Other Biochemistry, Biophysics, and Structural Biology Commons^™

Reactive Oxygen Species In Chronic Obstructive Pulmonary Disease, Samia Boukhenouna, Mark A. Wilson, Karim Bahmed, Beata Kosmider

Department of Biochemistry: Faculty Publications

Chronic obstructive pulmonary disease (COPD) includes chronic bronchitis and emphysema. Environmental exposure, primarily cigarette smoking, can cause high oxidative stress and is the main factor of COPD development. Cigarette smoke also contributes to the imbalance of oxidant/antioxidant due to exogenous reactive oxygen species (ROS). Moreover, endogenously released ROS during the inflammatory process and mitochondrial dysfunction may contribute to this disease progression. ROS and reactive nitrogen species (RNS) can oxidize different biomolecules such as DNA, proteins, and lipids leading to epithelial cell injury and death. Various detoxifying enzymes and antioxidant defense systems can be involved in ROS removal. In this review, …

Role Of Selenof As A Gatekeeper Of Secreted Disulfide-Rich Glycoproteins, Sun Hee Yim, Robert A. Everley, Frank A. Schildberg, Sang-Goo Lee, Andrea Orsi, Zachary R. Barbati, Kutay Karatepe, Dmitry E. Fomenko, Petra A. Tsuji, Hongbo R. Luo, Steven P. Gygi, Roberto Sitia, Arlene H. Sharpe, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Selenof (15-kDa selenoprotein; Sep15) is an endoplasmic reticulum (ER)-resident thioredoxin-like oxidoreductase that occurs in a complex with UDPglucose: glycoprotein glucosyltransferase. We found that Selenof deficiency in mice leads to elevated levels of non-functional circulating plasma immunoglobulins and increased secretion of IgM during in vitro splenic B cell differentiation. However, Selenof knockout animals show neither enhanced bacterial killing capacity nor antigen-induced systemic IgM activity, suggesting that excess immunoglobulins are not functional. In addition, ER-to-Golgi transport of a target glycoprotein was delayed in Selenof knockout embryonic fibroblasts, and proteomic analyses revealed that Selenof deficiency is primarily associated with antigen presentation and ER-to-Golgi …

Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle E. Howell, Karin V. Van Dijk, Christine S. Booth, Tomáš Helikar, Brian A. Couch, Rebecca Roston

Department of Biochemistry: Faculty Publications

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7).

Structural Basis For The Substrate Inhibition Of Proline Utilization A By Proline, David A. Korasick, Travis A. Pemberton, Benjamin W. Arentson, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) is a bifunctional flavoenzyme that catalyzes the two-step oxidation of L-proline to L-glutamate using spatially separated proline dehydrogenase (PRODH) and L-glutamate-y-semialdehyde dehydrogenase (GSALDH) active sites. Substrate inhibition of the coupled PRODH-GSALDH reaction by proline is a common kinetic feature of PutAs, yet the structural basis for this phenomenon remains unknown. To understand the mechanism of substrate inhibition, we determined the 2.15 Å resolution crystal structure of Bradyrhizobium japonicum PutA complexed with proline. Proline was discovered in five locations remote from the PRODH active site. Most notably, strong electron density indicated that proline bound tightly to the …

Lncrna Meg3 Protects Endothelial Function By Regulating The Dna Damage Response, Mohamed Sham Shihabudeen Haider Ali, Xiao Cheng, Matthew Moran, Stefan Haemmig, Michael J. Naldrett, Sophie Alvarez, Mark W. Feinberg, Xinghui Sun

Department of Biochemistry: Faculty Publications

The role of long non-coding RNAs (lncRNAs) in regulating endothelial function through the DNA damage response (DDR) remains poorly understood. In this study, we demonstrate that lncRNA maternally expressed gene 3 (Meg3) interacts with the RNA binding protein polypyrimidine tract binding protein 3 (PTBP3) to regulate gene expression and endothelial function through p53 signaling a major coordinator of apoptosis and cell proliferation triggered by the DDR. Meg3 expression is induced in endothelial cells (ECs) upon p53 activation. Meg3 silencing induces DNA damage, activates p53 signaling, increases the expression of p53 target genes, promotes EC apoptosis, and inhibits EC proliferation. Mechanistically, …

