Biochemistry, Biophysics, and Structural Biology Commons^™

Characterization Of Wssf; A Putative Acetyltransferase From Achromobacter Insuavis And Pseudomonas Fluorescens, Cody Reese

Theses and Dissertations (Comprehensive)

Biofilms are a survival mechanism commonly employed by communities of bacteria for adherence and protection. Bacteria produce a matrix of polymers (e.g. exopolysaccharides, such as cellulose) that allow them to exert control on their local environment. In the case of cellulose biofilms, acetylation (addition of acetate on carbohydrates) is paramount for polymer integrity and in some cases virulence. For this research, the wrinkly spreader (WS) genotype of the emergent human pathogen Achromobacter insuavis facilitates infections of the eyes of contact lens wearers and the lungs of Cystic Fibrosis patients (CF). Chronic infections have created a growing concern for the protective …

Expression, Purification, Functional Characterization And Crystallization Of Three Porphyromonas Gingivalis Gene Products, Katarina Mandic

Theses and Dissertations (Comprehensive)

Dental biofilms are coupled polymicrobial aggregates that have attached to solid surfaces in the oral cavity. These collections of microorganisms are known to cause periodontal diseases that commence as localized inflammation of the gingiva and if untreated, eventually lead to irreversible alveolar bone resorption and tooth loss. Porphyromonas gingivalis is one of three periodontal pathogens that make up the “Red Complex”; a bacterial consortium responsible for the production of polysaccharide-rich biofilms that are essential to the inception and progression of periodontal disease. The dysbiosis and destructive inflammation caused by these organisms propel a self-sustained feed-forward loop that perpetuates periodontal disease. …

Structural Investigation Of Bcsc: Insight Into Periplasmic Transport During Cellulose Export, William Scott, Joel T. Weadge

Theses and Dissertations (Comprehensive)

A biofilm can be defined by a community of microbes coexisting within a self-produced protective polymeric matrix. Exopolysaccharide (EPS) is a key component in biofilms and a contributor to their virulence and pathogenicity. The cellulose bacterial synthesis complex is one such EPS system that is found in many Enterobacteriaceae,including Escherichia coli and Salmonella spp., and is responsible for the production and secretion of the EPS cellulose. BcsC is the periplasmic protein responsible for the export of the exopolysaccharide cellulose and was the focus of this research. Sequence homology comparisons and structural predictions between BcsC, and the previously characterized alginate …

Ph-Induced Folding Of The Caspase-Cleaved Par-4 Tumor Suppressor: Evidence Of Structure Outside Of The Coiled Coil Domain, Andrea M. Clark, Komala Ponniah, Meghan S. Warden, Emily M. Raitt, Andrea C. Yawn, Stephen M. Pascal

Chemistry & Biochemistry Faculty Publications

Prostate apoptosis response-4 (Par-4) is a 38 kDa largely intrinsically disordered tumor suppressor protein that functions in cancer cell apoptosis. Par-4 down-regulation is often observed in cancer while up-regulation is characteristic of neurodegenerative conditions such as Alzheimer’s disease. Cleavage of Par-4 by caspase-3 activates tumor suppression via formation of an approximately 25 kDa fragment (cl-Par-4) that enters the nucleus and inhibits Bcl-2 and NF-ƙB, which function in pro-survival pathways. Here, we have investigated the structure of cl-Par-4 using biophysical techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and intrinsic tyrosine fluorescence. The results demonstrate pH-dependent folding of cl-Par-4, …

Role Of P300 Zz Domain In Chromatin Association And Histone Acetylation, Yongming Xue

Dissertations and Theses (Open Access)

Transcription is strictly regulated by numerous factors including transcription coactivators. The p300 protein and its close paralogue CREB-binding protein (CREBBP, aka CBP) are well-known transcriptional coactivators that have intrinsic lysine acetyltransferase activity. The functions of p300/CBP largely rely on their capabilities to bind to chromatin and to acetylate the histone substrates. However, the molecular mechanisms underlying the regulation of these processes are not fully understood.

