Biochemistry, Biophysics, and Structural Biology Commons^™

Redox-Dependent Stability, Protonation, And Reactivity Of Cysteine-Bound Heme Proteins, Fangfang Zhong, George P. Lisi, Daniel P. Collins, John H. Dawson, Ekaterina V. Pletneva

Dartmouth Scholarship

Cysteine-bound hemes are key components of many enzymes and biological sensors. Protonation (deprotonation) of the Cys ligand often accompanies redox transformations of these centers. To characterize these phenomena, we have engineered a series of Thr78Cys/Lys79Gly/Met80X mutants of yeast cytochrome c (cyt c) in which Cys78 becomes one of the axial ligands to the heme. At neutral pH, the protonation state of the coordinated Cys differs for the ferric and ferrous heme species, with Cys binding as a thiolate and a thiol, respectively. Analysis of redox-dependent stability and alkaline transitions of these model proteins, as well as comparisons to Cys …

Collisional Dynamic Elements Of The Pyrazine - N2o System:Middle And Low J States, La Moyne Tyler Mix

Theses and Dissertations

Unimolecular reactions based on the Lindemann - Hinchelwood mechanism are important to understanding combustion and atmospheric processes. The main feature of this mechanism is the energy transfer probability distribution function, P(E',E). We have chosen to study P(E',E) through gas phase collisional dynamics probed with IR transient absorption spectroscopy. Post-collision absorption line widths for the pyrazine-N2O system are used to calculate lab frame translational temperatures. The translational temperatures reveal that collisions with large rotational energy transfer also transfer large amounts of translational energy. For J states >47 the relationship is linear indicating a constant impact parameter. Line widths for J=47 through …

Understanding The Mechanism Of Glucose-Induced Relief Of Rgt1-Mediated Repression In Yeast, Adhiraj Roy, David Jouandot, Kyu Hong Cho, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

The yeast Rgt1 repressor inhibits transcription of the glucose transporter (HXT) genes in the absence of glucose. It does so by recruiting the general corepressor complex Ssn6-Tup1 and the HXT corepressor Mth1. In the presence of glucose, Rgt1 is phosphorylated by the cAMP-activated protein kinase A (PKA) and dissociates from the HXT promoters, resulting in expression of HXT genes. In this study, using Rgt1 chimeras that bind DNA constitutively, we investigate how glucose regulates Rgt1 function. Our results show that the DNA-bound Rgt1 constructs repress expression of the HXT1 gene in conjunction with Ssn6-Tup1 and Mth1, and that …

Measuring Radiation Exposure In Human Blood Using Gene Expression, Krystal Naranjo, Melissa Bentley, Harsha Konery, Matthew Coleman

STAR Program Research Presentations

Mammalian cells are known to express genes that are associated with repairing damaged DNA. The transcript CDKN1A is one of several cell cycle regulator genes expressed in response to cell damage by ionizing radiation (IR). In this study, male and female lymphocytes; previously exposed ex vivo to IR, were used to demonstrate linear gene expression responses that may vary between genders. We used qRT-PCR to generate response curves for CDKN1A. No differences were identified for the endogenous control gene GAPDH. CDKN1A expression demonstrated average fold changes well above three fold for three of the four healthy patient donors at 24 …

Glycosylation Of Cyclooxygenase-2 (Cox-2) Influences The Migratory And Invasive Potential Of Cells, Fahad Algaly, Julia Hand, Mary B. Sevigny

Natural Sciences and Mathematics | Faculty Research Posters

Prostaglandins are bioactive lipids involved in many physiological functions such as maintenance of the cardiovascular, immune, renal, and central nervous systems. They also play a role in certain diseases like arthritis, cancer, and Alzheimer’s. Cyclooxygenase-2 (COX-2) is the enzyme that catalyzes the initial rate-limiting step in the pathway that converts arachidonic acid to prostaglandins. COX-2 exists as two glycoforms with the molecular weights of 72 and 74 kDa, the latter resulting from the addition of a high mannose chain to the Asn580 residue ~50% of the time. The over-expression of COX-2 is believed to be linked to cancer progression and …

A Framework For Organizing Cancer-Related Variations From Existing Databases, Publications And Ngs Data Using A High-Performance Integrated Virtual Environment (Hive), Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Chrichton, Vahan Simonyan, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated …

High-Performance Integrated Virtual Environment (Hive) Tools And Applications For Big Data Analysis, Vahan Simonyan, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion. The platform contains a distributed storage library and a distributed computational powerhouse linked seamlessly. Resources available through the interface include algorithms, tools and applications developed exclusively for the HIVE platform, as well as commonly used external tools adapted to operate within the parallel architecture of the system. HIVE is …

Human Germline And Pan-Cancer Variomes And Their Distinct Functional Profiles, Yang Pan, Konstantinos Karagiannis, Haichen Zhang, Hayley Dingerdissen, Amirhossein Shamsaddini, Quan Wan, Vahan Simonyan, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 …

Strong Dna Deformation Required For Extremely Slow Dna Threading Intercalation By A Binuclear Ruthenium Complex, Ali A. Almaqwashi, Thayaparan Paramanathan, Per Lincoln, Ioulia Rouzina, Fredrik Westerlund, Mark C. Williams

Physics Faculty Publications

DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)₄Ru₂]⁴⁺ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that …

Alpha-Asarone Protects Endothelial Cells From Injury By Angiotensin Ii, Ha-Xia Shi, Jiajun Yang, Tao Yang, Yong-Liang Xue, Jun Liu, Ya-Juan Li, Dan-Dan Zhang, Ji-Wen Zhu, Ka Bian

Biochemistry and Molecular Medicine Faculty Publications

α-Asarone is the major therapeutical constituent of Acorus tatarinowii Schott. In this study, the potential protective effects of α-asarone against endothelial cell injury induced by angiotensin II were investigated in vitro. The EA.hy926 cell line derived from human umbilical vein endothelial cells was pretreated with α-asarone (10, 50, 100 µmol/L) for 1 h, followed by coincubation with Ang II (0.1 µmol/L) for 24 h. Intracellular nitric oxide (NO) and reactive oxygen species (ROS) were detected by fluorescent dyes, and phosphorylation of endothelial nitric oxide synthase (eNOS) at was determined by Western blotting. α-Asarone dose-dependently mitigated the Ang II-induced intracellular NO …

Census-Based Rapid And Accurate Metagenome Taxonomic Profiling, Amirhossein Shamsaddini, Yang Pan, W. Evan Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy Zanne, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Background

Understanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.

Results

Rapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive …

Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of …

Applications Of Epr With An Emphasis On Tau Fibril Structure, Virginia Meyer

Electronic Theses and Dissertations

Substances containing unpaired electrons have been studied by electron paramagnetic resonance (EPR) for nearly 70 years. With continual development and enhancement of EPR techniques, questions have arisen regarding optimum method selection for a given sample based on its properties. In this work, radiation defects, natural lattice defects, solid organic radicals, radicals in solution, and spin-labeled proteins were analyzed using CW, pulse, and rapid scan EPR to compare methods. Studies of solid BDPA, E' in quartz, N_s⁰ in diamond, and a-Si:H, showed that rapid scan could overcome many obstacles presented by other techniques, cementing rapid scan as an effective …

The Effects Of Lipoxin A4 (Lxa4) On Neutrophil Biology In Sepsis, Benedict Wu

Graduate School of Biomedical Sciences Theses and Dissertations

During sepsis, neutrophils are inappropriately activated and have prolonged lifespans, thus becoming dysfunctional. Excessive neutrophil activation can lead to tissue injury while neutrophil dysfunction can lead to decreased free radical production and reduced phagocytosis, preventing the host from clearing preexisting infections. Lipoxin A4 (LXA4) is a specialized pro-resolution mediator which reduces neutrophil migration and expression of proinflammatory mediators. Intact neutrophil functions are critical for the host to efficiently clear invading pathogens. The effects of LXA4 on neutrophil function in sepsis have not been established. Using the cecal ligation and puncture (CLP) model of sepsis, LXA4 administered 1 h after sepsis …

2014 Annual Report Department Of Biological Sciences, Ronald L. Frank, Chen Hou, Yue-Wern Huang, Melanie R. Mormile, Dev Niyogi, Katie Shannon, Julie A. Semon, Matthew S. Thimgan, David J. Westenberg, Terry Wilson

Biological Sciences Faculty Research & Creative Works

No abstract provided.

