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Chloride And Proton Binding In The E. Coli 2cl¯:1h+ Clc Exchanger, Catherine Chenal 2017 The Graduate Center, City University of New York

Chloride And Proton Binding In The E. Coli 2cl¯:1h+ Clc Exchanger, Catherine Chenal

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

The CLC family of membrane proteins is a ubiquitously expressed class of proton and usually voltage-activated chloride transporters involved in a myriad of physiological functions. Crystallographic structures identify up to three chloride binding sites: external, central and intracellular located in the inner half of the trans-membrane domain. The CLC proteins, except for the kidney isoforms, are gated by the extracellular side-facing gating Glutamate (Ex, E148 in CLC-ec1, the E. coli exchanger), which is thought to undergo a conformational change upon protonation.

To sort out how the thermodynamic paths to H+ coupled Cl¯ binding and conformational change in CLC-ec1 at the ...


Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan 2017 Cleveland State University

Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan

Partha Srinivasan

No abstract provided.


Shannon Information Entropy In The Canonical Genetic Code, Louis R. Nemzer 2016 Nova Southeastern University

Shannon Information Entropy In The Canonical Genetic Code, Louis R. Nemzer

Louis R Nemzer

The Shannon entropy measures the expected information value of messages. As with thermodynamic entropy, the Shannon entropy is only defined within a system that identifies at the outset the collections of possible messages, analogous to microstates, that will be considered indistinguishable macrostates. This fundamental insight is applied here for the first time to amino acid alphabets, which group the twenty common amino acids into families based on chemical and physical similarities. To evaluate these schemas objectively, a novel quantitative method is introduced based the inherent redundancy in the canonical genetic code. Each alphabet is taken as a separate system that ...


Shannon Information Entropy In The Canonical Genetic Code, Louis R. Nemzer 2016 Nova Southeastern University

Shannon Information Entropy In The Canonical Genetic Code, Louis R. Nemzer

Louis R Nemzer

The Shannon entropy measures the expected information value of messages. As with thermodynamic entropy, the Shannon entropy is only defined within a system that identifies at the outset the collections of possible messages, analogous to microstates, that will be considered indistinguishable macrostates. This fundamental insight is applied here for the first time to amino acid alphabets, which group the twenty common amino acids into families based on chemical and physical similarities. To evaluate these schemas objectively, a novel quantitative method is introduced based the inherent redundancy in the canonical genetic code. Each alphabet is taken as a separate system that ...


Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor 2016 Colby College

Teaching Systems Biology Of The Circadian Clock With Journal Articles And Matlab, Stephanie R. Taylor

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan 2016 Cleveland State University

Extracting Biochemical Parameters From Protein Distributions Of Vascular Cells, Partha Srinivasan

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Microfluidic Cantilever Detects Bacteria And Measures Their Susceptibility To Antibiotics In Small Confined Volumes, Hashem Etayash, M. F. Khan, Kamaljit Kaur, Thomas Thundat 2016 University of Alberta

Microfluidic Cantilever Detects Bacteria And Measures Their Susceptibility To Antibiotics In Small Confined Volumes, Hashem Etayash, M. F. Khan, Kamaljit Kaur, Thomas Thundat

Pharmacy Faculty Articles and Research

In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a ...


Insights From Molecular Dynamics On Substrate Binding And Effects Of Active Site Mutations In Delta1-Pyrroline-5-Carboxylate Dehydrogenase, Bogdan F. Ion, Mohamed M. Aboelnga, James W. Gauld 2016 University of Windsor

Insights From Molecular Dynamics On Substrate Binding And Effects Of Active Site Mutations In Delta1-Pyrroline-5-Carboxylate Dehydrogenase, Bogdan F. Ion, Mohamed M. Aboelnga, James W. Gauld

Chemistry and Biochemistry Publications

The NAD+-dependent enzyme, 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), has an important role in proline and hydroxyproline catabolism for humans. Specifically, this aldehyde dehydrogenase is responsible for the oxidation of both L-glutamate- -semialdehyde (GSA) and 4-erythro-hydroxy-L-glutamate- -semialdehyde (4-OH-GSA) to their respective L-glutamate product forms. We have performed a detailed molecular dynamics (MD) study of both the reactant and product complex structures of P5CDH to gain insights into ligand binding (i.e., GSA, 4-OH-GSA, NAD+, GLU) in the active site. Moreover, our investigations were further extended to examine the structural impact of S352L, S352A, and E314A mutations on the deficiency in the P5CDH ...


