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Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss

Dissertations, Theses, and Capstone Projects

All forms of life are based on biopolymers, which are made up of a selection of simple building blocks, such as amino acids, nucleotides, fatty acids and sugars. Their individual properties govern their interactions, giving rise to complex supramolecular structures with highly specialized functionality, including ligand recognition, catalysis and compartmentalization. In this thesis, we aim to answer the question whether short peptides could have acted as precursors of modern proteins during prebiotic evolution. Using a combination of experimental and computational techniques, we screened a large molecular search space for peptide sequences that are capable of forming supramolecular complexes with adenosine …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Synthesis Of Stimuli-Responsive Programmable Polymers Through Ring-Opening–Metathesis Cross-Metathesis (Rom-Cm), Courtney S. Dziewior, Sharon M. S. Strickland, Ping Li, Ken D. Shimizu

Journal of the South Carolina Academy of Science

Stimuli-responsive polymers can change their physical and/or chemical properties in response to external stimuli. These polymers have found great success in a number of important areas including molecular gels and biomedical engineering, as well as success in applications such as targeted drug delivery and biosensors. We have been working toward the development of programmable polymers that remember the response after a stimulus is withdrawn. To this end, we set out to synthesize specific functional monomers. While different types of reactions could potentially result in the desired target monomer, we studied the ring-opening metathesis–cross-metathesis reaction (ROM-CM). Previous work of ours synthesized …

Chronic Exposure To Complex Metal Oxide Nanoparticles Elicits Rapid Resistance In Shewanella Oneidensis Mr-1, Stephanie L. Mitchell, Natalie V. Hudson-Smith, Meghan S. Cahill, Benjamin N. Reynolds, Seth D. Frand, Curtis M. Green, Chenyu Wang, Mimi N. Hang, Rodrigo Tapia Hernandez, Robert J. Hamers, Z. Vivian Feng, Christy L. Haynes, Erin E. Carlson

Faculty Authored Articles

Engineered nanoparticles are incorporated into numerous emerging technologies because of their unique physical and chemical properties. Many of these properties facilitate novel interactions, including both intentional and accidental effects on biological systems. Silver-containing particles are widely used as antimicrobial agents and recent evidence indicates that bacteria rapidly become resistant to these nanoparticles. Much less studied is the chronic exposure of bacteria to particles that were not designed to interact with microorganisms. For example, previous work has demonstrated that the lithium intercalated battery cathode nanosheet, nickel manganese cobalt oxide (NMC), is cytotoxic and causes a significant delay in growth of Shewanella …

Anisotropic Singlet Fission In Single Crystalline Hexacene, Dezheng Sun, Gang-Hua Deng, Bolei Xu, Enshi Xu, Xia Li, Yajing Wu, Yuqin Qian, Yu Zhong, Colin Nuckolls, Avetik R. Harutyunyan, Hai-Lung Dai, Gugang Chen, Hanning Chen, Yi Rao

Chemistry and Biochemistry Faculty Publications

Singlet fission is known to improve solar energy utilization by circumventing the Shockley-Queisser limit. The two essential steps of singlet fission are the formation of a correlated triplet pair and its subsequent quantum decoherence. However, the mechanisms of the triplet pair formation and decoherence still remain elusive. Here we examined both essential steps in single crystalline hexacene and discovered remarkable anisotropy of the overall singlet fission rate along different crystal axes. Since the triplet pair formation emerges on the same timescale along both crystal axes, the quantum decoherence is likely responsible for the directional anisotropy. The distinct quantum decoherence rates …

Dna Recovery From Handwritten Documents Using A Novel Vacuum Technique, Patrick M. Mclaughlin

Student Theses

Investigations of many crimes such as robberies, kidnappings, and terrorism are often associated with the recovery of a paper document which has been written by the perpetrator. Paper can provide a variety of forensic evidence such as DNA, latent fingermarks, and indented writing. The focus of this study was the collection of probative DNA profiles from the text region of a handwritten note through a vacuum suction device without altering or destroying the document. Collection of DNA evidence was carried out in two separate groups. The first group involved 11 volunteers providing a handwritten note sample with unwashed hands. The …

Spectroscopic Description Of The E1 State Of Mo Nitrogenase Based On Mo And Fe X‑Ray Absorption And MöSsbauer Studies, Casey Van Stappen, Roman Davydov, Zhi-Yong Yang, Ruixi Fan, Yisong Guo, Eckhard Bill, Lance C. Seefeldt, Brian M. Hoffman, Serena Debeer

