Open Access. Powered by Scholars. Published by Universities.®

Structural Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

270 Full-Text Articles 689 Authors 21311 Downloads 49 Institutions

All Articles in Structural Biology

Faceted Search

270 full-text articles. Page 1 of 10.

Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary 2016 University of Chicago

Analyzing The Γδ T Cell Receptor Sequences Of Patients With Celiac Disease, Alanna P. Gary

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Frozen Brain Atlas, Natalie Andrea Builes, Dominick Joseph Casciato, Samantha Taylor Bergoine, Robert Speth 2016 Nova Southeastern University

Frozen Brain Atlas, Natalie Andrea Builes, Dominick Joseph Casciato, Samantha Taylor Bergoine, Robert Speth

Frozen Brain Atlas

The Frozen Brain Atlas provides students, educators, and scientists with a tool to further explore the architecture of the brain. Current brain atlases allow users to navigate sectioned brain tissue using histological staining; however, they fail to capture naturally visible structures post sectioning. Through immediate post sectioning image collection, the natural contrast of the brain reveals unique structural details that are rarely seen by traditional staining procedures. By utilizing indexing and interactive labeling, the Nova Southeastern University Frozen Brain Atlas will allow identification of brain regions when used as a correlative tool for modalities including receptor autoradiography, immunofluorescence, and other ...


Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager 2016 University of Wisconsin-La Crosse

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by ...


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 ...


Habitat Temperature And Precipitation Of Arabidopsis Thaliana Ecotypes Determine The Response Of Foliar Vasculature, Photosynthesis, And Transpiration To Growth Temperature, William W. Adams III, Jared J. Stewart, Christopher M. Cohu, Onno Muller, Barbara Demmig-Adams 2016 University of Colorado Boulder

Habitat Temperature And Precipitation Of Arabidopsis Thaliana Ecotypes Determine The Response Of Foliar Vasculature, Photosynthesis, And Transpiration To Growth Temperature, William W. Adams Iii, Jared J. Stewart, Christopher M. Cohu, Onno Muller, Barbara Demmig-Adams

Ecology & Evolutionary Biology Faculty Contributions

Acclimatory adjustments of foliar vascular architecture, photosynthetic capacity, and transpiration rate in Arabidopsis thaliana ecotypes (Italian, Polish [Col-0], Swedish) were characterized in the context of habitat of origin. Temperatures of the habitat of origin decreased linearly with increasing habitat latitude, but habitat precipitation was greatest in Italy, lowest in Poland, and intermediate in Sweden. Plants of the three ecotypes raised under three different growth temperature regimes (low, moderate, and high) exhibited highest photosynthetic capacities, greatest leaf thickness, highest chlorophyll a/b ratio and levels of β-carotene, and greatest levels of wall ingrowths in phloem transfer cells, and, in the Col-0 ...


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 ...


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.


Structure And Function Relationships Between Atpase Family, Aaa Domain Containing Protein 5, Proliferating Cell Nuclear Antigen, And Usp1-Associated Factor 1, Tam T. Bui 2016 The University of Western Ontario

Structure And Function Relationships Between Atpase Family, Aaa Domain Containing Protein 5, Proliferating Cell Nuclear Antigen, And Usp1-Associated Factor 1, Tam T. Bui

Electronic Thesis and Dissertation Repository

The genome is constantly damaged by intracellular and extracellular factors. At sites of DNA damage, replication forks are stalled, leading monoubiquitination of proliferating cell nuclear antigen (PCNA). Monoubiquitination of PCNA promote the switch from regular high-fidelity polymerases to Y-family polymerases for bypassing damaged DNA. Prolonged replication by these polymerases may lead to increased mutagenesis, so tight regulation of this process is required. ATAD5 recruits a deubiquitinase complex consisting of ubiquitin-specific protease 1 (USP1) and USP1-associated factor 1 (UAF1) to control PCNA monoubiquitination. The mechanism by which ATAD5 and PCNA interact has been previously unexplored. We show through biochemical and structural ...


Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas 2016 Graduate Center, City University of New York

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

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

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is ...


Purification, Optimization, And Growth Of New Delhi Metallo-Β-Lactamase-1 Protein Crystals Mixed With Nz218 Inhibitor, Brandon M. Wills 2016 Augustana College, Rock Island Illinois

Purification, Optimization, And Growth Of New Delhi Metallo-Β-Lactamase-1 Protein Crystals Mixed With Nz218 Inhibitor, Brandon M. Wills

Celebration of Learning

New Delhi metallo-β-lactamase-1 is a problematic gene found in certain strains of bacteria that cause them to become antibiotic resistant to nearly all known antibiotics. While some antibiotics are available to treat patients with a bacterial infection, most are toxic or do not have 100% success rates. With that being said, it is imperative that we search for a molecule that is successfully able to inhibit the effects of this gene every time. Such a discovery would help tremendously with new antibiotic drug development and also prevent further damage by these dangerous bacteria. In this presentation, I will describe the ...


