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Articles 1 - 9 of 9

Full-Text Articles in Molecular Biology

Modeling Of Dynamic Allostery In Proteins Enabled By Machine Learning, Mohsen Botlani-Esfahani Jul 2017

Modeling Of Dynamic Allostery In Proteins Enabled By Machine Learning, Mohsen Botlani-Esfahani

Graduate Theses and Dissertations

Regulation of protein activity is essential for normal cell functionality. Many proteins are regulated allosterically, that is, with spatial gaps between stimulation and active sites. Biological stimuli that regulate proteins allosterically include, for example, ions and small molecules, post-translational modifications, and intensive state-variables like temperature and pH. These effectors can not only switch activities on-and-off, but also fine-tune activities. Understanding the underpinnings of allostery, that is, how signals are propagated between distant sites, and how transmitted signals manifest themselves into regulation of protein activity, has been one of the central foci of biology for over 50 years. Today, the importance ...


An Enzymology And Structural Biology Approach Towards Elucidation Of E. Coli Fatty Acid Biosynthesis And Its Application To The Production Of Bio-Renewables, Aaron Michael Marcella Jan 2017

An Enzymology And Structural Biology Approach Towards Elucidation Of E. Coli Fatty Acid Biosynthesis And Its Application To The Production Of Bio-Renewables, Aaron Michael Marcella

Graduate Theses and Dissertations

Prokaryotic fatty acid biosynthesis is an important process to study due to its necessity for cell survival and production of highly reduced carbon chains. A characterization of several proteins involved in E. coli fatty acid biosynthesis is presented. This work provides a method for generating large amounts of pure malonyl acyl-carrier-protein using both the wild type malonyl-CoA:holo-ACP transacylase (FabD) and a variant studied further in our lab. This preparation overcomes the phenomena of a 50:50 mixture of malonyl and acetyl-ACP in the reaction and is crucial for the efficacy of future assays involving malonyl-ACP. A new assay has ...


Computational Modeling Of Allosteric Stimulation Of Nipah Virus Host Binding Protein, Priyanka Dutta Jul 2016

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 ...


Introducing Multiple Sites Of Acetylation To Histone H3 Via Nonsense Suppression, Isaac Young Jan 2016

Introducing Multiple Sites Of Acetylation To Histone H3 Via Nonsense Suppression, Isaac Young

Graduate Theses and Dissertations

A common post-translational modification (PTM) of proteins is lysine acetylation. This is an especially ubiquitous PTM in the histones of chromatin, and is important for helping to regulate both structural and mechanistic aspects of chromatin. The fundamental unit of chromatin is called the nucleosome and is made up of DNA that wraps around a histone protein octamer. Protruding from the nucleosome are 10 unstructured “tails” which protrude into the aqueous environment. A number of strategies exist for generating acetylated nucleosomes for the in-vitro study of chromatin including: Purification from eukaryotic organisms, chemical acetylation, amino acid analog incorporation, enzyme mediated acetylation ...


Investigation Of Snare Mediated Membrane Fusion And Its Regulation By Optimized Single Molecule Method, Yicheng Zhu Jan 2016

Investigation Of Snare Mediated Membrane Fusion And Its Regulation By Optimized Single Molecule Method, Yicheng Zhu

Graduate Theses and Dissertations

Neurotransmitter release going through synaptic vesicle cycle is one key step how signal is transported in our brains. The mechanism on molecular level has been under development and debated for decades. Many milestones have been made including, the identification of SNARE as core assembly machinery, the clarification of synaptotagmin as calcium sensor, the recognition of NSF and SNAP as disassembly apparatus, the determination of complexin and SM protein as regulatory protein. However, the sequence of their involvement in synaptic vesicle cycle, the relationship between the structure and psychological function, microscale fusion mechanism and are under further investigation. This puzzle is ...


Role Of Non-Catalytic Ligands In Macromolecule Function, Muneaki Watanabe Jan 2016

Role Of Non-Catalytic Ligands In Macromolecule Function, Muneaki Watanabe

Graduate Theses and Dissertations

Human hexokinase Type-I (HKI) binds to the outer mitochondrial membrane, and in so doing protects the mitochondrion, controls adenine nucleotide flux through the membrane and blocks mitochondrion-linked apoptosis. Adenosine 5’-triphosphate (ATP) releases HKI from the outer mitochondrial membrane, but the mechanism of ATP release is unclear. ATP-release is not due to the generation of glucose 6-phosphate (G6P) from ATP and glucose or by the binding of ATP to HKI at its catalytic or regulatory domains. Instead, the voltage dependent anion channel (VDAC) has a high affinity binding site for ATP as revealed by titrations using ATP and fluorescent analogs ...


Studies Of Integrins' Lateral Dynamics At A Single Particle Level, Dipak Mainali Jan 2014

Studies Of Integrins' Lateral Dynamics At A Single Particle Level, Dipak Mainali

Graduate Theses and Dissertations

One of the important factors in controlling the dynamics, structure, and functioning of the cell membrane is the lateral diffusion of membrane proteins and lipids. Integrins are one of the ubiquitous transmembrane proteins that are vital for numerous cellular functions. Integrins' lateral mobility and rearrangement is essential for integrins primary function of cell-extracellular matrix adhesion, cell-cell adhesion, and signaling. Lateral movement allows integrins to associate with extracellular ligand and other cytoplasmic and membrane proteins to incite biological activity such as signaling and downstream effects. This thesis describes the role of both downstream and upstream effectors, such as extracellular ligand, selected ...


A Single Molecular Study Of The Regulation Of Snare-Mediated Membrane Fusion, Jaekyun Song Jan 2014

A Single Molecular Study Of The Regulation Of Snare-Mediated Membrane Fusion, Jaekyun Song

Graduate Theses and Dissertations

The presynaptic membrane fusion is mediated by a protein set called SNARE (Soluble NSF Attachment protein REceptor) proteins. SNARE proteins form a ternary SNARE-complex that comprises minimal machinery for membrane fusion; the complex consists of three SNARE proteins: Syntaxin 1, SNAP-25 and Vamp 2, also called Synaptobrevin 2. The SNARE complex is a four-helix coiled coil with four SNARE motifs; two come from SNARE-25 and one each from Syntaxin 1 and Vamp 2. It is believed that a regulatory protein Complexin binds tightly to the SNARE complex and stabilizes the complex, preventing it from driving toward fusion. However, the detailed ...


Structural Basis For Ternary Complex Formation Between Tau, Hsp90, And Fkbp51, Alexander Steven Barrett Jan 2013

Structural Basis For Ternary Complex Formation Between Tau, Hsp90, And Fkbp51, Alexander Steven Barrett

Graduate Theses and Dissertations

The accumulation of the microtubule associated protein tau has been implicated in several neurological disorders; however, its interaction with chaperones along its normal degradation pathway remains largely uncharacterized at single residue resolution. In this study, nuclear magnetic resonance (NMR) spectroscopy was used to probe the interaction between tau, the molecular chaperone Hsp90, and the immunophilin FKBP51. Resonance intensity changes were observed for specific residues in the heteronuclear single quantum coherence (HSQC) spectra of 15N-labeled tau in the presence of Hsp90 and/or FKBP51. Analysis of the HSQC spectra identified the two hydrophobic hexapeptide motifs located at residues V275 - K280 and ...