Biochemistry Commons^™

Engineering And Application Of A Biosensor With Focused Ligand Specificity, Dennis Della Corte, Hugo L. Van Beek, Falk Syberg, Marcus Schallmey, Felix Tobola, Kai U. Cormann, Christine Schlicker, Philipp T. Baumann, Karin Krumbach, Sascha Sokolowsky, Connor J. Morris, Alexander Grünberger

Faculty Publications

Cell factories converting bio-based precursors to chemicals present an attractive avenue to a sustainable economy, yet screening of genetically diverse strain libraries to identify the best-performing whole-cell biocatalysts is a low-throughput endeavor. For this reason, transcriptional biosensors attract attention as they allow the screening of vast libraries when used in combination with fluorescence-activated cell sorting (FACS). However, broad ligand specificity of transcriptional regulators (TRs) often prohibits the development of such ultra-high-throughput screens. Here, we solve the structure of the TR LysG of Corynebacterium glutamicum, which detects all three basic amino acids. Based on this information, we follow a semi-rational engineering …

Retrieving Functional Pathways Of Biomolecules From Single-Particle Snapshots, Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee Des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd

Publications and Research

A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the …

A Review Of The Preclinical And Clinical Efficacy Of Remdesivir, Hydroxychloroquine, And Lopinavir-Ritonavir Treatments Against Covid-19, Dawid Maciorowski, Samir Z. El Idrissi, Yash Gupta, Brian J. Medernach, Michael B. Burns, Daniel P. Becker Ph.D., Ravi Durvasula, Prakasha Kempaiah

Chemistry: Faculty Publications and Other Works

In December of 2019, an outbreak of a novel coronavirus flared in Wuhan, the capital city of the Hubei Province, China. The pathogen has been identified as a novel enveloped RNA beta-coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus SARS-CoV-2 is associated with a disease characterized by severe atypical pneumonia known as coronavirus 2019 (COVID-19). Typical symptoms of this disease include cough, fever, malaise, shortness of breath, gastrointestinal symptoms, anosmia, and, in severe cases, pneumonia.¹ The high-risk group of COVID-19 patients includes people over the age of 60 years as well as people with existing cardiovascular …

A Practical Guide To Mechanistic Systems Modeling In Biology Using A Logic-Based Approach, Anna Niarakis, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These models provide a means to analyze the dynamics of the systems they describe, and to study and interrogate their properties, and provide insights about the emerging behavior of the system in the presence of single or combined perturbations. Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps. The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting …

Cautionary Tale Of Using Tris(Alkyl)Phosphine Reducing Agents With Nad+-Dependent Enzymes, Sagar M. Patel, Thomas G. Smith, Martha Morton, Kyle M. Stiers, Javier Seravalli, Stephen J. Mayclin, Thomas E. Edwards, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Protein biochemistry protocols typically include disulfide bond reducing agents to guard against unwanted thiol oxidation and protein aggregation. Commonly used disulfide bond reducing agents include dithiothreitol, β-mercaptoethanol, glutathione, and the tris(alkyl)phosphine compounds tris(2-carboxyethyl)phosphine (TCEP) and tris(3-hydroxypropyl)phosphine (THPP). While studying the catalytic activity of the NAD(P)H-dependent enzyme Δ¹-pyrroline-5-carboxylate reductase, we unexpectedly observed a rapid non-enzymatic chemical reaction between NAD⁺ and the reducing agents TCEP and THPP. The product of the reaction exhibits a maximum ultraviolet absorbance peak at 334 nm and forms with an apparent association rate constant of 231–491 M⁻¹ s⁻¹. The reaction is …

Indoline‐6‐Sulfonamide Inhibitors Of The Bacterial Enzyme Dape, Cory T. Reidl, Tahirah K. Heath, Iman Darwish, Rachel M. Torrez, Maxwell Moore, Elliot Gild, Boguslaw P. Nocek, Anna Starus, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Inhibitors of the bacterial enzyme dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18) hold promise as antibiotics with a new mechanism of action. Herein we describe the discovery of a new series of indoline sulfonamide DapE inhibitors from a high-throughput screen and the synthesis of a series of analogs. Inhibitory potency was measured by a ninhydrin-based DapE assay recently developed by our group. Molecular docking experiments suggest active site binding with the sulfonamide acting as a zinc-binding group (ZBG).

Rethinking Fda Regulation Of Complex Products, Philip E. Alford

Minnesota Journal of Law, Science & Technology

No abstract provided.

Estimating Partial Body Ionizing Radiation Exposure By Automated Cytogenetic Biodosimetry, Peter Rogan

Biochemistry Publications

Purpose: Inhomogeneous exposures to ionizing radiation can be detected and quantified with the Dicentric Chromosome Assay (DCA) of metaphase cells. Complete automation of interpretation of the DCA for whole body irradiation has significantly improved throughput without compromising accuracy, however low levels of residual false positive dicentric chromosomes (DCs) have confounded its application for partial body exposure determination.

