Biochemistry, Biophysics, and Structural Biology Commons^™

Improving Predicted Protein Loop Structure Ranking Using A Pareto-Optimality Consensus Method, Yaohang Li, Ionel Rata, See-Wing Chiu, Erik Jakobsson

Computer Science Faculty Publications

Background

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction.

Results

We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy …

Protein Folding, Aggregation And Unfolding In Monte Carlo Simulations, Sandipan Mohanty, Anders Irbäck, Simon Mitternacht, Giorgio Favrin, U. H.E. Hansmann

Michigan Tech Publications, Part 1

An implicit water all-atom model is used to study folding, aggregation and mechanical unfolding of small proteins. Physically reasonable results obtained for a variety of applications indicate healthy global properties of the interaction potential.

Studies On Inositol Polyphosphates And Their Role In Programmed Cell Death, Rakhee Agarwal

Theses and Dissertations

The agents that induce apoptosis in cancerous cells are considered as potential candidates for cancer therapy. Inositol polyphosphates, the naturally occurring compounds, regulate diverse cellular processes including induction of apoptosis in certain cancerous cells and hence can be considered as potential anticancer agents. The aim of this research dissertation was to establish firmly the role of inositol polyphosphates in induction of apoptosis by examining their mechanism of action. The overall hypothesis was that alterations in intracellular levels of inositol polyphosphates would bring about apoptotic changes. The hypothesis was tested by changing endogenous inositol polyphosphates by way of chemical treatments known …

The Danger Signal Adenosine Induces Persistence Of Chlamydial Infection Through Stimulation Of A2b Receptors, Matthew A. Pettengill, Verissa W. Lam, David M. Ojcius

All Dugoni School of Dentistry Faculty Articles

Infections with intracellular bacteria such as chlamydiae affect the majority of the world population. Infected tissue inflammation and granuloma formation help contain the short-term expansion of the invading pathogen, leading also to local tissue damage and hypoxia. However, the effects of key aspects of damaged inflamed tissues and hypoxia on continued infection with intracellular bacteria remain unknown. We find that development of Chlamydia trachomatis is reversibly retarded by prolonged exposure of infected cells to extracellular adenosine, a hallmark of hypoxia and advanced inflammation. In epithelial cells, this effect was mediated by the A2b adenosine receptor, unique in the adenosine receptor …

Progress Toward The Total Synthesis Of Lyconadin A, Yu Zhang

Theses and Dissertations

Lyconadin A is a pentacyclic Lycopodium alkaloid isolated from the club moss Lycopodium complanatum with antitumor properties. We have developed a novel 7-exo/6-exo acyl radical cascade cyclization as a method of making the bicyclo[5.4.0]undecane ring system of lyconadin A. The model products are trans-fused ring systems, while a cis-fused ring system is needed in lyconadin A. We have discovered a method to convert the trans-fused model cascade cyclization product into the desired cis isomer. Based on Donohoe's pyridone synthesis, we developed a method for the construction of 5-alkyl and 3,5-dialkyl-6-carbomethoxy-2-pyridones, the former of which …

Overexpression And Partial Purification Of Serine Hydroxymethyltransferase, Kimberly Rose Stevens

Chemistry and Biochemistry

No abstract provided.

Distribution And Diversity Of Archaeal And Bacterial Ammonia Oxidizers In Salt Marsh Sediments, Nicole S. Moin, Katelyn A. Nelson, Alexander Bush, Anne E. Bernhard

Biology Faculty Publications

Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP were equally distributed between the water column/sediment and soil/sediment clades, while AOA amoA sequences at SAS were primarily affiliated with the …

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charged-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.