Chemistry and Biochemistry Faculty Publications

Mo nitrogenase (N2ase) utilizes a two-component protein system, the catalytic MoFe and its electron-transfer partner FeP, to reduce atmospheric dinitrogen (N₂) to ammonia (NH₃). The FeMo cofactor contained in the MoFe protein serves as the catalytic center for this reaction and has long inspired model chemistry oriented toward activating N₂. This field of chemistry has relied heavily on the detailed characterization of how Mo N2ase accomplishes this feat. Understanding the reaction mechanism of Mo N2ase itself has presented one of the most challenging problems in bioinorganic chemistry because of the ephemeral nature of its …

Fluorescence Microscopy Of Biophysical Protein Dynamics In Nanoporous Hydrogels, Anuj Saini, Lydia Kisley

Faculty Scholarship

Proteins within nanoporous hydrogels have important biotechnological applications in pharmaceutical purification, tissue engineering, water treatment, biosensors, and medical implants. Yet, oftentimes proteins that are functional in solution lose activity when in contact with soft, nanostructured, condensed phase materials due to perturbations in the folded state, conformation, diffusion, and adsorption dynamics of the protein by the material. Fluorescence microscopy experimentally measures the biophysical dynamics of proteins within hydrogels at the nanoscale and can overcome the limitations of conventional ensemble techniques. An explanation of the benefits of fluorescence is provided, and principles of fluorescence microscope instrumentation and analysis are discussed. Then several …

An Exploration Of Protein And Dna Components In Fingerprint Residue, Ashley Borrego

Student Theses

The main focus of this project was to investigate the protein and DNA components in both sebaceous and eccrine fingerprints. This study investigated the relative content of DNA and proteins in eccrine fingerprints to sebaceous fingerprints. All volunteers were instructed to wash and dry their hands prior to depositing parallel thumbprints. Twenty volunteers were instructed to touch their face to produce sebaceous prints, and 5 volunteers were instructed to wear gloves over a heat source to produce sweaty or eccrine prints. Microscopy was used to score the cellular debris of the right fingerprint on a scale of 1-4 based on …

Our Envirome, Spring/Summer 2019, Issue 40

Sustain Magazine

No abstract provided.

Plastic Pollution, Fall/Winter 2019, Issue 39.3

Sustain Magazine

No abstract provided.

A Panel Of Protein Kinase Chemosensors Distinguishes Different Types Of Fatty Liver Disease, Jon R. Beck, Fatima Cabral, Karuna Rasineni, Carol A. Casey, Edward N. Harris, Cliff I. Stains

Department of Chemistry: Faculty Publications

The worldwide incidence of fatty liver disease continues to rise, which may account for concurrent increases in the frequencies of more aggressive liver ailments. Given the existence of histologically identical fatty liver disease subtypes, there is a critical need for the identification of methods that can classify disease and potentially predict progression. Herein, we show that a panel of protein kinase chemosensors can distinguish fatty liver disease subtypes. These direct activity measurements highlight distinct differences between histologically identical fatty liver diseases arising from diets rich in fat versus alcohol and identify a previously unreported decrease in p38α activity associated with …

Global Sinusoidal Seasonality In Precipitation Isotopes, Scott T. Allen, Scott Jasechko, Wouter R. Berghuijs, Jeffrey M. Welker, Gregory R. Goldsmith, James W. Kirchner

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantifying seasonal variations in precipitation δ²H and δ¹⁸O is important for many stable isotope applications, including inferring plant water sources and streamflow ages. Our objective is to develop a data product that concisely quantifies the seasonality of stable isotope ratios in precipitation. We fit sine curves defined by amplitude, phase, and offset parameters to quantify annual precipitation isotope cycles at 653 meteorological stations on all seven continents. At most of these stations, including in tropical and subtropical regions, sine curves can represent the seasonal cycles in precipitation isotopes. Additionally, the amplitude, phase, and offset parameters of …

Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman

Publications and Research

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …

Hidden Bias In The Dud-E Dataset Leads To Misleading Performance Of Deep Learning In Structure-Based Virtual Screening, Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J. Dickson, Jose S. Duca, Viktor Hornak, David R. Koes, Tom Kurtzman

Publications and Research

Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliable protein-ligand x-ray structures and binding affinity data has required the use of constructed datasets for the training and evaluation of CNN molecular recognition models. Here, we outline various sources of bias in one such widely-used dataset, the Directory of Useful Decoys: Enhanced (DUDE). We have constructed and performed tests to investigate whether CNN models developed using DUD-E are properly learning the underlying physics of molecular …

Chemistry And Biochemistry News, Georgia Southern University

Biochemistry, Chemistry & Physics: News & Publications (2012-2023)

• Professor wins Jean Dreyfus Lectureship Grant
• Dr. Wu wins the University Excellence in Research Award 2019-20