Actin-Based Feedback Circuits In Cell Migration And Endocytosis, Xinxin Wang 2016 Washington University in St. Louis

Actin-Based Feedback Circuits In Cell Migration And Endocytosis, Xinxin Wang

Arts & Sciences Electronic Theses and Dissertations

In this thesis, we study the switch and pulse functions of actin during two important cellular processes, cell migration and endocytosis. Actin is an abundant protein that can polymerize to form a dendritic network. The actin network can exert force to push or bend the cell membrane. During cell migration, the actin network behaves like a switch, assembling mostly at one end or at the other end. The end with the majority of the actin network is the leading edge, following which the cell can persistently move in the same direction. The other end, with the minority of the actin ...


Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci 2016 University of Tennessee, Knoxville

Pinpointing The Molecular Basis For Metal Ion Effects On Plasminogen Activator Inhibitor-1 (Pai-1), Joel Cullen Bucci

Doctoral Dissertations

Plasminogen activator inhibitor type-1 (PAI-1) specifically inhibits the proteases tissue type plasminogen activator and urokinase plasminogen activator to control the activation of fibrinolysis. Vitronectin interacts with PAI-1 primarily through the somatomedin B (SMB) domain to stabilize and localize PAI-1 to sites of injury. Our laboratory observed that transition metals such as copper2+ have VN dependent, reciprocal effects on how long PAI-1 remains active. We aim to determine the molecular basis for effects of copper2+ on PAI-1 activity. We employed a computational algorithm (MUG) to predict metal binding clusters, and introduced mutations hypothesized to create metal binding deficiency. We ...


Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu 2016 Pacific Northwest National Laboratory

Comparative Analysis Of In Situ Fibronectin Using Tof-Sims, Spi-Ms, And Dropdesi-Ms In A Microfluidic Reactor, Shannon Fasing, Xiao-Ying Yu, Juan Yao, Jiachao Yu

STAR (STEM Teacher and Researcher) Presentations

Fibronectin is an important biomolecule due to its role in cell differentiation, growth, kinesis, and adhesion. Such biological responses are mediated through membrane recognition and signaling; where fibronectin is found. Studying the outer molecular surface of fibronectin allows deeper insight into the microbiological reactions that occur during these processes. In situ mass spectrometry analysis in aqueous solution accurately represents fibronectin’s chemical components, made possible by a vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface). SALVI was paired with the analytical tools: time-of-flight secondary ion mass spectrometer (ToF-SIMS), single photon ionization mass spectrometer (SPI-MS) and ...


Structural And Functional Characterization Of Acetoacetate Decarboxylase-Like Enzymes, Lisa Mueller 2016 University of Wisconsin-Milwaukee

Structural And Functional Characterization Of Acetoacetate Decarboxylase-Like Enzymes, Lisa Mueller

Theses and Dissertations

The acetatoacetate decarboxylase-like superfamily (ADCSF) is a largely unexplored group of enzymes that may be a potential source of new biocatalysts. Bioinformatic analysis has grouped these approximately 2000 enzymes into seven different families based on comparison of predicted active site residues. To date, only the prototypical ADCs (Family I) that catalyze the decarboxylation of acetoacetate have been studied. Analysis of gene context suggests that Family V contains predominantly enzymes predicted to be involved in secondary metabolism. On average, these share about 20% sequence identity to the true ADCs. To learn more about the diversity of chemistries performed by members of ...


Long-Range Acoustic Interactions In Insect Swarms: An Adaptive Gravity Model, Dan Gorbonos, Reuven Ianconescu, James G. Puckett, Rui Ni, Nicholas T. Ouellette, Nir S. Gov 2016 Weizmann Institute of Science

Long-Range Acoustic Interactions In Insect Swarms: An Adaptive Gravity Model, Dan Gorbonos, Reuven Ianconescu, James G. Puckett, Rui Ni, Nicholas T. Ouellette, Nir S. Gov

Physics and Astronomy Faculty Publications

The collective motion of groups of animals emerges from the net effect of the interactions between individual members of the group. In many cases, such as birds, fish, or ungulates, these interactions are mediated by sensory stimuli that predominantly arise from nearby neighbors. But not all stimuli in animal groups are short range. Here, we consider mating swarms of midges, which are thought to interact primarily via long-range acoustic stimuli. We exploit the similarity in form between the decay of acoustic and gravitational sources to build a model for swarm behavior. By accounting for the adaptive nature of the midges ...