Dietary Omega-3 And Omega-6 Polyunsaturated Fatty Acids Modulate Hepatic Pathology, Saraswoti Khadge, J. Graham Sharp, Geoffrey M. Thiele, Timothy R. Mcguire, Lynell W. Klassen, Michael J. Duryee, Holly C. Britton, Jordan Beck, Paul N. Black, Concetta Dirusso, James Talmadge

Department of Biochemistry: Faculty Publications

Recent evidence has suggested that dietary polyunsaturated fatty acids (PUFAs) modulate inflammation; however, few studies have focused on the pathobiology of PUFA using isocaloric and isolipidic diets and it is unclear if the associated pathologies are due to dietary PUFA composition, lipid metabolism or obesity, as most studies compare diets fed ad libitum. Our studies used isocaloric and isolipidic liquid diets (35% of calories from fat), with differing compositions of omega (ω)-6 or long chain (Lc) ω-3 PUFA that were pair-fed and assessed hepatic pathology, inflammation and lipid metabolism. Consistent with an isocaloric, pair-fed model we observed no significant difference …

Long-Chain Omega-3 Polyunsaturated Fatty Acids Modulate Mammary Gland Composition And Inflammation, Saraswoti Khadge, Geoffrey M. Thiele, J. Graham Sharp, Timothy R. Mcguire, Lynell W. Klassen, Paul N. Black, Concetta Dirusso, James Talmadge

Department of Biochemistry: Faculty Publications

Studies in rodents have shown that dietary modifications as mammary glands (MG) develop, regulates susceptibility to mammary tumor initiation. However, the effects of dietary PUFA composition on MGs in adult life, remains poorly understood. This study investigated morphological alterations and inflammatory microenvironments in the MGs of adult mice fed isocaloric and isolipidic liquid diets with varying compositions of omega (ω)-6 and long-chain (Lc)-ω3FA that were pair-fed. Despite similar consumption levels of the diets, mice fed the ω-3 diet had significantly lower body-weight gains, and abdominal-fat and mammary fat pad (MFP) weights. Fatty acid analysis showed significantly higher levels of Lc-ω-3FAs …

Adenosine Has Two Faces: Regionally Dichotomous Adenosine Tone In A Model Of Epilepsy With Comorbid Sleep Disorders, Ted J. Warren, Timothy A. Simeone, D. David Smith, Ryan Grove, Jiri Adamec, Kaeli K. Samson, Harrison M. Roundtree, Deepak Madhavan, Kristina A. Simeone

Department of Biochemistry: Faculty Publications

Objective: Adenosine participates in maintaining the excitatory/inhibitory balance in neuronal circuits. Studies indicate that adenosine levels in the cortex and hippocampus increase and exert sleep pressure in sleep-deprived and control animals, whereas in epilepsy reduced adenosine tone promotes hyperexcitability. To date, the role of adenosine in pathological conditions that result in both seizures and sleep disorders is unknown. Here, we determined adenosine tone in sleep and seizure regulating brain regions of Kv1.1 knockout (KO) mice, a model of temporal epilepsy with comorbid sleep disorders.

Methods: 1) Reverse phase-high performance liquid chromatography (RP-HPLC) was performed on brain tissue to determine levels …

Photosystem Ii Subunit S Overexpression Increases The Efficiency Of Water Use In A Field-Grown Crop, Katarzyna Glowacka, Johannes Kromdijk, Katherine Kucera, Jiayang Xie, Amanda P. Cavanagh, Lauriebeth Leonelli, Andrew D. B. Leakey, Donald R. Ort, Krishna K. Niyogi, Stephen P. Long

Department of Biochemistry: Faculty Publications

Insufficient water availability for crop production is a mounting barrier to achieving the 70% increase in food production that will be needed by 2050. One solution is to develop crops that require less water per unit mass of production. Water vapor transpires from leaves through stomata, which also facilitate the influx of CO2 during photosynthetic assimilation. Here, we hypothesize that Photosystem II Subunit S (PsbS) expression affects a chloroplastderived signal for stomatal opening in response to light, which can be used to improve wateruse efficiency. Transgenic tobacco plants with a range of PsbS expression, from undetectable to 3.7 …

