cantilever spring constant k spring is the proportionality factor. The cantilever spring constant dictates the flexibility and sensitivity of the cantilever and is defined by its dimensions and material constants. For a rectangular-shaped cantilever, k spring, is given by [18] $$ k_{spring}\frac{Ewt^{3}}{4l^3}
The surface defect dominated visible emission from one-dimensional multiferroic BiFeO 3 (BFO) nan... more The surface defect dominated visible emission from one-dimensional multiferroic BiFeO 3 (BFO) nanowires (NWs) is characterized by photoluminescence (PL) spectroscopy. The PL spectra of BFO NWs exhibit a weak near band emission (NBE) along with a strong defect-level emission (DLE). It is suggested that excess surface defects exist in BFO NWs which are responsible for strong visible green emission. Passivation of BFO NW surface with H 2 significantly improves the NBE emission while suppressing surface recombination. Such a surface enhanced emission promises many potential applications of BFO NWs not only in photonic devices such as LEDs but also in fluorescence-based chemical sensing.
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2014
Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal... more Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal growth and development. The human fungal pathogen Aspergillus fumigatus expresses RodA hydrophobins that self-assemble on the outer conidial surface into tightly organized nanorods known as rodlets. AFM investigation of the conidial surface allows us to evidence that RodA hydrophobins self-assemble into rodlets through bilayers. Within bilayers, hydrophilic domains of hydrophobins point inward, thus making a hydrophilic core, while hydrophobic domains point outward. AFM measurements reveal that several rodlet bilayers are present on the conidial surface thus showing that proteins self-assemble into a complex three-dimensional multilayer system. The self-assembly of RodA hydrophobins into rodlets results from attractive interactions between stacked β-sheets, which conduct to a final linear cross-β spine structure. A Monte Carlo simulation shows that anisotropic interactions are the main driving forces leading the hydrophobins to self-assemble into parallel rodlets, which are further structured in nanodomains. Taken together, these findings allow us to propose a mechanism, which conducts RodA hydrophobins to a highly ordered rodlet structure. The mechanism of hydrophobin assembly into rodlets offers new prospects for the development of more efficient strategies leading to disruption of rodlet formation allowing a rapid detection of the fungus by the immune system.
Nanoparticle chemistry is emerging in the field of nanomedicine and nanodiagnostics. In recent ti... more Nanoparticle chemistry is emerging in the field of nanomedicine and nanodiagnostics. In recent times quantum dots have been considered as potential probes for bioimaging. These particles can be beneficial when it comes to study neurodegenerative diseases such as Alzheimer's disease. Amyloid beta (1-42) (A (1-42)) is a polypeptide that is the major constituent of the plaques in Alzheimer's disease patients. We have examined the surface and spectroscopic properties of A (1-42) mixed with or conjugated to dihydrolipoic acid-and poly(ethylene glycol)-capped CdSe/ZnS quantum dots. Surface pressure-area isotherms and in situ UV-vis absorption and fluorescence spectroscopy were used to characterize the A (1-42) mixed with or conjugated to quantum dots at the air-water interface. The capping of quantum dots played a role in surface chemistry as was determined by surface pressure-area isotherms and spectroscopic properties of the Langmuir monolayer.
Surface pressure and surface potential-area isotherms were used to characterize a lysozyme Langmu... more Surface pressure and surface potential-area isotherms were used to characterize a lysozyme Langmuir monolayer. The compression-decompression cycles and stability measurements showed a homogeneous and stable monolayer at the air-water interface. Salt concentration in the subphase and pH of the subphase were parameters controlling the homogeneity and stability of the Langmuir monolayer. In situ UV-vis and fluorescence spectroscopies were used to verify the homogeneity of the lysozyme monolayer and to identify the chromophore residues in the lysozyme. Optimal experimental conditions were determined to prepare a homogeneous and stable lysozyme Langmuir monolayer.
Broad-spectrum biosensing technologies examine sensor signals using biomarkers, such as proteins,... more Broad-spectrum biosensing technologies examine sensor signals using biomarkers, such as proteins, DNA, antibodies, specific cells, and macromolecules, based on direct- or indirect-conformational changes. Here, we have investigated the pH-dependent conformational isomerization of human serum albumin (HSA) using microcantilevers as a sensing platform. Native and denatured proteins were immobilized on cantilever surfaces to understand the effect of pH on conformational changes of the protein with respect to the coupling ligand. Our results show that protonation and deprotonation of amino acid residues on proteins play a significant role in generating charge-induced cantilever deflection. Surface plasmon resonance (SPR) was employed as a complementary technique to validate the results.
The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigat... more The surface chemistry and spectroscopy of the reduced lysozyme Langmuir monolayer were investigated at different pH values to compare with the native one. It was found that the limiting molecular area of the reduced lysozyme was not subphase pH dependent as the native lysozyme. To explain this result in terms of the conformation and orientation of the lysozyme Langmuir monolayer at various subphase pH values, we have used infrared reflection absorption spectroscopy. The interpretation of the results make plausible change of the conformation and orientation of the native lysozyme Langmuir monolayer with the subphase pH 3, 6, and 11.
Lipid rafts being rich in cholesterol and sphingolipids are considered to provide ordered lipid e... more Lipid rafts being rich in cholesterol and sphingolipids are considered to provide ordered lipid environment in the neuronal membranes, where it is hypothesized that the cleavage of amyloid precursor protein (APP) to A (1-40) and A (1-42) takes place. It is highly likely that the interaction of lipid raft components like cholesterol, sphingomylein or GM1 leads to nucleation of A and results in aggregation or accumulation of amyloid plaques. One has investigated surface pressure-area isotherms of the lipid raft and A (1-40) Langmuir monolayer. The compression-decompression cycles and the stability of the lipid raft Langmuir monolayer are crucial parameters for the investigation of interaction of A (1-40) with the lipid raft Langmuir monolayer. It was revealed that GM1 provides instability to the lipid raft Langmuir monolayer. Adsorption of A (1-40) onto the lipid raft Langmuir monolayer containing neutral (POPC) or negatively charged phospholipid (DPPG) was examined. The adsorption isotherms revealed that the concentration of cholesterol was important for adsorption of A (1-40) onto the lipid raft Langmuir monolayer containing POPC whereas for the lipid raft Langmuir monolayer containing DPPG:cholesterol or GM1 did not play any role. In situ UV-vis absorption spectroscopy supported the interpretation of results for the adsorption isotherms.
Amyloid beta (1-40) and (1-42) peptides are the major constituents of hallmark senile plaques fou... more Amyloid beta (1-40) and (1-42) peptides are the major constituents of hallmark senile plaques found in Alzheimer's disease (AD) patients. Study of aggregation of Abeta (1-40) and (1-42) peptides and the truncated Abeta fragments could lead towards the mechanism of AD. Langmuir monolayer approach is one of the excellent methods to investigate the mechanism and origin of AD. Particularly, to study the steps involved in the formation and assembly of beta-sheet structures leading to formation of amyloid fibrils. Surface pressure- and surface potential-area isotherms provide information regarding the nature of short-range and long-range interactions between the molecules especially the lipids and the Abeta peptides. Spectroscopic methods like IRRAS, PM-IRRAS, FTIR-ATR, and GIXD at the air-water interface provide insight into the structural characterization, and orientation of the molecules in the Langmuir monolayer.
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Papers by Garima Thakur