Open Access. Powered by Scholars. Published by Universities.®
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Diabetes (2)
- Adducts (1)
- Amyloid Inhibition (1)
- Amyloid inhibition (1)
- Charge transfer (1)
-
- Computational chemistry (1)
- Density functional theory (1)
- EGFP (1)
- Enhanced green fluorescent protein (1)
- Excited states (1)
- Islet amyloid polypeptide (1)
- Lewis acids (1)
- Machine learning (1)
- Mononuclear iron catalyst (1)
- Mutagenesis (1)
- Natural Product Therapeutics (1)
- Protein characterization (1)
- Protein purification (1)
- Water oxidation (1)
Articles 1 - 30 of 30
Full-Text Articles in Physical Sciences and Mathematics
Computational Investigation Of Mononuclear Iron Water Oxidation Catalyst Design, Kristal Stevens, Emily Jarvis
Computational Investigation Of Mononuclear Iron Water Oxidation Catalyst Design, Kristal Stevens, Emily Jarvis
Chemistry and Biochemistry Faculty Works
Hydrogen production from non-carbon sources is an essential component of clean and sustainable technology for reducing greenhouse gas emissions from fuels. Water oxidation, which splits water molecules into hydrogen (protons) and molecular oxygen, is a thermodynamically challenging, multistep reaction achieved in photosynthetic organisms via photocatalysis by the Oxygen Evolving Complex (OEC) of Photosystem II. Mononuclear water oxidation catalysts that aim to mimic nature typically rely on heavy, rare metals such as ruthenium and iridium. Replacing these metals with iron is particularly appealing because it is abundant, benign, and inexpensive. We use density functional theory to characterize the catalytic ability of …
Quantum Chemistry–Machine Learning Approach For Predicting Properties Of Lewis Acid–Lewis Base Adducts, Hieu Huynh, Thomas J. Kelly, Linh Vu, Tung Hoang, Phuc An Nguyen, Tu C. Le, Emily Jarvis, Hung Phan
Quantum Chemistry–Machine Learning Approach For Predicting Properties Of Lewis Acid–Lewis Base Adducts, Hieu Huynh, Thomas J. Kelly, Linh Vu, Tung Hoang, Phuc An Nguyen, Tu C. Le, Emily Jarvis, Hung Phan
Chemistry and Biochemistry Faculty Works
Synthetic design allowing predictive control of charge transfer and other optoelectronic properties of Lewis acid adducts remains elusive. This challenge must be addressed through complementary methods combining experimental with computational insights from first principles. Ab initio calculations for optoelectronic properties can be computationally expensive and less straightforward than those sufficient for simple ground-state properties, especially for adducts of large conjugated molecules and Lewis acids. In this contribution, we show that machine learning (ML) can accurately predict density functional theory (DFT)-calculated charge transfer and even properties associated with excited states of adducts from readily obtained molecular descriptors. Seven ML models, built …
Thermostability And Excision Activity Of Polymorphic Forms Of Hogg1, Kathryn Mouzakis
Thermostability And Excision Activity Of Polymorphic Forms Of Hogg1, Kathryn Mouzakis
Chemistry and Biochemistry Faculty Works
Objectives: Reactive oxygen species (ROS) oxidize guanine residues in DNA to form 7,8-dihydro-oxo-2′-deoxyguanosine (8oxoG) lesions in the genome. Human 8-oxoguanine glycosylase-1 (hOGG1) recognizes and excises this highly mutagenic species when it is base-paired opposite a cytosine. We sought to characterize biochemically several hOGG1 variants that have been found in cancer tissues and cell lines, reasoning that if these variants have reduced repair capabilities, they could lead to an increased chance of mutagenesis and carcinogenesis. Results: We have over-expressed and purified the R46Q, A85S, R154H, and S232T hOGG1 variants and have investigated their repair efficiency and thermostability. The hOGG1 variants showed …
Green Chemistry In United States Science Policy, Emily Jarvis
Green Chemistry In United States Science Policy, Emily Jarvis
Chemistry and Biochemistry Faculty Works
Although optimizing each of the Twelve Principles of Green Chemistry is necessary for achieving the greenest possible chemistry in the lab, there are additional creative ways to promote green chemistry not encompassed by these. Communicating to society the importance of green chemistry beyond the laboratory is essential. Of course, doing this effectively presents distinct challenges to those encountered when designing chemical syntheses. Here, I discuss several observations from my time working in federal science policy as an American Association for the Advancement of Science/American Chemical Society Congressional Science Fellow in the United States Senate. I suggest a practical science policy …
The Stress Granule Transcriptome Reveals Principles Of Mrna Accumulation In Stress Granules, Sarah F. Mitchell
The Stress Granule Transcriptome Reveals Principles Of Mrna Accumulation In Stress Granules, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
