Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Microbiology (9)
- Molecular Biology (9)
- Physical Sciences and Mathematics (6)
- Chemistry (5)
- Genetics and Genomics (4)
-
- Biophysics (3)
- Biotechnology (3)
- Cell Biology (3)
- Cell and Developmental Biology (3)
- Genetics (3)
- Medicine and Health Sciences (3)
- Biology (2)
- Biomedical Engineering and Bioengineering (2)
- Cellular and Molecular Physiology (2)
- Engineering (2)
- Microbial Physiology (2)
- Molecular Genetics (2)
- Other Biochemistry, Biophysics, and Structural Biology (2)
- Pathogenic Microbiology (2)
- Physiology (2)
- Plant Sciences (2)
- Amino Acids, Peptides, and Proteins (1)
- Analytical, Diagnostic and Therapeutic Techniques and Equipment (1)
- Bacteriology (1)
- Biochemical and Biomolecular Engineering (1)
- Biological Engineering (1)
- Cell Anatomy (1)
- Institution
-
- Western University (6)
- Dartmouth College (5)
- Old Dominion University (3)
- University at Albany, State University of New York (3)
- Bemidji State University (2)
-
- Portland State University (2)
- Thomas Jefferson University (2)
- Binghamton University (1)
- Chapman University (1)
- Dominican University of California (1)
- Northern Illinois University (1)
- Universitas Indonesia (1)
- University of Kentucky (1)
- University of Montana (1)
- University of Nebraska - Lincoln (1)
- University of South Carolina (1)
- Valparaiso University (1)
- Virginia Commonwealth University (1)
- Washington University in St. Louis (1)
- Wayne State University (1)
- Publication Year
- Publication
-
- Biochemistry Publications (6)
- Dartmouth Scholarship (4)
- Legacy Theses & Dissertations (2009 - 2024) (3)
- Department of Biochemistry and Molecular Biology Faculty Papers (2)
- Honors Capstones (2)
-
- Theses and Dissertations (2)
- Biological Sciences Faculty Publications (1)
- Biology Faculty Research (1)
- Biology, Chemistry, and Environmental Sciences Faculty Articles and Research (1)
- Chemistry & Biochemistry Theses & Dissertations (1)
- Chemistry Faculty Publications (1)
- Chemistry Faculty Publications and Presentations (1)
- Chemistry Honors Papers (1)
- Dartmouth College Ph.D Dissertations (1)
- Department of Biochemistry: Faculty Publications (1)
- Graduate Research Theses & Dissertations (1)
- Makara Journal of Science (1)
- Medical Student Research Symposium (1)
- Natural Sciences and Mathematics | Faculty Scholarship (1)
- OES Theses and Dissertations (1)
- Undergraduate Honors Theses (1)
- Undergraduate Theses, Professional Papers, and Capstone Artifacts (1)
- University Honors Theses (1)
- Publication Type
Articles 1 - 30 of 36
Full-Text Articles in Biochemistry
Analysis Of Bacterial Virulence And Resistance In A Model Of Recurrent Uti, Rachel L. Proper
Analysis Of Bacterial Virulence And Resistance In A Model Of Recurrent Uti, Rachel L. Proper
Undergraduate Honors Theses
Urinary tract infection (UTI) is a major women’s health issue, affecting approximately 40% of women during their lifetime. Formation of a biofilm by UTI-causing bacteria poses a major challenge in treatment, as the protection provided by the biofilm hinders both host defenses and antibiotic treatment. Failure to eradicate these infections causes them to become recurrent (rUTI). Previous research indicates that rUTI may be comorbid with a mutation in the SERPINE1 gene, which causes fibrin to accumulate within the body. Literature also indicates that fibrin provides a better scaffold for bacterial attachment and, subsequently, biofilm formation. In this work it was …
Mechanistic Insights Into E. Coli Recovery From Growth Arrest, Ahmed H. Hassan, Yuko Nakano, Howard Gamper, Isao Masuda, Ludmila Vesela, Matyas Pinkas, Sathya Narayanan Nagarajan, Jonathan Dworkin, Gregor Blaha, Ya-Ming Hou, Gabriel Demo
Mechanistic Insights Into E. Coli Recovery From Growth Arrest, Ahmed H. Hassan, Yuko Nakano, Howard Gamper, Isao Masuda, Ludmila Vesela, Matyas Pinkas, Sathya Narayanan Nagarajan, Jonathan Dworkin, Gregor Blaha, Ya-Ming Hou, Gabriel Demo
Department of Biochemistry and Molecular Biology Faculty Papers
Bacteria survive hostile conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an E. coli ΔrimM strain, which exhibits a prolonged growth arrest, as a model to investigate how bacteria recover from this state and restore protein synthesis. RimM is a conserved ribosome maturation factor for the 3'-major (head) domain of the 16S rRNA within the bacterial 30S subunit. The loss of RimM causes a longer delay in recovery than other 30S maturation factors, including RbfA. Cryo-EM analysis of ΔrimM ribosomes suggests a delayed recruitment of ribosomal proteins to the 30S head …
Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy
Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy
Makara Journal of Science
Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …
Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma
Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma
Dartmouth College Ph.D Dissertations
Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …
Viral Genome Delivery Across Bacterial Cell Surfaces, Stephano M. Iglesias, Fenglin Li, Federica Briani, Gino Cingolani
Viral Genome Delivery Across Bacterial Cell Surfaces, Stephano M. Iglesias, Fenglin Li, Federica Briani, Gino Cingolani
Department of Biochemistry and Molecular Biology Faculty Papers
In 1952, Hershey and Chase used bacteriophage T2 genome delivery inside Escherichia coli to demonstrate that DNA, not protein, is the genetic material. Over 70 years later, our understanding of bacteriophage structure has grown dramatically, mainly thanks to the cryogenic electron microscopy revolution. In stark contrast, phage genome delivery in prokaryotes remains poorly understood, mainly due to the inherent challenge of studying such a transient and complex process. Here, we review the current literature on viral genome delivery across bacterial cell surfaces. We focus on icosahedral bacterial viruses that we arbitrarily sort into three groups based on the presence and …
Assessing Lipid Composition Of Cell Membrane In Escherichia Coli Under Aerobic And Anaerobic Conditions, Isabelle Johnson
Assessing Lipid Composition Of Cell Membrane In Escherichia Coli Under Aerobic And Anaerobic Conditions, Isabelle Johnson
Undergraduate Theses, Professional Papers, and Capstone Artifacts
Escherichia coli is a highly studied model organism that is tightly tied to the mammalian gastrointestinal system. This microorganism has the capability to be a beneficial gut microbe or a life-threatening pathogen. In this study, the lipid membrane of Escherichia coli was investigated using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) to observe the change in its composition in aerobic and anaerobic conditions. Evidence of desaturation was discovered in the spectra, though more investigation is needed to understand the metabolic processes and drives that result in this change. Elucidation of these pathways in the future could result in …
Expression And Purification Of E. Coli Yoaa, A Putative Helicase, Mark Gregory, Vincent Sutera Mr., Susan Lovett Dr.
Expression And Purification Of E. Coli Yoaa, A Putative Helicase, Mark Gregory, Vincent Sutera Mr., Susan Lovett Dr.
Medical Student Research Symposium
All cells must maintain their genomic integrity to survive, which they achieve through several repair mechanisms that necessitate unwinding the damaged DNA by helicases. In Escherichia coli (E. coli), YoaA has been genetically shown to be involved in DNA repair and shares conserved sequences with helicase DinG. The goal of our study was to purify YoaA for further biochemical characterization. For expression, YoaA was fused to a His tag and overexpressed in MG1655 E.coli under the lacZ or T7 promoters for 2 hours, 4 hours, or overnight at 24oC, 30oC or 37oC. For purification, crude lysate was applied to a …
Characterization Of Potential Anti-Infective Agents By Targeting Burkholderia Pseudomallei And Escherichia Coli Ispf, Dakota Lane Grote
Characterization Of Potential Anti-Infective Agents By Targeting Burkholderia Pseudomallei And Escherichia Coli Ispf, Dakota Lane Grote
Graduate Research Theses & Dissertations
With the likelihood of contracting an antibiotic resistant infection increasing, the need for novel anti-infective agents is critical. The development of novel anti-infective agents benefits from the identification of new target pathways necessary for the survival of the pathogen. One such target is the methylerythritol phosphate (MEP) pathway, responsible for the synthesis of the isoprenoid precursors isopentyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) in bacteria and other pathogenic organisms. The MEP pathway is an attractive target because it is specific to a wide range of pathogenic organisms, while humans have a separate pathway, the mevalonate (MVA) pathway, for the biosynthesis …
The Role Of Redox Chemistry Of Disulfide Bonds In Cysteine Residues Of Membrane Proteins By Cuprous And Cupric Ions In Cell Death Of E. Coli, Morgan R. Stewart
The Role Of Redox Chemistry Of Disulfide Bonds In Cysteine Residues Of Membrane Proteins By Cuprous And Cupric Ions In Cell Death Of E. Coli, Morgan R. Stewart
University Honors Theses
The antimicrobial properties of copper have been thoroughly researched, but is still unclear what the actual mechanism of cell death is. This study explores the theory that copper ions and other copper sources act as an antibiotic for E. coli by cleaving the disulfide bonds of membrane proteins through redox chemistry, disrupting the cell membrane and causing cell death. The focus of this study is Cu(I) and Cu(II) interactions with the thiol containing amino acid, cysteine, and how these interactions may be responsible for copper’s toxicity. Cuprous ions have been found to be more toxic to E.coli than cupric …
Post-Translational Modifications And Functional Studies Of Dksa In Escherichia Coli, Andrew Charles Isidoridy