Rational Design Of An Epitope-Based Hepatitis C Virus Vaccine, Brian G. Pierce, Elisabeth N. Boucher, Ejemel Monir, William D. Thomas, Zhiping Weng, Yan Wang 2016 University of Maryland

Rational Design Of An Epitope-Based Hepatitis C Virus Vaccine, Brian G. Pierce, Elisabeth N. Boucher, Ejemel Monir, William D. Thomas, Zhiping Weng, Yan Wang

UMass Center for Clinical and Translational Science Research Retreat

Despite improving treatment methods and therapeutic options, hepatitis C virus (HCV) remains a major global disease burden, and a vaccine would help greatly in reducing its incidence. Due to its extremely high sequence variability, HCV can readily escape the immune response, thus a vaccine must elicit an immune response toward conserved, functionally important epitopes.

Using structural data of the broadly neutralizing antibody HCV1 in complex with a conserved linear epitope from the HCV E2 protein (aa 412-423, referred to as epitope I or domain E), we performed structure-based design to generate vaccine immunogens to induce antibody responses to this epitope ...


Structural And Molecular Analysis Of A Protective Epitope Of Lyme Disease Antigen Ospa And Antibody Interactions, Shivender Shandilya, Nese Kurt Yilmaz, Ejemel Monir, Andrew Sadowski, William D. Thomas, Mark S. Klempner, Celia A. Schiffer, Yan Wang 2016 University of Massachusetts Medical School

Structural And Molecular Analysis Of A Protective Epitope Of Lyme Disease Antigen Ospa And Antibody Interactions, Shivender Shandilya, Nese Kurt Yilmaz, Ejemel Monir, Andrew Sadowski, William D. Thomas, Mark S. Klempner, Celia A. Schiffer, Yan Wang

UMass Center for Clinical and Translational Science Research Retreat

The murine monoclonal antibody LA-2 recognizes a clinically protective epitope on outer surface protein (OspA) of Borrelia burgdorferi, the causative agent of Lyme disease in North America. Human antibody equivalence to LA-2 is the best serologic correlate of protective antibody responses following OspA vaccination. Understanding the structural and functional basis of the LA-2 protective epitope is important for developing OspA-based vaccines and discovering prophylactic antibodies against Lyme disease.

Here, we present a detailed structure-based analysis of the LA-2/OspA interaction interface and identification of residues mediating antibody recognition. Mutations were introduced into both OspA and LA-2 based on computational predictions ...


Characterization Of Glycine Rich Proteins From The Salivary Glands Of The Lone Star Tick Amblyomma Americanum, Rebekah Lynn Bullard 2016 University of Southern Mississippi

Characterization Of Glycine Rich Proteins From The Salivary Glands Of The Lone Star Tick Amblyomma Americanum, Rebekah Lynn Bullard

Dissertations

Ticks are blood sucking arthropods that feed on living hosts for up to three weeks. The ticks secrete a multitude of pharmacologically active proteins into the host during feeding which allow the tick to avoid the host immune response, establish a blood pool, and form a firm attachment. The firm attachment is facilitated by the formation of a cement cone which surrounds the tick mouthparts and intertwine between the host skin layers. In this study, gene expression of 44 A. americanum genes was measured throughout the bloodmeal to reveal the differential expression of these genes. Each of the genes tested ...


Stability Of Norwalk Virus Capsid Protein Interfaces Evaluated By In Silico Nanoindentation, Prakhar Bansal 2016 University of Connecticut

Stability Of Norwalk Virus Capsid Protein Interfaces Evaluated By In Silico Nanoindentation, Prakhar Bansal

University Scholar Projects

Studying the mechanical properties of viral capsids can give several insights into not only the lifecycle of the virus, but also into potential drug targets to thwart the progression of viral infection. Nanoindentation using an atomic force microscope is a useful technique for determining structural properties of small molecules and particles, and is commonly used to study viral capsids. This technique utilizes the probe of the microscope to push down on the capsid and record the forces along the indentation path. We ran this experiment in silico where we simulated the nanoindentation of Norwalk virus capsids using molecular dynamics. Running ...