Stress granules are mRNA-protein assemblies formed from nontranslating mRNAs. Stress granules are important in the stress response and may contribute to some degenerative diseases. Here, we describe the stress granule transcriptome of yeast and mammalian cells through RNA-sequencing (RNA-seq) analysis of purified stress granule cores and single-molecule fluorescence in situ hybridization (smFISH) validation. While essentially every mRNA, and some noncoding RNAs (ncRNAs), can be targeted to stress granules, the targeting efficiency varies from <1% to >95%. mRNA accumulation in stress granules correlates with longer coding and UTR regions and poor translatability. Quantifying the RNA-seq analysis by smFISH reveals that only 10% of …
Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David A. Moffet, Pei-Yu Kao, Evangeline Green, Catalina Pereirab, Shauna Ekimura, Dennis Juarez, Travis Whyte, Taylor Arhar, Bianca Malaspina, Luiza A. Nogaj
Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David A. Moffet, Pei-Yu Kao, Evangeline Green, Catalina Pereirab, Shauna Ekimura, Dennis Juarez, Travis Whyte, Taylor Arhar, Bianca Malaspina, Luiza A. Nogaj
Chemistry and Biochemistry Faculty Works
The aggregation of the 37-amino acid polypeptide islet amyloid polypeptide (IAPP, amylin), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type 2 diabetes. It is believed that inhibiting the aggregation of IAPP may slow down, if not prevent entirely, the progression of this disease. Extracts of thirteen different common fruits were analyzed for their ability to prevent the aggregation of amyloidogenic IAPP. Thioflavin T binding, immuno-detection and circular dichroism assays were performed to test the in vitro inhibitory potential of each extract. Atomic force microscopy was …
Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David Moffet
Inhibition Of Toxic Iapp Amyloid By Extracts Of Common Fruits, David Moffet
Chemistry and Biochemistry Faculty Works
The aggregation of the 37-amino acid polypeptide islet amyloid polypeptide (IAPP, amylin), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of pancreatic β-islet cells in type 2 diabetes. It is believed that inhibiting the aggregation of IAPP may slow down, if not prevent entirely, the progression of this disease. Extracts of 13 different common fruits were analyzed for their ability to prevent the aggregation of amyloidogenic IAPP. Thioflavin T binding, immuno-detection and circular dichroism assays were performed to test the in vitro inhibitory potential of each extract. Atomic force microscopy was …
Modifications On Translation Initiation, Sarah F. Mitchell
Modifications On Translation Initiation, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
Two studies by Meyer et al. and Wang et al. demonstrate a role for m6A modification of mRNA in stimulating translation initiation. These findings add to the growing number of diverse mechanisms for translation initiation in eukaryotes.
Dynamic Motions Of The Hiv-1 Frameshift Site Rna, Kathryn Mouzakis
Dynamic Motions Of The Hiv-1 Frameshift Site Rna, Kathryn Mouzakis
Chemistry and Biochemistry Faculty Works
The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal …
Global Shape Mimicry Of Trna Within A Viral Internal Ribosome Entry Site Mediates Translational Reading Frame Selection, Kathryn Mouzakis
Global Shape Mimicry Of Trna Within A Viral Internal Ribosome Entry Site Mediates Translational Reading Frame Selection, Kathryn Mouzakis
Chemistry and Biochemistry Faculty Works
The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the threehelical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and …
Identification And Characterization Of Functionally Critical, Conserved Motifs In The Internal Repeats And N-Terminal Domain Of Yeast Translation Initiation Factor 4b (Yeif4b), Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
EIF4B has been implicated in attachment of the 43 S preinitiation complex (PIC) to mRNAs and scanning to the start codon. We recently determined that the internal seven repeats (of ∼26 amino acids each) of Saccharomyces cerevisiae eIF4B (yeIF4B) compose the region most critically required to enhance mRNA recruitment by 43 S PICs in vitro and stimulate general translation initiation in yeast. Moreover, although the N-terminal domain (NTD) of yeIF4B contributes to these activities, the RNA recognition motif is dispensable. We have now determined that only two of the seven internal repeats are sufficient for wildtype (WT) yeIF4B function in …
Principles And Properties Of Eukaryotic Mrnps, Sarah F. Mitchell
Principles And Properties Of Eukaryotic Mrnps, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
The proper processing, export, localization, translation, and degradation of mRNAs are necessary for regulation of gene expression. These processes are controlled by mRNA-specific regulatory proteins, noncoding RNAs, and core machineries common to most mRNAs. These factors bind the mRNA in large complexes known as messenger ribonucleoprotein particles (mRNPs). Herein, we review the components of mRNPs, how they assemble and rearrange, and how mRNP composition differentially affects mRNA biogenesis, function, and degradation. We also describe how properties of the mRNP "interactome" lead to emergent principles affecting the control of gene expression.