Investigation Into The Cellular Actions Of Carnosine And C-Peptide, Emma H. Gardner

Theses, Dissertations and Capstones

Carnosine is a dipeptide composed of beta-alanine and histidine found exclusively in long-lived animal tissues. The cellular action of carnosine is still under extensive investigation; however, it has been proposed to have a role as an anti-oxidant and oxygen free radical scavenger, a physiological buffer, a heavy metal chelator, and has been implicated as an anti-aging agent.^2,4 Our lab has been studying the interaction between carnosine and heme by analyzing both the effect carnosine has on the glycation of the heme containing protein cytochrome c and the interaction of carnosine with free hemin. We have observed that the addition …

Competition Between Lone Pair-Π, Halogen Bond, And Hydrogen Bond In Adducts Of Water With Perhalogenated Alkenes C2clnf4-N (N = 0-4), U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A thorough search of the potential energy surface is carried out for heterodimers of water with C2ClnF4−n. Three different types of interactions are observed. Structures dominated by a lone pair–π interaction have the highest binding energies, and are stabilized by charge transfer from O lone pairs of H2O to the Csingle bondC π* antibonding orbital of the alkene. Halogen-bonded O⋯Cl complexes are slightly less strongly bound, followed by OH⋯X hydrogen bonds. The replacements of Cl by F atoms have only small effects upon binding energies. Inclusion of vibrational and entropic effects removes the clear energetic superiority of lp–π binding energies. …

A Td-Dft Study Of The Absorption Spectra Of Mono-Nitrated Fluoranthenes [Abstract], Kefa Karimu Onchoke

Faculty Publications

No abstract provided.

Vibrational Spectroscopy: Disease Diagnostics And Beyond, Hugh Byrne, Kamila Ostrowska, Haq Nawaz, Jennifer Dorney, Aidan Meade, Franck Bonnier, Fiona Lyng

Books/Book Chapters

Summary

This chapter outlines some developments in the applications of vibrational spectroscopy for disease diagnostics and demonstrates how the applications of the spectroscopic techniques can be extended to the analysis and evaluation of disease aetiology and the mechanisms of interaction and the cellular and subcellular responses to, for example chemotherapeutic agents and nanoparticles. The primary emphasis is on Raman spectroscopy, although some examples are based on infrared absorption spectroscopy. The studies presented are chosen to illustrate how a range of multivariate analytical techniques can be employed to maximize the potential benefits of the complex spectral information obtained from tissue or …

Complexation Of N So2 Molecules (N=1,2,3) With Formaldehyde And Thioformaldehyde, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio and density functional theory calculations are used to examine complexes formed between H2CO and H2CS with 1, 2, and 3 molecules of SO2. The nature of the interactions is probed by a variety of means, including electrostatic potentials, natural bond orbital, atoms in molecules, energy decomposition, and electron density redistribution maps. The dimers are relatively strongly bound, with interaction energies exceeding 5 kcal/mol. The structures are cyclic, containing both a O/S⋯S chalcogen bond and a CH⋯O H-bond. Addition of a second SO2 molecule leads to a variety of heterotrimer structures, most of which resemble the original dimer, where …

Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C···O bonds in the most stable heterodimer, bound by some 2 kcal mol(-1), NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O···O chalcogen bond. The NBO picture is that of two transfers in opposite …

Interaction Between Temozolomide And Water: Preferred Binding Sites, O. E. Kasende, A. Matondo, M. Muzomwe, J. T. Muya, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Computational methods are used to predict the most favorable site of temozolomide towards attack by a water molecule. The energetics of the various complexes are presented as well as their geometries, including perturbations of each subunit caused by the presence of the other. Molecular electrostatic potential and Natural Bond Orbital (NBO) data are used to understand the interactions which conclude the terminal amide group is the preferred attack site where water can act as simultaneous proton donor and acceptor. Other potential proton acceptor N atoms within the aromatic ring structure represent weaker binding sites. Some of the less strongly bound …

Substituent Effects In The Noncovalent Bonding Of So2 To Molecules Containing A Carbonyl Group. The Dominating Role Of The Chalcogen Bond, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of …

An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal …

Intrinsic Delocalization During The Decay Of Excitons In Polymeric Solar Cells, Thomas George, W. Chen, D. Jiang, R. Chen, S. Li

Chemistry & Biochemistry Faculty Works

In bulk heterojunction polymer solar cells, external photoexcitation results in localized excitons in the polymer chain. After hot exciton formation and subsequent relaxation, the dipole moment drives the electron to partially transfer to extended orbitals from the original localized ones, leading to self-delocalization. Based on the dynamic fluorescence spectra, the delocalization of excitons is revealed to be an intrinsic property dominated by exciton decay, acting as a bridge for the exciton to diffuse in the polymeric solar cell. The modification of the dipole moment enhances the efficiency of polymer solar cells.