Through combination of various biochemical, biophysical and molecular approaches, we show that the ZZ-type zinc finger (ZZ) domain of p300 functions as a histone reader that specifically binds the N-terminal tail of histone H3. Crystal …

A Crispr Platform For Rapid And Inducible Genome Editing In Human Non-Small Cell Lung Cancer Cells, Lloyd Bartley

Posters-at-the-Capitol

Non-small cell lung cancer (NSCLC) accounts for about 85% of lung cancer, which is the leading cause of cancer death in the world. High mortality rate associated with NSCLC is partially attributed to the limited understanding of NSCLC as well as ineffective therapeutic treatments. The initiation and progression of NSCLC involves genetic changes leading to alterations in the control of tissue development and homeostatic maintenance. Better knowledge about these genetic abnormalities is imperative for developing new chemotherapeutic drugs for NSCLC. Recent research demonstrates that the expression of paraoxonase 2 (PON2), a lactonase/arylesterase with anti-oxidant properties, are markedly enhanced in cancer …

Multi-Resolution Analysis Of Large Molecular Structures And Interactions, Kasra Manavi

Computer Science ETDs

Simulation of large molecular structures and their interactions has become a major component of modern biomolecular research. Methods to simulate these type of molecules span a wide array of resolutions, from all atom molecular dynamics to model interaction energetics to systems of linear equations to evaluate population kinetics. In recent years, there has been an acceleration of molecular structural information production, primarily from x-ray crystallography and electron microscopy. This data has provided modelers the ability to produce better representations of these molecular structures. The purpose of this research is to take advantage of this information to develop multi-resolution models for …

Combined High-Speed Single Particle Tracking Of Membrane Proteins And Super-Resolution Of Membrane-Associated Structures, Hanieh Mazloom Farsibaf, Keith A. Lidke

Shared Knowledge Conference

Many experiments have shown that the diffusive motion of lipids and membrane proteins are slower on the cell surface than those in artificial lipid bilayers or blebs. One hypothesis that may partially explain this mystery is the effect of the cytoskeleton structures on the protein dynamics. A model proposed by Kusumi [1] is the Fence-Picket Model which describes the cell membrane as a set of compartment regions, each ~ 10 to 200 nm in size, created by direct or indirect interaction of lipids and proteins with actin filaments just below the membrane. To test this hypothesis, we have assembled a …

Amino Acid Pop-Set: Model File Name: Amino-Acid-Wgrp-Pop_Sc3.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model for protein primary structure. It consists of four amino acids (tryptophan, proline, arginine, and glycine) depicted in stick and space-fill representations, five peptide bonds depicted in space-fill, and an N-terminus and a C-terminus depicted in space-fill. It is designed so that students can make various peptides to explore the amount of space of the electron clouds of the amino acids and bonds, and explore the psi and phi angles for the peptides. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Amino acid pop-set”. This model has …

Lipoprotein Signal Peptidase Ii: Model File Name: 5dir-Lipoii-Reps_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of lipoprotein signal peptidase II (PDB: 5DIR). It is designed with different regions of the protein depicted in space-filling, ribbon, stick, and backbone-only representations to explore protein secondary structure and illustrate how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lipoprotein signal peptidase II” and is intended to accompany the “Crambin”, “Cytochrome c” and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in …

3 Water Molecules: Model File Name: 3hoh-Final.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of 3 water molecules depicted in space-fill. It is designed to the same scale as the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models to illustrate the amount of space taken up by proteins. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “3 water molecules” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “Cytochrome c” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering …

Crambin: Model File Name: 2fd7-Crambin-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 2FD7). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Crambin” and is intended to accompany the “Lipoprotein signal peptidase II”, “Cytochrome c”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Cytochrome C: Model File Name: 1b7v-Cytc-Stick_Sc1-5.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of cytochrome c (PDB: 1B7V). It is designed in a stick representation to explore protein secondary structure and how much space the protein takes up. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Cytochrome c” and is intended to accompany the “Lipoprotein signal peptidase II”, “Crambin”, and “3 water molecules” models. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