Structure And Dynamics Of The Hiv-1 Frameshift Element Rna, Kathryn Mouzakis
Structure And Dynamics Of The Hiv-1 Frameshift Element Rna, Kathryn Mouzakis
Chemistry and Biochemistry Faculty Works
The HIV-1 ribosomal frameshift element is highly structured, regulates translation of all virally encoded enzymes, and is a promising therapeutic target. The prior model for this motif contains two helices separated by a three-nucleotide bulge. Modifications to this model were suggested by SHAPE chemical probing of an entire HIV-1 RNA genome. Novel features of the SHAPE-directed model include alternate helical conformations and a larger, more complex structure. These structural elements also support the presence of a secondary frameshift site within the frameshift domain. Here, we use oligonucleotide-directed structure perturbation, probing in the presence of formamide, and in-virion experiments to examine …
Iapp Aggregation And Cellular Toxicity Are Inhibited By 1,2,3,4,6-Penta-O-Galloyl-Β-D-Glucose, Edward Bruno, Catalina Pereira, Karla P. Roman, Marisa Takiguchi, Pei-Yu Kao, Luiza A. Nogaj, David A. Moffet
Iapp Aggregation And Cellular Toxicity Are Inhibited By 1,2,3,4,6-Penta-O-Galloyl-Β-D-Glucose, Edward Bruno, Catalina Pereira, Karla P. Roman, Marisa Takiguchi, Pei-Yu Kao, Luiza A. Nogaj, David A. Moffet
Chemistry and Biochemistry Faculty Works
The polyphenol, 1,2,3,4,6-penta-O-galloyl-β-D-glucose (PGG) has been found to exhibit a host of positive pharmacologic activities, including anti-cancer and anti-diabetic. Little is known about the mode of action of PGG in yielding these positive activities. We show here that PGG is a potent inhibitor of IAPP (islet amyloid polypeptide, amylin) aggregation. Preventing the initial aggregation event of IAPP is one strategy for slowing, and possibly preventing, the toxic effects of IAPP oligomeric intermediates. Equal molar ratios of PGG to IAPP substantially reduced the ability of IAPP to bind thioflavin T. Atomic force microscopy revealed that PGG prevented amyloid-based fiber formation under …
Yeast Eif4b Binds To The Head Of The 40s Ribosomal Subunit And Promotes Mrna Recruitment Through Its N-Terminal And Internal Repeat Domains, Sarah F. Mitchell
Yeast Eif4b Binds To The Head Of The 40s Ribosomal Subunit And Promotes Mrna Recruitment Through Its N-Terminal And Internal Repeat Domains, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
Eukaryotic translation initiation factor (eIF)4B stimulates recruitment of mRNA to the 43S ribosomal pre-initiation complex (PIC). Yeast eIF4B (yeIF4B), shown previously to bind single-stranded (ss) RNA, consists of an N-terminal domain (NTD), predicted to be unstructured in solution; an RNA-recognition motif (RRM); an unusual domain comprised of seven imperfect repeats of 26 amino acids; and a C-terminal domain. Although the mechanism of yeIF4B action has remained obscure, most models have suggested central roles for its RRM and ssRNA-binding activity. We have dissected the functions of yeIF4B's domains and show that the RRM and its ssRNA-binding activity are dispensable in vitro …
Hiv-1 Frameshift Efficiency Is Primarily Determined By The Stability Of Base Pairs Positioned At The Mrna Entrance Channel Of The Ribosome, Kathryn Mouzakis
Hiv-1 Frameshift Efficiency Is Primarily Determined By The Stability Of Base Pairs Positioned At The Mrna Entrance Channel Of The Ribosome, Kathryn Mouzakis
Chemistry and Biochemistry Faculty Works
The human immunodeficiency virus (HIV) requires a programmed -1 ribosomal frameshift for Pol gene expression. The HIV frameshift site consists of a heptanucleotide slippery sequence (UUUUUUA) followed by a spacer region and a downstream RNA stem-loop structure. Here we investigate the role of the RNA structure in promoting the -1 frameshift. The stem-loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. No correlation between overall stability and frameshift efficiency is observed. In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3-4 bp in …
Photochemical Modeling Of Glyoxal At A Rural Site: Observations And Analysis From Bearpex 2007, Nicole Bouvier-Brown
Photochemical Modeling Of Glyoxal At A Rural Site: Observations And Analysis From Bearpex 2007, Nicole Bouvier-Brown
Chemistry and Biochemistry Faculty Works