Electron Decoupling With Chirped Microwave Pulses For Magic Angle Spinning Dynamic Nuclear Polarization Nuclear Magnetic Resonance Spectroscopy, Edward Paul Saliba

Arts & Sciences Graduate Student Theses and Dissertations

Dynamic nuclear polarization (DNP) is a method of generating hyperpolarization of nuclear spins for nuclear magnetic resonance (NMR) spectroscopy. Coherent, time domain techniques make the possibility of DNP directly to spins of interest at room temperature and higher feasible in magic angle spinning (MAS) NMR, allowing for optimal experimental repetition times to be limited by the T_1 of the electron, rather than a much longer T_1DNP, with excellent resolution. The strong hyperfine couplings that make such direct DNP transfers possible, however, can lead to short nuclear relaxation times that result in broadening of nuclear resonances and reduce sensitivity. This dissertation …

Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott

Arts & Sciences Graduate Student Theses and Dissertations

This work is focused on iron trafficking through ABC transporters in Staphylococcus aureus and combatting the growing antimicrobial resistance crisis by exploiting virulence factors as therapeutic targets. Specifically, the goal was to understand the role of a siderophore-binding lipoprotein FhuD2 in S. aureus iron trafficking. While S. aureus endogenously produces three metallophores for metal sequestration from the host, FhuD2 is thought to scavenge metals from hydroxamate-based xenosiderophores encountered in the host environment. FhuD2 is a critical virulence factor and vaccine candidate (Novartis) for MRSA. Since xenosiderophore scavenging systems are often dispensable, it was hypothesized that FhuD2 must be playing another …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Graduate Student Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and for …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Graduate Student Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and for …

Siderophore-Dependent Transport Paradigms For Iron Across The Bacterial Cell Envelope In The Human Pathogen Staphylococcus Aureus, Nathaniel Endicott

Arts & Sciences Graduate Student Theses and Dissertations

This work is focused on iron trafficking through ABC transporters in Staphylococcus aureus and combatting the growing antimicrobial resistance crisis by exploiting virulence factors as therapeutic targets. Specifically, the goal was to understand the role of a siderophore-binding lipoprotein FhuD2 in S. aureus iron trafficking. While S. aureus endogenously produces three metallophores for metal sequestration from the host, FhuD2 is thought to scavenge metals from hydroxamate-based xenosiderophores encountered in the host environment. FhuD2 is a critical virulence factor and vaccine candidate (Novartis) for MRSA. Since xenosiderophore scavenging systems are often dispensable, it was hypothesized that FhuD2 must be playing another …

Self-Assembly Of Conducting Polymer Nano- And Microstructures For Energy Storage, Luciano Matteo Santino

Arts & Sciences Graduate Student Theses and Dissertations

Plastics are materials composed of many long chains of molecules with repeating subunits; strong interactions between neighboring molecules lead to the material used throughout the world. Plastics are commonly thought to be insulating, in stark contrast to the conductivity of metals. However, certain polymer structures were discovered to exhibit semiconducting properties, the subject of the Nobel Prize in Chemistry in 2000. Conducting polymers have a unique molecular structure with an electronically conjugated backbone, allowing electrons to freely travel both across the chain and in between chains. This work focuses on controlling the kinetics of the reaction between the vapors of …

Solid-State Nmr Of Co2 Mineralization And Nmr Crystallography, Jinlei Cui

Arts & Sciences Graduate Student Theses and Dissertations

The work described in this dissertation has been accomplished by using solid-state nuclear magnetic resonance (SSNMR) spectroscopy to investigate CO2 mineralization and to refine the positions of protons in the crystalline system. The reaction of forsterite (Mg2SiO4) and 13CO2 is presented here, which is measured using in-situ 13C NMR spectroscopy without removing the sample from the reactor. 29Si SSNMR is used to investigate the reaction of forsterite with 13CO2 in the presence of water or NaCl brine as a function of depth in the sample. Additionally, we also show that NMR crystallography can significantly improve structure refinement of hydrogens’ positions …

Novel Self-Assembly Of Fullerene-Based Dyads, Ashley D. Anderson

Theses and Dissertations

Eventual depletion and environmental toxicity of natural non-renewable energy resources are two issues pushing research toward alternative energy resources. Nature’s process of renewable, unlimited, clean energy production is photosynthesis and porphyrins are a critical component due to their ability to undergo photoinduced electron transfer. This property also makes porphyrins excellent candidates for applications such as solar cells, water splitting, and optical sensing. Researchers have previously tethered porphyrins to fullerene (C60), an excellent electron acceptor, to mimic the reaction centers in photosynthesis. Photoinduced electron transfer in these donor-acceptor dyads has been investigated with particular focus on factors such as the donor, …