Cloning Of "Animal Cryptochrome" Cdna From The Model Organism Chlamydomonas Reinhardtii For Functional Analysis Of Its Protein Product, Shobha Lavanya Silparasetty

Masters Theses & Specialist Projects

reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases …

Computational Prediction Of The Agregated Structure Of Denatured Lysozyme, Pongsathorn Chotikasemsri

Masters Theses & Specialist Projects

Mis-folded proteins and their associated aggregates are a contributing factor in some human diseases. In this study we used the protein lysozyme as a model to define aggregation structures under denaturing conditions. Sasahara et al. (2007), Frare et al. (2009, 2006), and Rubin et al. (2008) observed conditions where heat denatured lysozyme formed fibril structures that were observed to be 8-17 nanometers in diameter under the electron microscope. Even though the crystal structure of lysozyme is known, the denatured form of this protein is still unknown. Therefore, we used Rosetta++ protein folding and blind docking software to create in silico …

Low-Dose Of Sodium Arsenite Causes Delayed Differentiation In C2c12 Mouse Myoblast Cells Through The Repression Of The Transcription Factor Myogenin, Amanda Steffens

All Theses

A number of epidemiological studies have correlated arsenic exposurwith cancer, skin diseases, cardiovascular diseases, and adverse developmental outcomes such as stillbirths, spontaneous abortions, neonatal mortality, low birth weight, and delays in the use of musculature. The current study used C2C12 mouse myoblast cells to examine whether low concentrations of arsenic could alter their differentiation into myotubes, which would indicate that arsenic has the ability to act as a developmental toxicant. Myoblast cells were exposed to 20nM sodium arsenite and allowed to differentiate into myotubes and expression of the muscle-specific transcription factor myogenin, along with the expression of myosin light chain …

Pot1 Proteins In Green Algae And Land Plants: Dna-Binding Properties And Evidence Of Co-Evolution With Telomeric Dna, Eugene V. Shakirov, Xiangyu Song, Jessica A. Joseph, Dorothy E. Shippen

Biological Sciences Faculty Research

Telomeric DNA terminates with a single-stranded 3′ G-overhang that in vertebrates and fission yeast is bound by POT1 (Protection Of Telomeres). However, no in vitro telomeric DNA binding is associated with Arabidopsis POT1 paralogs. To further investigate POT1–DNA interaction in plants, we cloned POT1 genes from 11 plant species representing major branches of plant kingdom. Telomeric DNA binding was associated with POT1 proteins from the green alga Ostreococcus lucimarinus and two flowering plants, maize and Asparagus. Site-directed mutagenesis revealed that several residues critical for telomeric DNA recognition in vertebrates are functionally conserved in plant POT1 proteins. However, the plant proteins …

Seeing The Future: Biology Research Allows Undergraduates New Insight Into Their Own Futures, Merideth Krevosky, Jeffery Bowen

Bridgewater Review

No abstract provided.

Inactivation Of The Fliy Gene Encoding A Flagellar Motor Switch Protein Attenuates Mobility And Virulence Of Leptospira Interrogans Strain Lai, Sumei Liao, Ai-Hua Sun, David M. Ojcius, Senlin Wu, Jinfang Zhao, Jie Yan

All Dugoni School of Dentistry Faculty Articles

Background: Pathogenic Leptospira species cause leptospirosis, a zoonotic disease of global importance. The spirochete displays active rotative mobility which may contribute to invasion and diffusion of the pathogen in hosts. FliY is a flagellar motor switch protein that controls flagellar motor direction in other microbes, but its role in Leptospira, and paricularly in pathogenicity remains unknown.

Results: A suicide plasmid for the fliY gene of Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai strain Lai that was disrupted by inserting the ampicillin resistance gene (bla) was constructed, and the inactivation of fliY gene in a mutant (fliY-) was confirmed by PCR and …

The Physiological And Biochemical Understanding Of 5’-Amp Induced Deep Hypometabolism, William G. O'Brien

Dissertations and Theses (Open Access)

Our laboratory’s ability to induce deep hypometabolism (DH) via an injection of adenosine monophosphate (5’-AMP) followed by placement in an ambient temperature (Ta) around 15oC currently can last about 3-9 hours. While we have insight into how 5’-AMP induced hypometabolism is initiated, it remains unclear how arousal from hypometabolism is controlled. Other laboratory members have been unable to prolong this process safely and effectively with previous attempts of re-injecting a dose of 5’-AMP upon arousal or by decreasing the Ta. While these methods worked in suppressing arousal, the mortality rate is also increased. To gather a better understanding of the …