We present roughly one month of high time-resolution, direct, in situ measurements of gas-phase glyoxal acquired during the BEARPEX 2007 field campaign. The research site, located on a ponderosa pine plantation in the Sierra Nevada mountains, is strongly influenced by biogenic volatile organic compounds (BVOCs); thus this data adds to the few existing measurements of glyoxal in BVOC-dominated areas. The short lifetime of glyoxal of ~1 h, the fact that glyoxal mixing ratios are much higher during high temperature periods, and the results of a photochemical model demonstrate that glyoxal is strongly influenced by BVOC precursors during high temperature periods. …
The Chemistry Of Atmosphere-Forest Exchange (Cafe) Model-Part 2: Application To Bearpex-2007 Observations, Nicole C. Bouvier-Brown
The Chemistry Of Atmosphere-Forest Exchange (Cafe) Model-Part 2: Application To Bearpex-2007 Observations, Nicole C. Bouvier-Brown
Chemistry and Biochemistry Faculty Works
In a companion paper, we introduced the Chemistry of Atmosphere-Forest Exchange (CAFE) model, a vertically-resolved 1-D chemical transport model designed to probe the details of near-surface reactive gas exchange. Here, we apply CAFE to noontime observations from the 2007 Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX-2007). In this work we evaluate the CAFE modeling approach, demonstrate the significance of in-canopy chemistry for forest-atmosphere exchange and identify key shortcomings in the current understanding of intra-canopy processes.
CAFE generally reproduces BEARPEX-2007 observations but requires an enhanced radical recycling mechanism to overcome a factor of 6 underestimate of hydroxyl (OH) concentrations observed …
Ribosome Recycling Step In Yeast Cytoplasmic Protein Synthesis Is Catalyzed By Eef3 And Atp, Sarah F. Mitchell
Ribosome Recycling Step In Yeast Cytoplasmic Protein Synthesis Is Catalyzed By Eef3 And Atp, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
After each round of protein biosynthesis, the posttermination complex (PoTC) consisting of a ribosome, mRNA, and tRNA must be disassembled into its components for a newround of translation. Here, we show that a Saccharomyces cerevisiae model PoTC was disassembled by ATP and eukaryotic elongation factor 3 (eEF3). GTP or ITP functioned with less efficiency and adenosine 5γ′-(β,γ-imido)triphosphate did not function at all. The kcat of eEF3 was 1.12 min-1, which is comparable to that of the in vitro initiation step. The disassembly reaction was inhibited by aminoglycosides and cycloheximide. The subunits formed from the yeast model PoTC remained separated under …
The 5'-7-Methylguanosine Cap On Eukaryotic Mrnas Serves Both To Stimulate Canonical Translation Initiation And To Block An Alternative Pathway, Sarah F. Mitchell
The 5'-7-Methylguanosine Cap On Eukaryotic Mrnas Serves Both To Stimulate Canonical Translation Initiation And To Block An Alternative Pathway, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
Translational control is frequently exerted at the stage of mRNA recruitment to the initiating ribosome. We have reconstituted mRNA recruitment to the 43S preinitiation complex (PIC) using purified S. cerevisiae components. We show that eIF3 and the eIF4 factors not only stabilize binding of mRNA to the PIC, they also dramatically increase the rate of recruitment. Although capped mRNAs require eIF3 and the eIF4 factors for efficient recruitment to the PIC, uncapped mRNAs can be recruited in the presence of eIF3 alone. The cap strongly inhibits this alternative recruitment pathway, imposing a requirement for the eIF4 factors for rapid and …
Observations Of Elevated Formaldehyde Over A Forest Canopy Suggest Missing Sources From Rapid Oxidation Of Arboreal Hydrocarbons, Nicole Bouvier-Brown
Observations Of Elevated Formaldehyde Over A Forest Canopy Suggest Missing Sources From Rapid Oxidation Of Arboreal Hydrocarbons, Nicole Bouvier-Brown
Chemistry and Biochemistry Faculty Works
To better understand the processing of biogenic VOCs (BVOCs) in the pine forests of the US Sierra Nevada, we measured HCHO at Blodgett Research Station using Quantum Cascade Laser Spectroscopy (QCLS) during the Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX) of late summer 2007. Four days of the experiment exhibited particularly copious HCHO, with midday peaks between 15–20 ppbv, while the other days developed delayed maxima between 8–14 ppbv in the early evening. From the expansive photochemical data set, we attempt to explain the observed HCHO concentrations by quantifying the various known photochemical production and loss terms in its …