Post-Translational Modifications And Functional Studies Of Dksa In Escherichia Coli, Andrew Charles Isidoridy
Legacy Theses & Dissertations (2009 - 2024)
DksA is a bacterial gene regulator that functions synergistically with the stress alarmone ppGpp to mediate the stringent response. DksA also functions independently of ppGpp to regulate transcription of a number of genes. DksA function is dependent on its binding affinity to RNA polymerase and requires specific interactions between RNAP and catalytic amino acids located on the coiled coil tip, D74 and A76. While much of the previous work on DksA has focused on understanding the mechanisms of action and the numerous gene targets for transcriptional regulation, little is known about the mechanisms by which DksA expression and function may …
Transcriptional Regulation Of Dksa In E. Coli, Daniel Thomas Woods
Transcriptional Regulation Of Dksa In E. Coli, Daniel Thomas Woods
Legacy Theses & Dissertations (2009 - 2024)
DksA is a global transcription factor that binds RNAP directly to regulate the expression of many genes and operons, including ribosomal RNA, in a ppGpp-dependent or ppGpp–independent manner. It is also involved in facilitating the process of DNA replication by removing stalled transcription elongation complexes that could block the progress of the replication fork. In addition, DksA is important for colonization, establishment of biofilms, and pathogenesis. In order to sustain these various functions, an adequate level of cellular DksA is required. This work tested the hypothesis that the E. coli dksA is substantially regulated at the level of transcription. Using …
Defining And Harnessing Nature's Selection Of Geranylation In Rna Modification, Phensinee Haruehanroengra
Defining And Harnessing Nature's Selection Of Geranylation In Rna Modification, Phensinee Haruehanroengra
Legacy Theses & Dissertations (2009 - 2024)
Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. Geranylated-2-thiouridine is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, namely E. coli, E. aerogenes, P. aeruginosa and S. typhimurium by Liu group. It has been found as a post-transcription modification on the wobble position of anticodon of tRNAs specific for glutamic acid, glutamine and lysine. Geranylated-tRNA was shown to correct the frameshifting during the translation of E. coli. However, the reason of the existing of the modification is still largely unclear. To understand why nature incorporates such a hydrophobic group in …
Data On Spectrum-Based Fluorescence Resonance Energy Transfer Measurement Of E. Coli Multidrug Transporter Acrb, Yuguang Cai, Thomas E. Wilkop, Yinan Wei
Data On Spectrum-Based Fluorescence Resonance Energy Transfer Measurement Of E. Coli Multidrug Transporter Acrb, Yuguang Cai, Thomas E. Wilkop, Yinan Wei
Chemistry Faculty Publications
This paper presented the dataset of correction parameters used in the determination of the energy transfer efficiencies from the spectrum-based fluorescence resonance energy transfer (FRET) measurement in a trimeric membrane protein AcrB. The cyan fluorescent protein (CFP) and yellow fluorescent protein (YPet) were used as the donor and acceptor, respectively. Two AcrB fusion proteins were constructed, AcrB-CFP and AcrB-YPet. The proteins were co-expressed in Escherichia coli cells, and energy transfer efficiency were determined in live cells. To obtain reliable energy transfer data, a complete set of correction parameters need to be first determined to accommodate for factors such as background …
Codon Usage Revisited: Lack Of Correlation Between Codon Usage And The Number Of Trna Genes In Enterobacteria, Joaquín Rojas, Gabriel Castillo, Lorenzo Eugenio Leiva, Sara Elgamal, Omar Orellana, Michael Ibba, Assaf Katz
Codon Usage Revisited: Lack Of Correlation Between Codon Usage And The Number Of Trna Genes In Enterobacteria, Joaquín Rojas, Gabriel Castillo, Lorenzo Eugenio Leiva, Sara Elgamal, Omar Orellana, Michael Ibba, Assaf Katz
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
It is widely believed that if a high number of genes are found for any tRNA in a rapidly replicating bacteria, then the cytoplasmic levels of that tRNA will be high and an open reading frame containing a higher frequency of the complementary codon will be translated faster. This idea is based on correlations between the number of tRNA genes, tRNA concentration and the frequency of codon usage observed in a limited number of strains as well as from the fact that artificially changing the number of tRNA genes alters translation efficiency and consequently the amount of properly folded protein …
Study Of Abc Membrane Transporters In Single Live Cells, Preeyaporn Songkiatisak
Study Of Abc Membrane Transporters In Single Live Cells, Preeyaporn Songkiatisak
Chemistry & Biochemistry Theses & Dissertations
