Biochemistry, Biophysics, and Structural Biology Commons^™

Analysis Of Critical Amino Acid Residues In Unc-45 Necessary For Its Interaction With Myosin Using Site-Directed Mutagenesis, Amanda H. Nolan

Undergraduate Research Conference

UNC-45 is an important protein for muscle contraction and heart formation. The UNC-45 protein is a chaperone for the myosin heavy chain head, and UNC-45 only binds to the UCS domain of the myosin head. In our research for the interaction of myosin and UNC-45. The mutation was accomplished using the multiple sequence alignment method and site-directed mutagenesis. The mutations were generated in UNC-45 of Mus musculus (mouse), and the specific amino acids that were mutated were: L741A and L860F. The mutant proteins were sequenced and over-expressed for analysis.

Generation, Cloning, And Expression Of Full-Length Human Evc Gene, Trey Polvadore

Undergraduate Research Conference

No abstract provided.

Arctic Mustard Flower Color Polymorphism Controlled By Petal-Specific Downregulation At The Threshold Of The Anthocyanin Biosynthetic Pathway, Cynthia A. Dick, Jason Buenrostro, Timothy Butler, Matthew L. Carlson, Daniel J. Kliebenstein, Justen B. Whittall

Biology

Intra- and interspecific variation in flower color is a hallmark of angiosperm diversity. The evolutionary forces underlying the variety of flower colors can be nearly as diverse as the colors themselves. In addition to pollinator preferences, non-pollinator agents of selection can have a major influence on the evolution of flower color polymorphisms, especially when the pigments in question are also expressed in vegetative tissues. In such cases, identifying the target(s) of selection starts with determining the biochemical and molecular basis for the flower color variation and examining any pleiotropic effects manifested in vegetative tissues. Herein, we describe a widespread purple-white …

Constructing A Vector For Over Expressing Nitrobenzene Dioxygenase In E. Coli, Paul Davis

Honors Student Works

Due to extensive use of nitroaromatic compounds in the production of dyes, pesticides, explosives, and their harmful effects on the environment, studying the enzyme mechanisms of bacteria capable of utilizing these compounds as nutrient sources have become a recent field of development. One example, the Comamonas sp. strain JS765, grows on nitrobenzene as its sole carbon, nitrogen and energy source. This bacterium contains a nitrobenzene dioxygenase enzyme system that incorporates O2 into the nitrobenzene ring to form catechol and nitrite. In this project, the genes that code for the dioxygenase enzyme were cloned and then transformed into an expression vector …

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 89th Annual Meeting of the Virginia Academy of Science, May 25-27, 2011, University of Richmond, Richmond VA.

Section Abstracts: Structural Biology, Biochemistry, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 89th Annual Meeting of the Virginia Academy of Science, May 25-27, 2011, University of Richmond, Richmond, VA.

Practical Approach To Bioinformatics, Nigel Yarlett, Melissa Grigione

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Bioinformatics, Thermodynamics And Kinetics Analysis Of An All Alpha Helical Protein With A Gree-Key Topology, Hai Li

Chemistry & Biochemistry Theses & Dissertations

Computational and experimental studies focusing on the role of conserved residues for folding and stability is an active and promising area of research. To further expand our understanding we present the results of a bioinformatics analysis of the death domain superfamily. The death domain superfamily fold consists of six α-helices arranged in a Greek-key topology, which is shared by the all β-sheet immunoglobulin and mixed α/β-plait superfamilies. Our sequence and structural studies have identified a group of conserved hydrophobic residues and corresponding long-range interactions, which we propose are important in the formation and stabilization of the hydrophobic core and native …

Organometallic Iron(Iii)-Salophene Exerts Cytotoxic Properties In Neuroblastoma Cells Via Mapk Activation And Ros Generation, Kyu Kwang Kim, Rakesh K. Singh, Robert M. Strongin, Richard G. Moore, Laurent Brard, Thilo S. Lange

Chemistry Faculty Publications and Presentations

The objective of the present study was to investigate the specific effects of Iron(III)-salophene (Fe-SP) on viability, morphology, proliferation, cell cycle progression, ROS generation and pro-apoptotic MAPK activation in neuroblastoma (NB) cells. A NCI-DTP cancer screen revealed that Fe-SP displayed high toxicity against cell lines of different tumor origin but not tumor type-specificity. In a viability screen Fe-SP exhibited high cytotoxicity against all three NB cell lines tested. The compound caused cell cycle arrest in G1 phase, suppression of cells progressing through S phase, morphological changes, disruption of the mitochondrial membrane depolarization potential, induction of apoptotic markers as well as …