From Gene Mutation To Protein Characterization, David A. Moffet
From Gene Mutation To Protein Characterization, David A. Moffet
Chemistry and Biochemistry Faculty Works
A seven-week “gene to protein” laboratory sequence is described for an undergraduate biochemistry laboratory course. Student pairs were given the task of introducing a point mutation of their choosing into the well studied protein, enhanced green fluorescent protein (EGFP). After conducting literature searches, each student group chose the mutation they wanted to introduce into EGFP. Students designed their sequence-specific mutagenic primers and constructed their desired mutation. The resulting EGFP mutant proteins were expressed in E. coli, purified and characterized. This laboratory sequence connected the major concepts of molecular biology and biochemistry, while incorporating the thrill of novel discovery in …
In-Situ Ambient Quantification Of Monoterpenes, Sesquiterpenes And Related Oxygenated Compounds During Bearpex 2007: Implications For Gas-And Particle-Phase Chemistry, Nicole Bouvier-Brown
In-Situ Ambient Quantification Of Monoterpenes, Sesquiterpenes And Related Oxygenated Compounds During Bearpex 2007: Implications For Gas-And Particle-Phase Chemistry, Nicole Bouvier-Brown
Chemistry and Biochemistry Faculty Works
We quantified ambient mixing ratios of 9 monoterpenes, 6 sesquiterpenes, methyl chavicol, the oxygenated terpene linalool, and nopinone using an in-situ gas chromatograph with a quadrupole mass spectrometer (GC-MS). These measurements were a part of the 2007 Biosphere Effects on AeRosols and Photochemistry EXperiment (BEARPEX) at Blodgett Forest, a ponderosa pine forest in the Sierra Nevada Mountains of California. To our knowledge, these observations represent the first direct in-situ ambient quantification of the sesquiterpenes α-bergamotene, longifolene, α-farnesene, and β-farnesene. From average diurnal mixing ratio profiles, we show that α-farnesene emissions are dependent mainly on temperature whereas α-bergamotene and β-farnesene emissions …
Methyl Chavicol: Characterization Of Its Biogenic Emission Rate, Abundance, And Oxidation Products In The Atmosphere, Nicole Bouvier-Brown
Methyl Chavicol: Characterization Of Its Biogenic Emission Rate, Abundance, And Oxidation Products In The Atmosphere, Nicole Bouvier-Brown
Chemistry and Biochemistry Faculty Works
We report measurements of ambient atmospheric mixing ratios for methyl chavicol and determine its biogenic emission rate. Methyl chavicol, a biogenic oxygenated aromatic compound, is abundant within and above Blodgett Forest, a ponderosa pine forest in the Sierra Nevada Mountains of California. Methyl chavicol was detected simultaneously by three in-situ instruments – a gas chromatograph with mass spectrometer detector (GC-MS), a proton transfer reaction mass spectrometer (PTR-MS), and a thermal desorption aerosol GC-MS (TAG) – and found to be abundant within and above Blodgett Forest. Methyl chavicol atmospheric mixing ratios are strongly correlated with 2-methyl-3-buten-2-ol (MBO), a light- and temperature-dependent …
Carbonyl Sulfide (Ocs): Large Scale Distributions Over North America During Intex-Na And Relationship To Co2, Lambert Doezema
Carbonyl Sulfide (Ocs): Large Scale Distributions Over North America During Intex-Na And Relationship To Co2, Lambert Doezema
Chemistry and Biochemistry Faculty Works
An extensive set of carbonyl sulfide (OCS) observations were made as part of the NASA Intercontinental Chemical Transport Experiment-North America (INTEX-NA) study, flown from 1 July to 14 August 2004 mostly over the eastern United States and Canada. These data show that summertime OCS mixing ratios at low altitude were dominated by surface drawdown and were highly correlated with CO2. Although local plumes were observed on some low-altitude flight legs, anthropogenic OCS sources were small compared to this sink. These INTEX-NA observations were in marked contrast to the early springtime 2001 Transport and Chemical Evolution over the Pacific experiment, which …
Should I Stay Or Should I Go? Eukaryotic Translation Initiation Factors 1 And 1a Control Start Codon Recognition, Sarah F. Mitchell
Should I Stay Or Should I Go? Eukaryotic Translation Initiation Factors 1 And 1a Control Start Codon Recognition, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
