Matching Items (45)
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Description
My research focuses on studying the interaction between spatiotemporally encoded electric field (EF) and living cells and biomolecules. In this thesis, I report two projects that I have been working on to address these questions. My first project studies the EF modulation of the extracellular-signal-regulated kinase (ERK) pathway. I demonstrated

My research focuses on studying the interaction between spatiotemporally encoded electric field (EF) and living cells and biomolecules. In this thesis, I report two projects that I have been working on to address these questions. My first project studies the EF modulation of the extracellular-signal-regulated kinase (ERK) pathway. I demonstrated modulation of ERK activities using alternative current (AC) EFs in a new frequency range applied through high-k dielectric passivated microelectrodes with single-cell resolution without electrochemical process induced by the EF stimulation. Further experiments pinpointed a mechanism of phosphorylation site of epidermal growth factor (EGF) receptor to activate the EGFR-ERK pathway that is independent of EGF. AC EFs provide a new strategy to precisely control the dynamics of ERK activation, which may serve as a powerful platform for control of cell behaviors with implications in wide range of biomedical applications. In the second project, I used solid-state nanopore system as the base platform for single molecule experiments, and developed a scalable bottom-up process to construct planar nanopore devices with self-aligned transverse tunneling junctions, all embedded on a nanofluidic chip, based on feedback-controlled reversible electrochemical deposition in a confined nanoscale space. I demonstrated the first simultaneous detection of translocating DNA molecules from both the ionic channel and the tunneling junction with very high yield. Meanwhile, the signal amplitudes from the tunneling junction are unexpectedly high, indicating that these signals are probably dominated by transient currents associated with the fast motion of charged molecules between the transverse electrodes. This new platform provides the flexibility and reproducibility required to study quantum-tunneling-based DNA detection and sequencing. In summary, I have developed two platforms that engineer heterogenous EF at different length scales to modulate live cells and single biomolecules. My results suggest that the charges and dipoles of biomolecules can be electrostatically manipulated to regulate physiological responses and to push detection resolution to single molecule level. Nevertheless, there are still many interesting questions remain, such as the molecular mechanism of EF-protein interaction and tunneling signal extraction. These will be the topics for future investigations.
ContributorsWang, Yuan (Author) / Qing, Quan (Thesis advisor) / Lindsay, Stuart (Committee member) / Wang, Shaopeng (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2021
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Description
Traditionally, allostery is perceived as the response of a catalytic pocket to perturbations induced by binding at another distal site through the interaction network in a protein, usually associated with a conformational change responsible for functional regulation. Here, I utilize dynamics-based metrics, Dynamic Flexibility Index and Dynamic Coupling Index to

Traditionally, allostery is perceived as the response of a catalytic pocket to perturbations induced by binding at another distal site through the interaction network in a protein, usually associated with a conformational change responsible for functional regulation. Here, I utilize dynamics-based metrics, Dynamic Flexibility Index and Dynamic Coupling Index to provide insight into how 3D network of interactions wire communications within a protein and give rise to the long-range dynamic coupling, thus regulating key allosteric interactions. Furthermore, I investigate its role in modulating protein function through mutations in evolution. I use Thioredoxin and β-lactamase enzymes as model systems, and show that nature exploits "hinge-shift'' mechanism, where the loss in rigidity of certain residue positions of a protein is compensated by reduced flexibility of other positions, for functional evolution. I also developed a novel approach based on this principle to computationally engineer new mutants of the promiscuous ancestral β-lactamase (i.e., degrading both penicillin and cephatoxime) to exhibit specificity only towards penicillin with a better catalytic efficiency through population shift in its native ensemble.I investigate how allosteric interactions in a protein can regulate protein interactions in a cell, particularly focusing on E. coli ribosome. I describe how mutations in a ribosome can allosterically change its associating with magnesium ions, which was further shown by my collaborators to distally impact the number of biologically active Adenosine Triphosphate molecules in a cell, thereby, impacting cell growth. This allosteric modulation via magnesium ion concentrations is coined, "ionic allostery''. I also describe, the role played by allosteric interactions to regulate information among proteins using a simplistic toy model of an allosteric enzyme. It shows how allostery can provide a mechanism to efficiently transmit information in a signaling pathway in a cell while up/down regulating an enzyme’s activity.
The results discussed here suggest a deeper embedding of the role of allosteric interactions in a protein’s function at cellular level. Therefore, bridging the molecular impact of allosteric regulation with its role in communication in cellular signaling can provide further mechanistic insights of cellular function and disease development, and allow design of novel drugs regulating cellular functions.
ContributorsModi, Tushar (Author) / Ozkan, Sefika (Thesis advisor) / Beckstein, Oliver (Committee member) / Vaiana, Sara (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2020
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Description