Computational Investigation Of The Bioactive Selenium Compounds Ebselen And Selenious Acid, Sonia Antony

Chemistry & Biochemistry Theses & Dissertations

Selenium, a toxic element, is required in trace quantities for the proper functioning of biological systems. The experimental mechanistic study of the reactions of ebselen and selenious acid is difficult due to complexity of the reaction mixtures and the presence of short-lived intermediates. Computational modeling of the reactivity of these species can give us an insight into their mechanisms, but the process is complicated by proton exchanges associated with the mechanistic steps. In gas phase modeling, this may be corrected to a certain level using the solvent assisted proton exchange (SAPE) method. SAPE is a modeling technique that mimics solvent …

An Observation Of Immunological Effect, A Diet Enhanced With Spirulina And Treatment With Fractalkine In Models Of Parkinson's Disease, Mibel M. Pabón

USF Tampa Graduate Theses and Dissertations

In my dissertation research we used use human wild type α-synuclein gene expression using an adeno-associated viral vector (AAV9) that induced a slowly progressive loss of dopamine (DA) neurons in the Substantia nigra (SN) as one of our animal model of Parkinson’s disease (PD). It is our hypothesis that neuroinflammation predisposes the brain to susceptibility to neurodegenerative diseases. Thus we examined the progression of a PD lesion and examined the manipulations of the immune system to understand further the inflammatory role when we administered exogenous soluble fractalkine.

The specific etiology of neurodegeneration in PD is unknown, but the inflammatory mechanisms …

Structural Study Of Mcry2: A Circadian Rhythm Regulator, Brenda L. Rodarte^, Gustavo A. Avila, Adrian S. Enriquez, Nicolas D. Silva, Tiffany H. Blankenship, Erquan Eric Zhang*, Chuan Xiao*

COURI Symposium Abstracts, Spring 2011

A circadian clock is a 24 hour biological rhythm that regulates physiological, psychological and behavioral processes in living organisms. Understanding the regulation mechanism of such circadian rhythms can have great impact in certain diseases such as sleeping disorders and cancers. There are many genes regulating circadian rhythms in different species. Cryptochromes (CRY) are photosensory receptors mediating light regulation of growth and development in certain species. Mouse cryptochrome protein mCRY2 has been found to encode a blue light photoreceptor and is important for mice circadian rhythm. The main goal of the project is to determine the atomic structure of mCRY2, via …

Biochemical Characterization And X-Ray Crystallography Of A Lysozyme Encoded By Pseudomonas Aeruginosa Bacteriophage Sn, Nadia Herrera^, Maxim V. Filchikov, Zacariah L. Hildenbrand, Sudheer K. Molugu, Vadim V. Mesyanzhinov, Konstantin A. Miroshnikov, Ricardo A. Bernal*

COURI Symposium Abstracts, Spring 2011

Bacteriophage SN is a virulent phage that selectively infects the bacterium Pseudomonas aeruginosa. It was isolated from Lake Chernoe in Russia and it is related to the PB1-like species of the Myoviridae family. The DNA genome is composed of 66,391 base pairs, has 89 predicted open reading frames, and encodes more than 20 structural proteins. One of the open reading frames of this newly discovered bacteriophage has high sequence identity to other lysozyme and chitinase genes. It is therefore assumed that this protein encoded by bacteriophage SN is utilized for digestion of the host cell wall prior to injection of …

Initialization Of Structural Proteomic Studies Of The Giant Marine Virus Crov, Duer Bolotaulo^, Nancy Rondeau, Gustavo A. Avila, Matthias G. Fischer, Curtis A. Suttle, Chuan Xiao*

COURI Symposium Abstracts, Spring 2011

The existence of cellular genes in viruses such as the nucleocytoplasmic large DNA viruses (NCLDV) has led to not only the redefinition of the virus but also the mystery of the origin of these genes. Cafeteria roenbergensis virus (CroV) is a giant marine virus in the NCLDV clade. Information obtained from structural proteomics studies of CroV can be compared with known cellular counterparts, elucidating the evolutionary relationship between virus and cell in a three-dimensional structural aspect. CroV's major capsid protein gene (MCP) and five CroV genes, (CDS 84, 115, 143, 149,152) including a photolyase and an oxidoreductase, have been chosen …

Enzymatic Characterization Of An Endolysin Mediated By Chaperonin In Bacteriophage Phi El, Diana A. Tafoya^, Nadia Herrera, Sudheer Molugu, Zachariah Hildenbrand, Maxim V. Filchikov, Vadim V. Mesyanzhinov, Konstantin A. Miroshnikov, Ricardo A. Bernal*