Materials and Methods: We describe a method of estimating and correcting for false positive DCs in digitally processed images of metaphase cells. Nearly all DCs detected in unirradiated calibration samples are introduced by digital image processing. DC frequencies of irradiated calibration …

Electronic-Cigarette Vehicles And Flavoring Affect Lung Function And Immune Responses In A Murine Model, Brittany N. Szafran, Rakeysha Pinkston, Zakia Perveen, Matthew K. Ross, Timothy Morgan, Daniel B. Paulsen, Arthur L. Penn, Barbara L. F. Kaplan, Alexandra Noel

Faculty Publications

The use of electronic nicotine delivery systems (ENDS), also known as electronic-cigarettes (e-cigs), has raised serious public health concerns, especially in light of the 2019 outbreak of e-cig or vaping product use-associated acute lung injury (EVALI). While these cases have mostly been linked to ENDS that contain vitamin E acetate, there is limited research that has focused on the chronic pulmonary effects of the delivery vehicles (i.e., without nicotine and flavoring). Thus, we investigated lung function and immune responses in a mouse model following exposure to the nearly ubiquitous e-cig delivery vehicles, vegetable glycerin (VG) and propylene glycol (PG), used …

Mesenchymal Stem Cells And Their Extracellular Vesicles: A Potential Game Changer For The Covid-19 Crisis, Dina H. Kassem, Mohamed M. Kamal

Pharmacy

Corona virus disease 2019 (COVID-19) is a global public health crisis. The high infectivity of the disease even from non-symptomatic infected patients, together with the lack of a definitive cure or preventive measures are all responsible for disease outbreak. The severity of COVID-19 seems to be mostly dependent on the patients’ own immune response. The over-activation of the immune system in an attempt to kill the virus, can cause a “cytokine storm” which in turn can induce acute respiratory distress syndrome (ARDS), as well as multi-organ damage, and ultimately may lead to death. Thus, harnessing the immunomodulatory properties of mesenchymal …

Synthesis, Structure Elucidation And Selected Biological Activities Of Ag(I) And Au(I) Complexes Constructed From Thiosemicarbazone And Phosphine Ligands, Syahrina Nur ‘Ain Abdul Halim

Student Works (2020-2029)

New Ag(I) and Au(I) mixed ligand complexes were synthesised using thiosemicarbazone and phosphine in search of a new biologically active compounds. CHN elemental analysis, powder X-ray diffraction (PXRD), single crystal X-ray diffraction as well as several spectroscopic techniques such as FT-IR, Energy-dispersive X-ray (EDX), 1H, 13C, and 31P{1H} NMR were performed to elucidate the structure of these complexes. Elemental analysis suggested that the stoichiometry of the complexes formed by the reaction of Ag nitrate with thiosemicarbazone in the presence of phosphine was indeed 1:2:1 molar ratio, while for the Au to be in 1:1:1 molar ratio. The Ag and Au …

Pressure Driven Desalination Utilizing Nanomaterials, Fangyou Xie

Master's Theses

Nanomaterials such as graphene oxide and carbon nanotubes, have demonstrated excellent properties for membrane desalination, including decrease of maintenance, increase of flux rate, simple solution casting, and impressive chemical inertness. Here, two projects are studied to investigate nanocarbon based membrane desalination. The first project is to prepare hybrid membranes with amyloid fibrils intercalated with graphene oxide sheets. The addition of protein amyloid fibrils expands the interlayer spacing between graphene oxide nanosheets and introduces additional functional groups in the diffusion pathways, resulting in increase of flux rate and rejection rate for the organic dyes. Amyloid fibrils also provide structural assistance to …

Berry Phenolic And Volatile Extracts Inhibit Pro-Inflammatory Cytokine Secretion In Lps-Stimulated Raw264.7 Cells Through Suppression Of Nf-Κb Signaling Pathway, Inah Gu, Cindi Brownmiller, Nathan Blaine Stebbins, Andy Mauromostakos, Luke Howard, Sun-Ok Lee

Food Science Faculty Publications and Presentations

Berries are a rich source of phytochemicals, especially phenolics well known for protective activity against many chronic diseases. Berries also contain a complex mixture of volatile compounds that are responsible for the unique aromas of berries. However, there is very limited information on the composition and potential health benefits of berry volatiles. In this study, we isolated phenolic and volatile fractions from six common berries and characterized them by HPLC/HPLC-MS and GC/GC-MS, respectively. Berry phenolic and volatile fractions were evaluated for an anti-inflammatory effect using lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells by measuring levels of pro-inflammatory cytokines and the nuclear factor-kappa …

Pointing The Zinc Finger On Protein Folding: Energetic Investigation Into The Role Of The Metal-Ion In The Metal-Induced Protein Folding Of Zinc Finger Motifs, Inna Bakman-Sanchez