Ribosome*Rela Structures Reveal The Mechanism Of Stringent Response Activation, Anna B. Loveland, Eugene Bah, Rohini Madireddy, Ying Zhang, Axel F. Brilot, Nikolaus Grigorieff, Andrei A. Korostelev 2016 University of Massachusetts Medical School

Ribosome*Rela Structures Reveal The Mechanism Of Stringent Response Activation, Anna B. Loveland, Eugene Bah, Rohini Madireddy, Ying Zhang, Axel F. Brilot, Nikolaus Grigorieff, Andrei A. Korostelev

Open Access Articles

Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 A wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the ...


Assessment Of Post-Treatment Imaging Changes Following Radiotherapy Using Magnetic Susceptibility Techniques, Jean-Guy Belliveau 2016 The University of Western Ontario

Assessment Of Post-Treatment Imaging Changes Following Radiotherapy Using Magnetic Susceptibility Techniques, Jean-Guy Belliveau

Electronic Thesis and Dissertation Repository

Radiation therapy (RT) is a common treatment for brain neoplasms and is used alone or in combination with other therapies. The use of RT has been found to be successful in controlling tumors and extending the overall survival of patients; however, there are many unanswered questions regarding radiotherapy effects in the normal brain surrounding or infiltrated by tumor. Changes to the vascular and parenchyma have been documented, and more recently inflammatory mechanisms have been postulated to play a role in radiation injury. Traditional imaging techniques used within the clinic (CT and MRI) are often lacking in their ability to differentiate ...


Computational Modeling Of Allosteric Stimulation Of Nipah Virus Host Binding Protein, Priyanka Dutta 2016 University of South Florida

Computational Modeling Of Allosteric Stimulation Of Nipah Virus Host Binding Protein, Priyanka Dutta

Graduate Theses and Dissertations

Nipah belongs to the family of paramyxoviruses that cause numerous fatal diseases in humans and farm animals. There are no FDA approved drugs for Nipah or any of the paramyxoviruses. Designing antiviral therapies that are more resistant to viral mutations require understanding of molecular details underlying infection. This dissertation focuses on obtaining molecular insights into the very first step of infection by Nipah. Such details, in fact, remain unknown for all paramyxoviruses. Infection begins with the allosteric stimulation of Nipah virus host binding protein by host cell receptors. Understanding molecular details of this stimulation process have been challenging mainly because ...


Closing The Net On Retroviruses, Jeremy Luban 2016 University of Massachusetts Medical School

Closing The Net On Retroviruses, Jeremy Luban

Open Access Articles

Structural studies reveal how an antiviral factor forms a molecular net to restrict retroviruses including HIV-1.


Differential Association Of Vitronectin And Fibronectin With Glass And Electrospun Fibers Of A Poly (D-Lysine) /Poly (Acrylic Acid), Syed Muhammad Sohaib Zafar Zafar 2016 University of South Florida

Differential Association Of Vitronectin And Fibronectin With Glass And Electrospun Fibers Of A Poly (D-Lysine) /Poly (Acrylic Acid), Syed Muhammad Sohaib Zafar Zafar

Graduate Theses and Dissertations

Proteins represent major constituent of the extracellular matrix which plays an important role in the formation, maintenance and remodeling of tissues, this project focuses on adsorption of two specific serum proteins fibronectin (FN) and vitronectin (VTN) responsible for mediating cell matrix interaction through integrin binding, tripeptide Arg-Gly-Asp (RGD) sequence found in these protein features are recognized by αβV3 integrin which ultimately helps in clot formation.


Inquiry Of Lipid Membranes Interacting With Functional Peptides And Polyphenol Drug Molecules, Chian Sing Ho 2016 University of South Florida

Inquiry Of Lipid Membranes Interacting With Functional Peptides And Polyphenol Drug Molecules, Chian Sing Ho

Graduate Theses and Dissertations

Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those ...


Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham 2016 Florida International University

Conformational Dynamics And Stability Associated With Magnesium Or Calcium Binding To Dream In The Regulation Of Interactions Between Dream And Dna Or Presenilins, Khoa Ngoc Pham

FIU Electronic Theses and Dissertations

Downstream regulatory element antagonist modulator (DREAM) is involved in various interactions with targets both inside and outside of the nucleus. In the cytoplasm, DREAM interacts with the C-terminal fragments of presenilins to facilitate the production of β-amyloid plaques in Alzheimer’s disease. In the nucleus, Ca2+ free DREAM directly binds to specific downstream regulatory elements of prodynorphin/c-fos gene to repress the gene transcription in pain modulation. These interactions are regulated by Ca2+ and/or Mg2+ association at the EF-hands in DREAM. Therefore, understanding the conformational dynamics and stability associated with Ca2+ and/or Mg ...


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