The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) – a main carrier of cholesterol in the blood stream – to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the

The process, how lipids are removed from the circulation and transferred from high density lipoprotein (HDL) – a main carrier of cholesterol in the blood stream – to cells, is highly complex. HDL particles are captured from the blood stream by the scavenger receptor, class B, type I (SR-BI), the so-called HDL receptor. The details in subsequent lipid-transfer process, however, have not yet been completely understood. The transfer has been proposed to occur directly at the cell surface across an unstirred water layer, via a hydrophobic channel in the receptor, or after HDL endocytosis. The role of the target lipid membrane for the transfer process, however, has largely been overlooked. Here, we studied at the single molecule level how HDL particles interact with synthetic lipid membranes. Using (high-speed) atomic force microscopy and fluorescence correlation spectroscopy (FCS) we found out that, upon contact with the membrane, HDL becomes integrated into the lipid bilayer. Combined force and single molecule fluorescence microscopy allowed us to directly monitor the transfer process of fluorescently labelled amphiphilic lipid probe from HDL particles to the lipid bilayer upon contact.

ContributorsPlochberger, Birgit (Author) / Rohrl, Clemens (Author) / Preiner, Johannes (Author) / Rankl, Christian (Author) / Brameshuber, Mario (Author) / Madl, Josef (Author) / Bittman, Robert (Author) / Ros, Robert (Author) / Sezgin, Erdinc (Author) / Eggeling, Christian (Author) / Hinterdorfer, Peter (Author) / Stangl, Herbert (Author) / Schutz, Gerhard J. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2017-11-21
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Description

Mechanical interactions between cells and their microenvironment dictate cell phenotype and behavior, calling for cell mechanics measurements in three-dimensional (3D) extracellular matrices (ECM). Here we describe a novel technique for quantitative mechanical characterization of soft, heterogeneous samples in 3D. The technique is based on the integration of atomic force microscopy

Mechanical interactions between cells and their microenvironment dictate cell phenotype and behavior, calling for cell mechanics measurements in three-dimensional (3D) extracellular matrices (ECM). Here we describe a novel technique for quantitative mechanical characterization of soft, heterogeneous samples in 3D. The technique is based on the integration of atomic force microscopy (AFM) based deep indentation, confocal fluorescence microscopy, finite element (FE) simulations and analytical modeling. With this method, the force response of a cell embedded in 3D ECM can be decoupled from that of its surroundings, enabling quantitative determination of the elastic properties of both the cell and the matrix. We applied the technique to the quantification of the elastic properties of metastatic breast adenocarcinoma cells invading into collagen hydrogels. We found that actively invading and fully embedded cells are significantly stiffer than cells remaining on top of the collagen, a clear example of phenotypical change in response to the 3D environment. Treatment with Rho-associated protein kinase (ROCK) inhibitor significantly reduces this stiffening, indicating that actomyosin contractility plays a major role in the initial steps of metastatic invasion.

ContributorsStaunton, Jack (Author) / Doss, Bryant (Author) / Lindsay, Stuart (Author) / Ros, Robert (Author) / College of Liberal Arts and Sciences (Contributor)
Created2016-01-27
Description
The goal of this study was to investigate the possibility of catch bond formation between nectin and actin during cellular adhesion by modeling the actin-filament binding protein, afadin, out of equilibrium. This was done through the in silico methodology of Molecular Dynamics (MD); more specifically using Steered Molecular Dynamics (SMD)

The goal of this study was to investigate the possibility of catch bond formation between nectin and actin during cellular adhesion by modeling the actin-filament binding protein, afadin, out of equilibrium. This was done through the in silico methodology of Molecular Dynamics (MD); more specifically using Steered Molecular Dynamics (SMD) and Replica Exchange Molecular Dynamics (REMD). The methodology of this experiment centered around generating physiologically probable structures through REMD, then using MD and SMD methods to generate structures in the absence and presence of force respectively. These structures were then analyzed through Solvent Accessible Surface Area (SASA) measurements to assess the overall compactness of the structure, which led to implicit observations on the overall resistance of force that this structure has. Overall, it was found that the structure displayed more compact conformations in the presence of force as the SASA values of the binding pocket and individual residues involved in the system tend to decrease as force was applied. This is indicative of more stable conformations and a force resistant quality that is indicative of catch bonding, thus leading to the natural conclusion that this structure displays catch bond character.
ContributorsChapman, Jonathan (Author) / Singharoy, Abhishek (Thesis director) / Beckstein, Oliver (Committee member) / Ros, Robert (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2024-05