COURI Symposium Abstracts, Spring 2011

Bacteriophage phi-EL is a virus that attacks the human pathogen Pseudomonas aeruginosa. One of the gene products from phi-EL is a putative endolysin. Endolysin is an enzyme produced during gene expression in the lytic cycle of the bacteriophage. Its function is to digest the peptidoglycan layer of the host cell wall, thereby releasing the newly formed virions. In order to confirm the identity of this putative endolysin, the gene product was transformed into competent E. coli cells, expressed to high levels and purified to high homogeneity using nickel affinity and size exclusion chromatography. The peptidoglycan-hydrolyzing activity of the protein …

Human Endogenous Sodium Pump Inhibitors Measurement, Source, Synthesis And Regulation, Jie Ma

Theses and Dissertations

The sodium pump (SP or Na+,K+-ATPase) is a membrane embedded protein complex that pumps 3 sodium ions out and 2 potassium ions into the cell per cycle and in so doing creates a cell membrane electrochemical potential. The membrane potential is critical for any functional cell. In the vasculature, reduction in the voltage potential causes vascular smooth muscle contraction and a narrowing of blood vessels (vasoconstriction) which can lead to increased blood pressure (hypertension). Substantial research over the past several decades has provided a vast amount of research on SP inhibitors, sometimes called endogenous digitalis-like factors (EDLF). Increased levels of …

Super Collision Energy Transfer Studies In Single Collisions Between Vibrationally Hot Benzene Like Molecules And Ground State Bath Molecules: The Effect Of Physical Properties Of Donor And Bath Molecules On Super Collision Energy Transfer, Kilyoung Kim

Theses and Dissertations

This research is focused on single-collision energy transfer events between highly vibrationally excited benzene-like donor molecules and small bath molecules, CO2 and N2O in the vibrational ground level. Measuring how much energy is transferred from donors to bath molecules was accomplished by probing bath molecules scattered into specific-rotational states using a tunable Δv=0.0003 cm-1 solid state diode laser. The normalized energy transfer probability distribution function, P(E,E'), determined from energy gain information, is very useful in comparing collisional energy transfer efficiency between various collision systems. P(E,E') is also used to investigate the effects of donor and bath physical properties on collisional …

A Novel Use Of Digoxin Immune Fab Fragment In Identification And Isolation Of An Endogenous Digitalis-Like Factor Found In Preeclampsia, Moana Lee Hopoate-Sitake

Theses and Dissertations

The mechanisms mediating the hypertension of preeclampsia (PE) are unclear. Endogenous digitalis-like factors (EDLFs) are specific sodium pump (SP) inhibitors implicated in essential and experimental hypertension, but they have not been fully explored in the setting of PE. This study uses a digoxin antibody Fab fragment to address the question of whether such factors are present and increased in PE, to investigate a possible treatment of PE, and to isolate and characterize all EDLFs present in PE. Sera and placenta from women with PE did show a significant increase in SP inhibition in comparison to women with normal pregnancy and …

Surface Modification, Fabrication, And Characterization Of Silicon, Polymer, And Nanotube Composite Materials, Lei Pei

Theses and Dissertations

In my research, I have performed many characterization and fabrication experiments that are based on tools of analytical chemistry, materials chemistry, and surface science. My research projects are as follows. (1) Fabrication of transparent polymer templates for nanostructured amorphous silicon photovoltaics was done using low-cost nanoimprint lithography of polydimethylsiloxane. This approach provides a test bed for absorption studies in nanostructured film geometries and should result in improved light capturing designs in thin-film solar cells. Nanopatterned polymer films were characterized by scanning electron microscopy and optical measurements. (2) A straightforward method for fabricating freely suspended, thin, carbon nanotube (CNT) membranes infiltrated …

Two Rotary Motors In F-Atp Synthase Are Elastically Coupled By A Flexible Rotor And A Stiff Stator Stalk., André Wächter, Yumin Bi, Stanley D Dunn, Brian D Cain, Hendrik Sielaff, Frank Wintermann, Siegfried Engelbrecht, Wolfgang Junge

Biochemistry Publications

ATP is synthesized by ATP synthase (F(O)F(1)-ATPase). Its rotary electromotor (F(O)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (F(1)). Elastic power transmission between F(O) and F(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. A particularly compliant elastic domain is located on the central rotor (c(10-15)/ε/γ), right between the two sites of torque generation and consumption. The hinge on the active lever on subunit β adds further compliance. It is under contention whether or not the peripheral stalk (and the "stator" as a whole) …