Simulation Of Stimulation: Cytokine Dosage And Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation, Matteo Barberis, Tomáš Helikar, Paul Verbruggen

Department of Biochemistry: Faculty Publications

Triggering an appropriate protective response against invading agents is crucial to the effectiveness of human innate and adaptive immunity. Pathogen recognition and elimination requires integration of a myriad of signals from many different immune cells. For example, T cell functioning is not qualitatively, but quantitatively determined by cellular and humoral signals. Tipping the balance of signals, such that one of these is favored or gains advantage on another one, may impact the plasticity of T cells. This may lead to switching their phenotypes and, ultimately, modulating the balance between proliferating and memory T cells to sustain an appropriate immune response. …

Computational Systems Biology Approach For The Study Of Rheumatoid Arthritis: From A Molecular Map To A Dynamical Model, Vidisha Singh, Marek Ostaszewski, George D. Kalliolias, Gilles Chiocchia, Robert Olaso, Elisabeth Petit-Teixeira, Tomáš Helikar, Anna Niarakis

Department of Biochemistry: Faculty Publications

In this work we present a systematic effort to summarize current biological pathway knowledge concerning Rheumatoid Arthritis (RA). We are constructing a detailed molecular map based on exhaustive literature scanning, strict curation criteria, re-evaluation of previously published attempts and most importantly experts’ advice. The RA map will be web-published in the coming months in the form of an interactive map, using the MINERVA platform, allowing for easy access, navigation and search of all molecular pathways implicated in RA, serving thus, as an on line knowledgebase for the disease. Moreover the map could be used as a template for Omics data …

The Colomoto Interactive Notebook: Accessible And Reproducible Computational Analyses For Qualitative Biological Networks, Aurelien Naldi, Celine Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loic Pauleve

Department of Biochemistry: Faculty Publications

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together,many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users’ learning curve of these technologies. The framework …

A Mechanistic Computational Model Reveals That Plasticity Of Cd4+ T Cell Differentiation Is A Function Of Cytokine Composition And Dosage, Bhanwar Lal Puniya, Robert G. Todd, Akram Mohammed, Deborah M. Brown, Matteo Barberis, Tomáš Helikar

Department of Biochemistry: Faculty Publications

CD4+ T cells provide cell-mediated immunity in response to various antigens. During an immune response, naïve CD4+ T cells differentiate into specialized effector T helper (Th1, Th2, and Th17) cells and induced regulatory (iTreg) cells based on a cytokine milieu. In recent studies, complex phenotypes resembling more than one classical T cell lineage have been experimentally observed. Herein, we sought to characterize the capacity of T cell differentiation in response to the complex extracellular environment. We constructed a comprehensive mechanistic (logical) computational model of the signal transduction that regulates T cell differentiation. The model’s dynamics were characterized and analyzed under …

Structural Features And Domain Movements Controlling Substrate Binding And Cofactor Specificity In Class Ii Hmg-Coa Reductase, Bradley R. Miller, Yan Kung

Chemistry Faculty Research and Scholarship

The key mevalonate pathway enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) uses the cofactor NAD(P)H to reduce HMG-CoA to mevalonate in the production of countless metabolites and natural products. Although inhibition of HMGR by statin drugs is well-understood, several mechanistic details of HMGR catalysis remain unresolved, and the structural basis for the wide range of cofactor specificity for either NADH or NADPH among HMGRs from different organisms is also unknown. Here, we present crystal structures of HMGR from Streptococcus pneumoniae (SpHMGR) alongside kinetic data of the enzyme’s cofactor preferences. Our structure of SpHMGR bound with its kinetically preferred NADPH cofactor …

Manipulating Graded Exercise Test Variables Affects The Validity Of The Lactate Threshold And Vo2peak, Nicholas A. Jamnick, Javier Botella, David B. Pyne, David Bishop

Research outputs 2014 to 2021

Background To determine the validity of the lactate threshold (LT) and maximal oxygen uptake (V_ O2max) determined during graded exercise test (GXT) of different durations and using different LT calculations. Trained male cyclists (n = 17) completed five GXTs of varying stage length (1, 3, 4, 7 and 10 min) to establish the LT, and a series of 30-min constant power bouts to establish the maximal lactate steady state (MLSS). V_ O2 was assessed during each GXT and a subsequent verification exhaustive bout (VEB), and 14 different LTs were calculated from four of the GXTs (3, 4, 7 and 10 …

Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae, Megann Michelle Schmidt

Honors Program Theses

Whole genome duplication (WGD) is a process in which the entire genome of an organism is duplicated, making redundant genes which are subject to unique evolutionary forces. Various modes of selection create different genetic fates such as retention of ancestral function, development of new function, or loss of function. Because of these differing fates, WGD is hypothesized to be a major driving force behind diversification. In this project, DNA sequences from fish species in the family Catostomidae were examined to observe patterns of evolution following a known WGD. Gene trees were generated for 179 loci to determine the amount of …

Impact Of Phosphoinositides On Regulation Of K-Atp By Atp And Hydrogen Sulfide, Tyler Hendon

Theses and Dissertations

Hydrogen sulfide (H2S) reduces ischemia reperfusion (IR) injury by stimulating adenosine triphosphate (ATP) sensitive potassium channels (KATP) [1-5]. Demonstrating H2S stimulation is unique to KATP, as other inwardly rectifying potassium (Kir) channels demonstrate inhibition or are unaffected [6]. We recently showed that H2S inhibits Kir2 and Kir3 by decreasing channel sensitivity to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2 or PIP2) [6]. Here, we test the hypothesis that H2S regulation of Kir6.2, a pore-forming subunit of the KATP channel, is also dependent on PIP2. Using whole-cell patch-clamp we show that H2S increases the activity of Kir6.2 channels expressed in HEK-293 cells. To study the …

Cancerdiscover: An Integrative Pipeline For Cancer Biomarker And Cancer Class Prediction From High-Throughput Sequencing Data, Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Accurate identification of cancer biomarkers and classification of cancer type and subtype from High Throughput Sequencing (HTS) data is a challenging problem because it requires manual processing of raw HTS data from various sequencing platforms, quality control, and normalization, which are both tedious and timeconsuming. Machine learning techniques for cancer class prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. To date, great research efforts have been taken for cancer biomarker identification and cancer class prediction. However, currently available tools and pipelines lack flexibility in data preprocessing, running multiple feature selection methods and learning algorithms, therefore, developing …

Endosomal Escape Of Antisense Oligonucleotides Internalized By Stabilin Receptors Is Regulated By Rab5c And Eea1 During Endosomal Maturation, Colton M. Miller, W. Brad Wan, Punit P. Seth, Edward N. Harris

Department of Biochemistry: Faculty Publications

Second-generation (Gen 2) Antisense oligonucleotides (ASOs) show increased nuclease stability and affinity for their RNA targets, which has translated to improved potency and therapeutic index in the clinic. Gen 2 ASOs are typically modified using the phosphorothioate (PS) backbone modification, which enhances ASO interactions with plasma, cell surface, and intracellular proteins. This facilitates ASO distribution to peripheral tissues and also promotes cellular uptake after injection into animals. Previous work identified that Stabilin receptors specifically internalize PS-ASOs in the sinusoidal endothelial cells of the liver and the spleen. By modulating expression of specific proteins involved in the trafficking and maturation of …

3-O Sulfation Of Heparin Leads To Hepatotropism And Longer Circulatory Half-Life, Colton M. Miller, Yongmei Xu, Katrina M. Kudrna, Blake E. Hass, Brianna M. Kellar, Andrew W. Egger, Jian Liu, Edward N. Harris

Department of Biochemistry: Faculty Publications

Introduction: Heparins are common blood anticoagulants that are critical for many surgical and biomedical procedures used in modern medicine. In contrast to natural heparin derived from porcine gut mucosa, synthetic heparins are homogenous by mass, polymer length, and chemistry.

Materials & methods: Stable cell lines expressing the human and mouse Stabilin receptors were used to evaluate endocytosis of natural and synthetic heparin. We chemoenzymatically produced synthetic heparin consisting of 12 sugars (dodecamers) containing 14 sulfate groups resulting in a non-3-O sulfated structure (n12mer). Half of the n12mer was modified with a 3-O sulfate on a single GlcNS sugar producing the …