Cloning And Expression Of Porcine Dicer And Argonaute-2, Heather Stowe

All Theses

In vitro-produced embryos exhibit aberrations in development, but the reasons for these developmental problems are unknown. Recently, a class of small non-coding RNA called microRNA (miRNA) has been described and reported to have roles in normal mammalian embryonic development. These miRNAs are encoded in the genome, transcribed by RNA pol II and processed into fragments approximately 22 nt in length by ribonuclease enzymes, the final one being a protein called Dicer. miRNA work through the RNA-induced silencing complex (RISC), of which the argonaute gene family are key proteins. Argonaute-2 (Ago2) has been identified as the only member possessing endonuclease activity, …

Characterization And Functional Regulation Of Bioactive Peptides In Avian Macrophages And Heterophils, Lakshmi Kannan

Graduate Theses and Dissertations

Oligopeptides and low molecular weight polypeptides play central roles as effectors and signal transducers acting as hormones, neurotransmitters, growth factors, toxins, and antimicrobial factors that are important for the survival of the organism. Owing to the ubiquitous involvement of peptides in many key regulatory processes, we have been interested to identify native peptides in different cells and tissues and understand their functions. To conduct our studies, we used avian macrophages and heterophils as models of specialized cells which constitute central components of innate immunity. These studies involved (a) qualitative identification and characterization of the peptides associated with high intensity mass …

Applications Of Variable Number Tandem Repeat Genotyping In The Validation Of An Animal Medical Model And Gene Flow Studies In Threatened Populations Of Reptiles, Candace D. Smith

Graduate Theses and Dissertations

We used variable number tandem repeats (VNTR) to validate the chicken as a human medical model for Pulmonary Arterial Hypertension. We identified seven regions on four chromosomes and interrogated for VNTR markers that significantly associate with Pulmonary Hypertension Syndrome/ascites. In those regions, we identified 7 candidate genes; AGTR1, ACE, p38MAPK, SST, 5HT2B, NET1, and CALM3 for further analysis as significantly contributing QTL for ascites/PHS. We also used variable number tandem repeats to measure gene flow and gather evidence for multiple paternity in a population of Timber rattlesnakes, Crotalus horridus. We were able to verify 1 VNTR that can be used …

The Role Of Multiple Ccaat-Binding Factors In Candida Albicans Gene Expression, Lashall Lynn Bates

Graduate Theses and Dissertations

The CCAAT-binding factor is a heterooligomeric transcription factor that is evolutionarily conserved in eukaryotes. In yeast, the DNA-binding component that interacts with the CCAAT consensus sequence in promoters consists of the subunits termed Hap2p, Hap3p and Hap5p. In yeast and fungi, a fourth subunit, Hap4p, is required for regulating gene expression. The goal of this research is to understand the function of the Candida albicans CCAAT-binding factor and how it relates to virulence and pathogenicity. C. albicans is a human opportunistic pathogen responsible for a variety of mucosal and systemic infections that result in significant morbidity and mortality, particularly in …

Subcutaneous Administration Of Tc007 Reduces Disease Severity In An Animal Model Of Sma, Virginia B. Mattis, Marina Y. Fosso, Cheng-Wei Tom Chang, Christian L. Lorson

Chemistry and Biochemistry Faculty Publications

Background Spinal Muscular Atrophy (SMA) is the leading genetic cause of infantile death. It is caused by the loss of functional Survival Motor Neuron 1 (SMN1). There is a nearly identical copy gene, SMN2, but it is unable to rescue from disease due to an alternative splicing event that excises a necessary exon (exon 7) from the majority of SMN2-derived transcripts. While SMNΔ7 protein has severely reduced functionality, the exon 7 sequences may not be specifically required for all activities. Therefore, aminoglycoside antibiotics previously shown to suppress stop codon recognition and promote translation read-through have been examined to increase the …