Start codon selection is a key step in translation initiation as it sets the reading frame for decoding. Two eukaryotic initiation factors, eIF1 and eIF1A, are key actors in this process. Recent work has elucidated many details of the mechanisms these factors use to control start site selection. eIF1 prevents the irreversible GTP hydrolysis that commits the ribosome to initiation at a particular codon. eIF1A both promotes and inhibits commitment through the competing influences of its two unstructured termini. Both factors perform their tasks through a variety of interactions with other components of the initiation machinery, in many cases mediated …
Dissociation Of Eif1 From The 40s Ribosomal Subunit Is A Key Step In Start Codon Selection In Vivo, Sarah F. Mitchell
Dissociation Of Eif1 From The 40s Ribosomal Subunit Is A Key Step In Start Codon Selection In Vivo, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
Selection of the AUG start codon is a key step in translation initiation requiring hydrolysis of GTP in the eIF2·GTP·Met-tRNA iMet ternary complex (TC) and subsequent Pi release from eIF2·GDP·Pi. It is thought that eIF1 prevents recognition of non-AUGs by promoting scanning and blocking P i release at non-AUG codons. We show that Sui? mutations in Saccharomyces cerevisiae eIF1, which increase initiation at UUG codons, reduce interaction of eIF1 with 40S subunits in vitro and in vivo, and both defects are diminished in cells by overexpressing the mutant proteins. Remarkably, Sui? mutation ISQLG93-97ASQAA (abbreviated 93-97) accelerates eIF1 dissociation and Pi …
A Molecular Switch Created By In Vitro Recombination Of Nonhomologous Genes, Sarah F. Mitchell
A Molecular Switch Created By In Vitro Recombination Of Nonhomologous Genes, Sarah F. Mitchell
Chemistry and Biochemistry Faculty Works
We have created a molecular switch by the in vitro recombination of nonhomologous genes and subjecting the recombined genes to evolutionary pressure. The gene encoding TEM1 β-lactamase was circularly permuted in a random fashion and subsequently randomly inserted into the gene encoding Escherichia coli maltose binding protein. From this library, a switch (RG13) was identified in which its β-lactam hydrolysis activity was compromised in the absence of maltose but increased 25-fold in the presence of maltose. Upon removal of maltose, RG13's catalytic activity returned to its premaltose level, illustrating that the switching is reversible. The modularity of RG13 was demonstrated …
Extensive Regional Atmospheric Hydrocarbon Pollution In The Southwestern United States, Lambert A. Doezema
Extensive Regional Atmospheric Hydrocarbon Pollution In The Southwestern United States, Lambert A. Doezema
Chemistry and Biochemistry Faculty Works
Light alkane hydrocarbons are present in major quantities in the near-surface atmosphere of Texas, Oklahoma, and Kansas during both autumn and spring seasons. In spring 2002, maximum mixing ratios of ethane [34 parts per 109 by volume (ppbv)], propane (20 ppbv), and n-butane (13 ppbv) were observed in north-central Texas. The elevated alkane mixing ratios are attributed to emissions from the oil and natural gas industry. Measured alkyl nitrate mixing ratios were comparable to urban smog values, indicating active photochemistry in the presence of nitrogen oxides, and therefore with abundant formation of tropospheric ozone. We estimate that 4-6 teragrams of …
Stably Folded De Novo Proteins From A Designed Combinatorial Library, David Moffet
Stably Folded De Novo Proteins From A Designed Combinatorial Library, David Moffet
Chemistry and Biochemistry Faculty Works
Binary patterning of polar and nonpolar amino acids has been used as the key design feature for constructing large combinatorial libraries of de novo proteins. Each position in a binary patterned sequence is designed explicitly to be either polar or nonpolar; however, the precise identities of these amino acids are varied extensively. The combinatorial underpinnings of the "binary code" strategy preclude explicit design of particular side chains at specified positions. Therefore, packing interactions cannot be specified a priori. To assess whether the binary code strategy can nonetheless produce well-folded de novo proteins, we constructed a second-generation library based upon a …