A Physics-Based Intermolecular Potential For Biomolecular Simulation, Joshua Andrew Rackers

Arts & Sciences Graduate Student Theses and Dissertations

The grand challenge of biophysics is to use the fundamental laws of physics to predict howbiological molecules will move and interact. The atomistic HIPPO (Hydrogen-likeIntermolecular Polarizable Potential) force field is meant to address this challenge. It does so bybreaking down the intermolecular potential energy function of biomolecular interactions intophysically meaningful components (electrostatics, polarization, dispersion, and exchangerepulsion)and using this function to drive molecular dynamics simulations. This force field isable to achieve accuracy within 1 kcal/mol for each component when compared with ab initioSymmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy becauseit introduces a model electron density on every …

Solid-State Nmr Of Co2 Mineralization And Nmr Crystallography, Jinlei Cui

Arts & Sciences Graduate Student Theses and Dissertations

The work described in this dissertation has been accomplished by using solid-state nuclear magnetic resonance (SSNMR) spectroscopy to investigate CO2 mineralization and to refine the positions of protons in the crystalline system. The reaction of forsterite (Mg2SiO4) and 13CO2 is presented here, which is measured using in-situ 13C NMR spectroscopy without removing the sample from the reactor. 29Si SSNMR is used to investigate the reaction of forsterite with 13CO2 in the presence of water or NaCl brine as a function of depth in the sample. Additionally, we also show that NMR crystallography can significantly improve structure refinement of hydrogens’ positions …

Systematic Optimization For Production Of The Anti-Mrsa Antibiotics Wap-8294a In An Engineered Strain Of Lysobacter Enzymogenes, Xusheng Chen, Shanren Li, Lingjun Yu, Amanda Miller, Liangcheng Du

Department of Chemistry: Faculty Publications

WAP-8294A is a group of cyclic lipodepsipeptides and considered as the first-in-class new chemical entity with potent activity against methicillin-resistant Staphylococcus aureus. One of the roadblocks in developing the WAP-8294A antibiotics is the very low yield in Lysobacter. Here, we carried out a systematic investigation of the nutritional and environmental conditions in an engineered L. enzymogenes strain for the optimal production of WAP-8294A. We developed an activity-based simple method for quick screening of various factors, which enabled us to optimize the culture conditions. With the method, we were able to improve the WAP-8294A yield by 10-fold in small-scale cultures and …

Β-Fluorofentanyls Are Ph-Sensitive Mu Opioid Receptor Agonists, Ricardo Rosas Jr., Xi-Ping Huang, Bryan L. Roth, Chris Dockendorff

Chemistry Faculty Research and Publications

The concept recently postulated by Stein and co-workers (Science2017, 355, 966) that mu opioid receptor (MOR) agonists possessing amines with attenuated basicity show pH-dependent activity and can selectively act at damaged, low pH tissues has been additionally supported by in vitro studies reported here. We synthesized and tested analogs of fentanyl possessing one or two fluorine atoms at the beta position of the phenethylamine side chain, with additional fluorines optionally added to the benzene ring of the side chain. These compounds were synthesized in 1 to 3 steps from commercial building blocks. The novel bis-fluorinated analog …

Using An Extended Broken Symmetry Approximation To Characterize Structure And Spectroscopic Properties Of 2fe-2s Clusters, Ashlyn M. Koval

Electronic Theses and Dissertations

Iron-sulfur proteins perform a wide variety of biological functions that assist in mediating protein function via electron transfer reactions. The Rieske and mitoNEET iron-sulfur clusters have been shown to undergo proton coupled electron transfer facilitated by a histidine ligand. The protonation state of the histidine residue is key to understanding the mechanism of proton coupled electron transfer. This work reports a study of the 2Fe-2S ferredoxin, Rieske, and mitoNEET clusters using the extended broken symmetry approximation. Calculations were performed on the ferredoxin cluster to establish appropriate methodologies. Calculations were then performed for Rieske and mitoNEET clusters to suggest experiments capable …

Triple Functionalization Of Titanium Aluminum Vanadium For Orthopedic Implant Applications, Ashley Blystone

Electronic Theses and Dissertations

Orthopedic implant surgeries are on the rise in the United States, with well over a million surgeries performed annually. Common materials used for these applications include titanium and its alloy, titanium aluminum vanadium (Ti-6Al-4V). Ti-6Al-4V is chosen for this application due to its mechanical strength and corrosion resistance. However, Ti-6Al-4V does not support osseointegration and is susceptible to bacterial colonization. Therefore, these implants suffer from aseptic loosening and infection, necessitating removal and replacement. Revision surgery and treatment is financially burdensome and taxing on the patient. Current approaches focus on modifying the surface of Ti-6Al-4V through a variety of means to …