Dissertations, Theses, and Capstone Projects

Interactions between inorganic metal-ion cofactors and organic protein scaffolds are important for the proper structure and function of metalloproteins. Zinc finger proteins (ZFPs) are an example of proteins with such crucial metal-protein interactions. Incorporation of the Zn(II)-ion into ZFPs allows for their correct folding into structures that can carry out vital biological functions which include gene expression and tumor suppression. In addition, engineered ZFPs have shown to be promising genetic therapeutics in the clinic. And yet, there is still a gap in a quantitative understanding of the energetic contribution of the metal-protein interactions towards the structure and function of these …

Machine Learning Applications For Drug Repurposing, Hansaim Lim

Dissertations, Theses, and Capstone Projects

The cost of bringing a drug to market is astounding and the failure rate is intimidating. Drug discovery has been of limited success under the conventional reductionist model of one-drug-one-gene-one-disease paradigm, where a single disease-associated gene is identified and a molecular binder to the specific target is subsequently designed. Under the simplistic paradigm of drug discovery, a drug molecule is assumed to interact only with the intended on-target. However, small molecular drugs often interact with multiple targets, and those off-target interactions are not considered under the conventional paradigm. As a result, drug-induced side effects and adverse reactions are often neglected …

Small Molecule Synthetic Carbohydrate Receptors, Marcelo F. Bravo Carranco

Dissertations, Theses, and Capstone Projects

Carbohydrate – receptor interactions are often involved in the attachment of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered “undruggable”, meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs) – small molecules that bind carbohydrates – could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of …

Microglia Induced Neuroinflammation Through The Nlrp3 Inflammasome Following Blast Traumatic Brain Injury, Daniel Younger

Dissertations

The incidence of traumatic brain injury (TBI) among military personnel have been steadily increasing with modern conflicts. A recent RAND report estimated 320,000 service members, totaling 20% of deployed forces, suffer from TBI. However, of this population roughly 60% have not seen a medical professional specifically for TBI. Unlike the civilian population, the primary cause of TBI for active-duty military personnel is blast exposure. Blasts now account for over 70% of all US military casualties in operation Iraqi Freedom (OIF) and Operation enduring freedom (OEF) and are the major cause of TBI. Among many pathological mechanisms associated with blast TBI, …

Capsaicin Is A Negative Allosteric Modulator Of The 5-Ht3 Receptor, Eslam El Nebrisi, Tatiana Prytkova, Dietrich Ernst Lorke, Luke Howarth, Asma Hassan Alzaabi, Keun-Hang Susan Yang, Frank Christopher Howarth, Murat Oz

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this study, effects of capsaicin, an active ingredient of the capsicum plant, were investigated on human 5-hydroxytryptamine type 3 (5-HT₃) receptors. Capsaicin reversibly inhibited serotonin (5-HT)-induced currents recorded by two-electrode voltage clamp method in Xenopus oocytes. The inhibition was time- and concentration-dependent with an IC₅₀ = 62 μM. The effect of capsaicin was not altered in the presence of capsazepine, and by intracellular BAPTA injections or trans-membrane potential changes. In radio-ligand binding studies, capsaicin did not change the specific binding of the 5-HT₃ antagonist [³H]GR65630, indicating that it is a noncompetitive inhibitor of …

Investigating Photosynthetic Stability: Relation Between Thylakoid Lipid Content And The Stability Of The Cytochrome B6f Complex, Marina Mehling

The Journal of Purdue Undergraduate Research

The cytochrome b₆f complex is an enzyme found in plants, cyanobacteria, and green algae that catalyzes the transport of electrons in the rate-limiting step of oxygenic photosynthesis. This dimeric complex has an extensive lipid architecture that is primarily composed of five distinct lipid classes: monogalactosyl diacylglycerol (MGDG), digalactosyl diacylglycerol (DGDG), phosphatidyl glycerol (PG), monoglucosyl diacylglycerol (GlcDG), and sulfoquinovosyl diacylglycerol (SQDG). While these lipid classes have been identified, their precise role in the function of the cytochrome complex are only beginning to be understood. Mechanisms describing the relation between thylakoid lipid content on the stability of the b_{6 …}

Aerosol Mass And Optical Properties, Smoke Influence On O3, And High No3 Production Rates In A Western U.S. City Impacted By Wildfires, Vanessa Selimovic, Robert J. Yokelson, Gavin R. Mcmeeking, Sarah Coefield

Chemistry and Biochemistry Faculty Publications

Evaluating our understanding of smoke from wild and prescribed fires can benefit from downwind measurements that include inert tracers to test production and transport and reactive species to test chemical mechanisms. We characterized smoke from fires in coniferous forest fuels for >1,000 hr over two summers (2017 and 2018) at our Missoula, Montana, surface station and found a narrow range for key properties. ΔPM2.5/ΔCO was 0.1070 ± 0.0278 (g/g) or about half the age-independent ratios obtained at free troposphere elevations (0.2348 ± 0.0326). The average absorption Ångström exponent across both years was 1.84 ± 0.18, or about half the values …