The Distinctive Regulatory Mechanisms Of Bacterial Acetyl-Coa Carboxylase, Alexandra Leigh Evans

LSU Doctoral Dissertations

Metabolic Regulation is a complex system used to control cellular metabolism in response to conditions in the cell’s environment. For most enzymes, the cell can rely upon a minimal amount of regulation; however, critical enzymes, such as acetyl-CoA carboxylase, must be regulated at multiple levels. Acetyl-CoA carboxylase catalyzes the first committed step in fatty acid synthesis. In bacteria, acetyl-CoA carboxylase forms a complex of three subunits–biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase–which catalyze the carboxylation of acetyl-CoA to form malonyl-CoA via two half-reactions. In the first half-reaction, biotin covalently linked to biotin carboxyl carrier protein is carboxylated by biotin …

Human Hexokinase I - Allosteric Regulation: Model File Name: 1dgk-Editb22-Allostery_Sc06.Stl, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

This is a teaching model of human Hexokinase I in a surface representation with small molecules ADP and G6P included (PDB: 1DGK). It is designed to be hollow with a lever to mimic allosteric regulation. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Human Hexokinase I - Allosteric regulation model”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Accurate Flexible Refinement Of Atomic Models Against Medium-Resolution Cryo-Em Maps Using Damped Dynamics, Julio A. Kovacs, Vitold E. Galkin, Willy Wriggers

Mechanical & Aerospace Engineering Faculty Publications

Background: Dramatic progress has recently been made in cryo-electron microscopy technologies, which now make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. However, the need persists for fitting and refinement approaches that address those cases that require modeling assistance.

Methods: In this paper, we describe algorithms to optimize the performance of such medium-resolution refinement methods. These algorithms aim to automatically optimize the parameters that define the density shape of the flexibly fitted model, as well as the time-dependent damper cutoff distance. Atomic distance constraints can be prescribed for cases where extra containment of parts of …

Towards An Atomic Level Model Of The Structure And Calmodulin Mediated Activation Of Eef-2k, Nathan E. Will

Dissertations, Theses, and Capstone Projects

Eukaryotic elongation factor 2 kinase (eEF-2K), the only calmodulin (CaM) dependent member of the a-kinase, phosphorylates eukaryotic elongation factor 2 (eEF-2) on a specific residue (Thr-56), decreasing its affinity for the ribosome and reducing the rate of peptide chain elongation during protein translation. In contrast to the “release-of-inhibition’ mechanism operative in most CaM-dependent proteins kinases, the activation of eEF-2K is proposed to occur through a two-step process subsequent to the engagement of CaM and involves (1) auto-phosphorylation on T348 and (2) engagement of an allosteric site by phospho-T348 leading to a state with the highest activity towards the substrate eEF-2. …

Structural And Functional Characterization Of Hyper-Phosphorylated Grk5 Protein Expressed From E. Coli, Joseph M. Krampen, John Tesmer, Qiuyan Chen

The Summer Undergraduate Research Fellowship (SURF) Symposium

G protein-coupled receptor (GPCR) kinases (GRKs) are proteins in the cell responsible for regulating GPCRs located on the cell membrane. GRKs regulate active GPCRs by phosphorylating them at certain sites which causes them to stop normal signaling on the membrane. This ultimately affects how the cell responds to its environment. GRK5 is a kinase of particular interest due to its involvement in the pathology of diseases such as cardiac failure, cancers, and diabetes. Understanding the structure and function of GRK5 is essential for discovering ways to manipulate its behavior with these diseases, but not much is known about how GRK5 …

Structural Characterization Of The Dep Domains Of P-Rex1, Samantha R. Allgood, John J.G. Tesmer, Sandeep K. Ravala