Ceramide Kinase Regulates Phospholipase C And Phosphatidylinositol 4, 5, Bisphosphate In Phototransduction, Ujjaini Dasgupta, Takeshi Bamba, Salvatore Chiantia, Pusha Karim, Ahmad N. Abou Tayoun

Dartmouth Scholarship

Phosphoinositide-specific phospholipase C (PLC) is a central effector for many biological responses regulated by G-protein-coupled receptors including Drosophila phototransduction where light sensitive channels are activated downstream of NORPA, a PLCbeta homolog. Here we show that the sphingolipid biosynthetic enzyme, ceramide kinase, is a novel regulator of PLC signaling and photoreceptor homeostasis. A mutation in ceramide kinase specifically leads to proteolysis of NORPA, consequent loss of PLC activity, and failure in light signal transduction. The mutant photoreceptors also undergo activity-dependent degeneration. Furthermore, we show that a significant increase in ceramide, resulting from lack of ceramide kinase, perturbs the membrane microenvironment of …

Quantifying And Resolving Multiple Vector Transformants In S. Cerevisiae Plasmid Libraries, Thomas C. Scanlon, Elizabeth C. Gray, Karl E. Griswold

Dartmouth Scholarship

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the …

Synthesis And Evaluation Of N6,5'-Bis-Ureido-5'-Amino-5'-Deoxyadenosine Derivatives: Novel Nucleosides With Antiproliferative And Protein Kinase Binding Activities, Marcelio Oliveira

Theses and Dissertations

A new series of N6,5'-bis-ureido-5'-amino-5'-deoxyadenosine derivatives was prepared and evaluated for anticancer activities using the NCI 60 panel of human cancers. Certain of the derivatives showed promising activities (low micromolar GI50's) against several of the representative cancers. These included cell lines from the following general cell types in the NCI 60: Leukemia, Breast, Central Nervous System, Non-Small Cell Lung, Ovarian, Prostate, Renal, and Colon cancers. Select compounds were also screened for their affinities for protein kinases. The synthesis of the compounds was straightforward and involved N6 acylation with arylisocyanates, preceded by activation and nucleophilic substitution of the 5'-position to give …

Expression And Function Of Hypoxia Inducible Factor-1 Alpha In Human Melanoma Under Non-Hypoxic Conditions, Caroline N. Mills, Sandeep S. Joshi, Richard M. Niles

Biochemistry and Microbiology

Background

Hypoxia inducible factor-1 alpha (HIF-1α) protein is rapidly degraded under normoxic conditions. When oxygen tensions fall HIF-1α protein stabilizes and transactivates genes involved in adaptation to hypoxic conditions. We have examined the normoxic expression of HIF-1α RNA and protein in normal human melanocytes and a series of human melanoma cell lines isolated from radial growth phase (RGP), vertical growth phase (VGP) and metastatic (MET) melanomas.

Results

HIF-1α mRNA and protein was increased in RGP vs melanocytes, VGP vs RGP and MET vs VGP melanoma cell lines. We also detected expression of a HIF-1α mRNA splice variant that lacks part …

Identification Of Functional Lsrb-Like Autoinducer-2 Receptors, C. S. Pereira, Anna Katherine De Regt , '09, P. H. Brito, Stephen T. Miller, K. B. Xavier

Chemistry & Biochemistry Faculty Works

Although a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (AI-2) to regulate multiple behaviors, the molecular mechanisms of AI-2 recognition and signal transduction remain poorly understood. To date, two types of AI-2 receptors have been identified: LuxP, present in Vibrio spp., and LsrB, first identified in Salmonella enterica serovar Typhimurium. In S. Typhimurium, LsrB is the ligand binding protein of a transport system that enables the internalization of AI-2. Here, using both sequence analysis and structure prediction, we establish a set of criteria for identifying functional AI-2 receptors. We test our predictions experimentally, …