Preliminary Study Of Kleptoplasty In Foraminifera Of South Carolina, Shawnee Lechliter

Bridges: A Journal of Student Research

Recent studies of living foraminifera, microscopic aquatic protists, indicate that some species have the ability to steal photosynthetic plastids from other microorganism and keep them viable through a process called kleptoplasty. Studying the symbiotic relationships within these diverse protists gives insight not only into evolutionary history, but also their importance to the ecosystem. We determined the presence of these kleptoplastic species and identified presence and origin of sequestered plastids based on morphological identification and molecular data from samples collected at Waties Island, South Carolina. We identified two kleptoplastic genera (Elphidium and Haynesina) and two non-kleptoplastic genera (Ammonia and Quinqueloculina) present …

The Role Of Mammalian Cyclin C In Stress Response And Thyroid Disease Progression, Kun Wang

Graduate School of Biomedical Sciences Theses and Dissertations

The cellular response to stress involves changes in gene expression programs as well as the remodeling of subcellular organelles including the mitochondria. Important for this study, the mitochondria undergo extensive fragmentation when the cell is exposed to a variety of stressors. The cyclin C-Cdk8 kinase is a highly conserved transcription factor that associates with the RNA polymerase II holoenzyme. Using cyclin C knockout (CCNC^-/-) mouse embryonic fibroblast (MEF) cells, I revealed that cyclin C is required for the extensive mitochondrial fragmentation following treatment with pro-oxidants or the anti-cancer drug cisplatin. However, Cdk8 is not required for this process …

Field Measurements Of Trace Gases Emitted By Prescribed Fires In Southeastern Us Pine Forests Using An Open-Path Ftir System, S. K. Akagi, I. R. Burling, A. Mendoza, T. J. Johnson, M. Cameron, David W. T. Griffith, C. Paton-Walsh, D. R. Weise, J. Reardon, Robert Yokelson

Chemistry and Biochemistry Faculty Publications

We report trace-gas emission factors from three pine-understory prescribed fires in South Carolina, US measured during the fall of 2011. The fires were more intense than many prescribed burns because the fuels included mature pine stands not subjected to prescribed fire in decades that were lit following an extended drought. Emission factors were measured with a fixed open-path Fourier transform infrared (OP-FTIR) system that was deployed on the fire control lines. We compare these emission factors to those measured with a roving, point sampling, land-based FTIR and an airborne FTIR deployed on the same fires. We also compare to emission …

Aerosol Single Scattering Albedo Dependence On Biomass Combustion Efficiency: Laboratory And Field Studies, Shang Liu, Allison C. Aiken, Caleb Arata, Manvendra K. Dubey, C. Stockwell, Robert Yokelson, Elizabeth A. Stone, Thilina Jayarathne, Allen L. Robinson, Paul J. Demott, Sonia M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Single scattering albedo (ω) of fresh biomass burning (BB) aerosols produced from 92 controlled laboratory combustion experiments of 20 different woods and grasses was analyzed to determine the factors that control the variability in ω. Results show that ω varies strongly with fire-integrated modified combustion efficiency (MCE_FI)—higher MCE_FI results in lower ω values and greater spectral dependence of ω. A parameterization of ω as a function of MCE_FI for fresh BB aerosols is derived from the laboratory data and is evaluated by field observations from two wildfires. The parameterization suggests that MCE_FI explains 60% of …

Validation Of Predicted Mrna Splicing Mutations Using High-Throughput Transcriptome Data., Coby Viner, Stephanie N Dorman, Ben C Shirley, Peter K Rogan

Biochemistry Publications

Interpretation of variants present in complete genomes or exomes reveals numerous sequence changes, only a fraction of which are likely to be pathogenic. Mutations have been traditionally inferred from allele frequencies and inheritance patterns in such data. Variants predicted to alter mRNA splicing can be validated by manual inspection of transcriptome sequencing data, however this approach is intractable for large datasets. These abnormal mRNA splicing patterns are characterized by reads demonstrating either exon skipping, cryptic splice site use, and high levels of intron inclusion, or combinations of these properties. We present, Veridical, an in silico method for the automatic validation …