Computational Investigations Into The Molecular Underpinnings Of Eyesight Signaling Pathways, Shaan Kamal 2016 University of Connecticut

Computational Investigations Into The Molecular Underpinnings Of Eyesight Signaling Pathways, Shaan Kamal

University Scholar Projects

Phosphodiesterase 6 (PDE6) is a critical enzyme in the eyesight-signaling pathway. When activated, PDE6 hydrolyzes cGMP to GMP, which deactivates cGMP- gated ion channels, causing hyperpolarization of the cell and activating the sensory neurons responsible for vision. Within the PDE family, PDE6 is the only enzyme known to have an inhibitory subunit (PDE6-γ), which allows for the regulation of cGMP levels. When PDE6-γ is bound to PDE6, the enzyme is turned “off” and cannot catalyze cGMP. The α subunit of the G-protein transducin removes PDE6-γ and activates PDE6. PDE6 has proven problematic to isolate, making it difficult to study experimentally ...


Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu 2016 University of Tennessee - Knoxville

Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu

Doctoral Dissertations

Internal structural motions in proteins are essential to their functions. In this present dissertation, we present the results from an extensive set of molecular dynamics simulations of three very different globular proteins and demonstrate that the structural fluctuations observed are highly complex, manifesting in non-ergodic and self-similar subdiffusive dynamics with non-exponential relaxation behavior. The characteristic time of the motion observed at a given timescale is dependent on the length of the observation time, indicating an aging effect. By comparing the simulation results to the existing single-molecule fluorescence spectroscopic data on other globular proteins, we found the characteristic relaxation time for ...


Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel 2016 University of Arkansas, Fayetteville

Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel

Chemistry & Biochemistry Undergraduate Honors Theses

Fibroblast growth factors (FGFs) are family of proteins that belong to a group of growth factors that are found in mammals and play an important role in angiogenesis, differentiation, organogenesis, and tissue repair. In summary, their main functionality is involved in cell division and proliferation. Because FGFs plays such a vital role in cell proliferation, they are mainly involved in the process of wound healing and injuries. FGF binds to its ligand, heparin—a heavily sulfated glycosaminoglycan. The binding of heparin to FGF occurs through electrostatic interactions, specifically between the negatively charged sulfate groups on heparin and positively charged residues ...


The Effect Of Transformed Escherichia Coli On The Mouse Intestine Microbiome: The Microbial Metabolic Enhancement Hypothesis, Bryar P. Kader 2016 Liberty University

The Effect Of Transformed Escherichia Coli On The Mouse Intestine Microbiome: The Microbial Metabolic Enhancement Hypothesis, Bryar P. Kader

Senior Honors Theses

Metabolic disorders affect around thirty-four percent of the population in the United States. Among these disorders is lactose intolerance, which results from diminished production of the human lactase enzyme. This disorder and others like it are genetically determined and cannot be cured. However, the use of transformed bacteria implanted in the colon may provide a means by which the faulty pathway can be bypassed. To test whether transformed bacteria have the capability to aid in the digestion of normally indigestible compounds, a transformed strain of Escherichia coli overexpressing the beta-galactosidase enzyme encoded by the lacZ gene was colonized in the ...


Structural Characterization Of The Iron-Sulfur Clusters In Metalloproteins, Andrew L. Schacht, Limei Zhang 2016 University of Nebraska-Lincoln

Structural Characterization Of The Iron-Sulfur Clusters In Metalloproteins, Andrew L. Schacht, Limei Zhang

UCARE Research Products

Iron-Sulfur ([Fe-S]) proteins refer to a group of metalloproteins containing cofactor(s) consisting of multiple iron and inorganic sulfur atoms. The [Fe-S] proteins are ubiquitous all the living organisms and play critical roles in a broad range of biological processes including redox reactions, stress and responses. Some examples of these are the WhiB proteins in Mycobacterium tuberculosis, which contain iron-sulfur cofactors that sense changes in redox hemostasis in the environment. Due to the their importance in the survival and virulence to the bacterial pathogens, these [Fe-S] proteins have become extensively studied within the last decades. Throughout my current experiences with ...


The Nmr Solution Structure And Function Of Rpa3313: A Hypothetical Protein From R. Palustris, Austin J. Lowe, Jonathan Catazaro, Cheryl Arrowsmith, Robert Powers 2016 University of Nebraska-Lincoln

The Nmr Solution Structure And Function Of Rpa3313: A Hypothetical Protein From R. Palustris, Austin J. Lowe, Jonathan Catazaro, Cheryl Arrowsmith, Robert Powers

UCARE Research Products

Protein function elucidation often relies heavily on amino acid sequence analysis and other bioinformatics approaches. The reliance is further extended to structure homology modeling for ligand docking and protein-protein interaction mapping. However, sequence analysis of RPA3313 exposes a large, unannotated class of hypothetical proteins mostly from the Rhizobiales order. In the absence of sequence and structure information, further functional elucidation of this class of proteins has been significantly hindered. A high quality NMR structure of RPA3313 reveals that the protein forms a novel split βαβ fold with a conserved ligand binding pocket between the first β-strand and the N-terminus of ...


Digital Commons powered by bepress