Trnas: Cellular Barcodes For Amino Acids, Ranat Banerjee, Shawn Chen, Kiley Dare, Marla Gilreath, Mette Praetorius-Ibba, Medha Raina, Noah M. Reynolds, Theresa E. Rogers, Hervé Roy, Srujana S. Yadavalli, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl‐tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of …

Yeast Ste23p Shares Functional Similarities With Mammalian Insulin-Degrading Enzymes, Benjamin Alper, Jarrad W. Rowse, Walter K. Schmidt

Chemistry & Physics Faculty Publications

The S. cerevisiae genome encodes two M16A enzymes: Axl1p and Ste23p. Of the two, Ste23p shares significantly higher sequence identity with M16A enzymes from other species, including mammalian insulin-degrading enzymes (IDEs). In this study, recombinant Ste23p and R. norvegicus IDE (RnIDE) were isolated from E. coli, and their enzymatic properties compared. Ste23p was found to cleave established RnIDE substrates including the amyloid-β peptide (Aβ 1-40) and insulin B chain. A novel internally quenched fluorogenic substrate (Abz-SEKKDNYIIKGVnitroY-OH) based on the polypeptide sequence of the yeast P2 a-factor mating propheromone was determined to be a suitable substrate for …

Methods And Compositions For Vaccnation Of Animals With Prrsv Antigens With Improved Immunogenicity, Israrul H. Ansari, Fernando A. Osorio, Asit K. Pattnaik,

School of Veterinary and Biomedical Sciences: Faculty Publications

Pigs challenged with hypoglycosylated variants of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) major surface protein GP5 exhibited increased production of PRRSV-neutralizing antibodies relative to the levels of neutralizing antibodies produced by pigs immunized with wild type (wt) or glycosylated GP5. This invention provides for methods of obtaining improved immune responses in pigs to PRRSV, compositions useful for obtaining the improved immune responses as well as isolated polynucleotides that encode hypoglycosylated variants of PRRSV major surface protein GP5.

Integral Membrane Proteins Brr6 And Apq12 Link Assembly Of The Nuclear Pore Complex To Lipid Homeostasis In The Endoplasmic Reticulum, Christine A. Hodge, Vineet Choudhary, Michael J. Wolyniak, John J. Scarcelli, Roger Schneiter, Charles N. Cole

Dartmouth Scholarship

Cells of Saccharomyces cerevisiae lacking Apq12, a nuclear envelope (NE)-endoplasmic reticulum (ER) integral membrane protein, are defective in assembly of nuclear pore complexes (NPCs), possibly because of defects in regulating membrane fluidity. We identified BRR6, which encodes an essential integral membrane protein of the NE-ER, as a dosage suppressor of apq12 Delta. Cells carrying the temperature-sensitive brr6-1 allele have been shown to have defects in nucleoporin localization, mRNA metabolism and nuclear transport. Electron microscopy revealed that brr6-1 cells have gross NE abnormalities and proliferation of the ER. brr6-1 cells were hypersensitive to compounds that affect membrane biophysical properties and to …

The Leishmania Donovani Lipophosphoglycan Excludes The Vesicular Proton-Atpase From Phagosomes By Impairing The Recruitment Of Synaptotagmin V, Adrien F. Vinet, Mitsunori Fukuda, Salvatore J. Turco, Albert Descoteaux

Molecular and Cellular Biochemistry Faculty Publications

We recently showed that the exocytosis regulator Synaptotagmin (Syt) V is recruited to the nascent phagosome and remains associated throughout the maturation process. In this study, we investigated the possibility that Syt V plays a role in regulating interactions between the phagosome and the endocytic organelles. Silencing of Syt V by RNA interference revealed that Syt V contributes to phagolysosome biogenesis by regulating the acquisition of cathepsin D and the vesicular proton-ATPase. In contrast, recruitment of cathepsin B, the early endosomal marker EEA1 and the lysosomal marker LAMP1 to phagosomes was normal in the absence of Syt V. As Leishmania …