The Summer Undergraduate Research Fellowship (SURF) Symposium

P-Rex1 is a guanine nucleotide exchange factor for Rho-GTPases, which is indirectly involved in the regulation of cell migration and proliferation. It contains a tandem DH/PH domain archetypal of the Dbl family of GEFs, two DEP and two PDZ domains, and a C-terminal end with weak homology to inositol polyphosphate 4-phosphatase. P-Rex1 is regulated by both intra-domain interactions and interactions with other proteins such as G-protein beta gamma, PKA and phosphatidylinositol (3,4,5)-trisphosphate. Upregulation of P-Rex1 has been found in multiple human cancers, making it a potential target for anti-cancer drug therapies. Therefore, structural characterization of P-Rex1 is critical. Currently, only …

The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn

Electronic Theses and Dissertations

Protein, DNA, and RNA methyltransferases have an ever-expanding list of novel substrates and catalytic activities. Even within families and between homologs, it is becoming clear the intricacies of methyltransferase specificity and regulation are far more diverse than originally thought. In addition to specific substrates and distinct methylation levels, methyltransferase activity can be altered through formation of complexes with close homologs. This work involves the N-terminal methyltransferase homologs NRMT1 and NRMT2. NRMT1 is a ubiquitously expressed distributive trimethylase. NRMT2 is a monomethylase expressed at low levels and in a tissue-specific manner. They are both nuclear methyltransferases with overlapping target consensus sequences …

The Regulation Of Notch Signaling By Src Kinase And Polyphenolic Compounds, Bryce David Lafoya

Boise State University Theses and Dissertations

Cellular signaling pathways provide cells with the means to sense their environment and communicate with other cells. The Notch signaling pathway is comprised of a set of protein machines which work in unison to coordinate cellular processes in response to stimuli coming from neighboring cells and changing microenvironmental conditions. Notch signaling is an important mode of cellular communication which is crucial to many processes involved in development and disease. During Notch activation, information about the extracellular environment is fed into the cell and relayed to the nucleus through a number of biochemical processes. The information-rich messages carried by Notch signaling …

Quantitative Studies Of Amyloidogenic Protein Residue Interaction Networks And Abnormal Ammonia Metabolism In Neurotoxicity And Disease, Jeddidiah Griffin

Electronic Theses and Dissertations

Investigating similarities among neurological diseases can provide insight into disease processes. Two prominent commonalities of neurological diseases are the formation of amyloid deposits and altered ammonia and glutamate metabolism. Computational techniques were used to explore these processes in several neurological diseases. Residue interaction networks (RINs) abstract protein structure into a series of nodes (representing residues) and edges (representing connections between residues likely to interact). Analyzing the RINs of monomeric forms of amyloidogenic proteins for common network features revealed similarities not previously known. First, amyloidogenic variants of lysozyme were used to demonstrate the usefulness of RINs to the study of amyloidogenic …

Identification And Folding Of Mirna Through Machine Learning, Xavier Pellow

The International Student Science Fair 2018

As of writing, there is currently no efficient way to accurately identify miRNA or predict the structure of miRNA without the usage of a lab. The purpose of this work is to provide a framework which allows for efficient identification of mature miRNA and folding of pre-miRNA using a feedforward neural network (FFNN) and probabilistic context-free grammar (PCFG) parsing, respectively. After training, the FFNN developed an accuracy of 98%. Out of all control cases using high confidence miRNA, the PCFG used returned folded structures that matched the canonical structures to an accuracy of 81%. The results of this work indicates …

Molecular Mechanism Of Early Amyloid Self-Assembly Revealed By Computational Modeling, Mohtadin Hashemi

Theses & Dissertations

Protein misfolding followed by the formation of aggregates, is an early step in the cascade of conformational changes in a protein that underlie the development of several neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. Efforts aimed at understanding this process have produced little clarity and the mechanism remains elusive.

Here, we demonstrate that the hairpin fold, a structure found in the early folding intermediates of amyloid b, induces morphological and stability changes in the aggregates of Aβ(14-23) peptide. We structurally characterized the interactions of monomer and hairpin using extended molecular dynamics (MD) simulations, which revealed a novel intercalated type complex. …

Towards The Identification Of The Molecular Mechanism Responsible For Rpa:Rad52 Complex Formation, Lucas Struble

Theses & Dissertations

Human cells are routinely exposed to DNA-damaging conditions, from both external sources like ionizing radiation and internal sources like normal oxidative metabolism. Damage in the form of double strand breaks (DSBs) is especially problematic. DSBs occurring outside of replication forks can be repaired through two forms of homologous recombination. The first of these is genetic conversion involving either RPA, BRCA1, PALB2, BRCA2, and RAD51, or RPA, RAD52, RAD51, and other unknown factors. The second is single strand annealing involving RPA and RAD52. Familial breast cancers, among numerous others, are characterized by homozygous pathological mutations in the BRCA2 pathway and must …

Ph Sensitivity Of Connexin 50 Hemichannels: H95 And Beyond, Leah Volk

Biology Theses

Gap junction channels formed by connexin proteins are critical for the health and function of the vertebrate lens. It is important to understand how these channels are affected by pH because a pH gradient exists in lens tissue. Intracellular pH (pH_i) is a regulator of gap junction coupling, and different connexins show different sensitivities to pH_i. A “Particle-Receptor” model for pH-dependent channel closure involves the intramolecular interaction between the cytoplasmic tail of the connexin and a region near the mouth of the channel dependent on a highly conserved histidine residue at position 95. While this model …

Binding Of Maize Necrotic Streak Virus (Mnesv) 3’ I-Shaped Structure (3’ Iss) To Eukaryotic Translation Factors (Eifs) And Implication In Eif4f Mediated Translation Initiation, Qiao Liu

Dissertations, Theses, and Capstone Projects

5' m⁷GpppN cap and the 3' poly adenosine (A) tail of eukaryotic mRNAs are key elements for recruiting translation initiation machinery in canonical translation initiation. Unlike host mRNAs, many viruses lack these elements and yet they are translated efficiently. Plant viruses, in particular, have complex structures within their untranslated regions (UTR) that allow them to bypass some cellular translation control steps. In Maize necrotic streak virus (MNeSV) 3' UTR, an I-Shaped RNA Structure (ISS) has been reported to mediate the virus translation initiation progress. 3’ ISS binding with eIF4F has been shown to facilitate translation. 5’ -3’ kissing …

Regulation Of The Tubulin Homolog Ftsz In Escherichia Coli, Monika S. Buczek

Dissertations, Theses, and Capstone Projects

Escherichia coli is a well-known pathogen, and importantly, a widely used model organism in all fields of biological sciences for cloning, protein purification, and as a model for Gram-negative bacterial species. And yet, researchers do not fully understand how this bacterium replicates and divides. Every year additional division proteins are discovered, which adds complexity to how we understand E. coli undergoes cell division. Due to their specific roles in cytokinesis, some of these proteins may be potential targets for development of antibacterials or bacteriostatics, which are much needed for fighting the current global antibacterial deficit. My thesis work focuses on …

Diversity, Structure And Sources Of Bacterial Communities In Earthworm Cocoons., Manuel Aira, Marcos Pérez-Losada, Jorge Domínguez

Computational Biology Institute

Animals start interactions with the bacteria that will constitute their microbiomes at embryonic stage. After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms Eisenia andrei and E. fetida, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts, Microbacteriaceae, Verminephrobacter and Ca. Nephrothrix, which accounted for 88% and 66% of the sequences respectively. Verminephrobacter and Ca. …

Data-Driven Computational Approach To Study Bio-Molecular Interactions, Misagh Naderi

LSU Doctoral Dissertations

Proteins commonly convey their functions in coordination with other proteins, small molecules and/or other biological assemblies such as sugars, lipids, DNA or RNA. Understanding the nature of these interactions is therefore central to improving our knowledge of biological systems. This body of work is a consolidation of three different computational approaches to study bio-molecular interactions: large-scale protein-ligand modeling, fragment-based cheminformatics, and computational analysis of interactions in single proteins.

The first issue that is addressed in this study is the scarcity of atomic crystal structures of protein-drug complexes. In general, a drug molecule’s affinity for multiple protein targets may causes unsolicited …