The multidrug ATP-binding cassette (ABC) membrane transporters (efflux pumps) are found in both prokaryotes and eukaryotes and they can extrude diverse structurally unrelated substrates, such as antibiotics and chemotherapeutic agents out of the cells. The efflux pumps are responsible for multidrug resistance (MDR) and the failure of numerous treatments in infections and cancers. All ABC membrane transporters share a common modular topology containing two transmembrane domains (TMDs) and two nucleotide binding domains (NBDs). The underlying molecular mechanisms regarding how the similar structural ABC membrane transporters could selectively extrude a wide variety of substrates and cause MDR, are not yet fully …
Physiological Evidence For Isopotential Tunneling In The Electron Transport Chain Of Methane-Producing Archaea, Nikolas Duszenko, Nicole R. Buan
Physiological Evidence For Isopotential Tunneling In The Electron Transport Chain Of Methane-Producing Archaea, Nikolas Duszenko, Nicole R. Buan
Department of Biochemistry: Faculty Publications
Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli. We found the quantity of MPh per …
Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver
Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver
Chemistry Honors Papers
The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …
The Study Of The Regulon Of Oxyr In Escherichia Coli And Porphyromonas Gingivalis, Christopher K. Pham
The Study Of The Regulon Of Oxyr In Escherichia Coli And Porphyromonas Gingivalis, Christopher K. Pham
Theses and Dissertations
The facultative anaerobe, Escherichia coli and the obligate anaerobe, Porphyromonas gingivalis are two bacteria that reside in our body. Although they reside in separate environments, they are both subject to hydrogen peroxide stress and have mechanisms to regulate the stress. OxyR is the primary transcriptional regulator/sensor of oxidative stress response caused by hydrogen peroxide. OxyR in P. gingivalis is not well-characterized compared to OxyR in E. coli. We sought to characterize and compare the two forms of OxyR in order to gain a better understanding of the protein. We determined the oligomeric state of both proteins: primarily a tetramer for …
Nmr-Based Structural Analysis Of Threonylcarbamoyl-Amp Synthase And Its Substrate Interactions, Kimberly A. Harris, Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, Paul F. Agris
Nmr-Based Structural Analysis Of Threonylcarbamoyl-Amp Synthase And Its Substrate Interactions, Kimberly A. Harris, Benjamin G. Bobay, Kathryn L. Sarachan, Alexis F. Sims, Yann Bilbille, Christopher Deutsch, Dirk Iwata-Reuyl, Paul F. Agris
Chemistry Faculty Publications and Presentations
The hypermodified nucleoside N(6)-threonylcarbamoyladenosine (t(6)A37) is present in many distinct tRNA species and has been found in organisms in all domains of life. This post-transcriptional modification enhances translation fidelity by stabilizing the anticodon/codon interaction in the ribosomal decoding site. The biosynthetic pathway of t(6)A37 is complex and not well understood. In bacteria, the following four proteins have been discovered to be both required and sufficient for t(6)A37 modification: TsaC, TsaD, TsaB, and TsaE. Of these, TsaC and TsaD are members of universally conserved protein families. Although TsaC has been shown to catalyze the formation of L-threonylcarbamoyl-AMP, a key intermediate in …
Characterization Of The Sufc Atpase During Fe-S Cluster Assembly By The Suf Pathway In Escherichia Coli, Khaleh Mykel Thomas
Characterization Of The Sufc Atpase During Fe-S Cluster Assembly By The Suf Pathway In Escherichia Coli, Khaleh Mykel Thomas
Theses and Dissertations
The gram-negative bacterium E. coli encodes the Suf pathway to assemble iron-sulfur (Fe-S) clusters under iron starvation and oxidative stress conditions. The ATPase activity of SufC is critical for in vivo Fe-S cluster assembly by the Suf pathway. SufC shares homology with the nucleotide binding domain (NBD) of ATP-binding cassette (ABC) transporters and belongs to the AAA+ (ATPases Associated with diverse cellular Activities) ATPase superfamily, a family of proteins that utilizes energy from ATP hydrolysis to perform a variety of cellular functions. SufC forms a stable SufBC2D complex with partner proteins SufB and SufD. The SufBC2D complex serves as a …
Comparison Of Two Separation Methods For Biological Particles: Field-Flow Fractionation (Fff) And Sucrose Density Gradients, Cody E. Garrison
Comparison Of Two Separation Methods For Biological Particles: Field-Flow Fractionation (Fff) And Sucrose Density Gradients, Cody E. Garrison
OES Theses and Dissertations
Sucrose gradient centrifugation and Field-flow fractionation (FFF) are two different particle separation methods that overcome the problems of similar size microorganisms clumping together during standard filtration methods. FFF separates particles based on size and density via the parabolic velocity profile of laminar flow in a ribbon-like channel. The sucrose method separates particles via centrifugation in a density gradient. Both techniques worked well in separating eukaryotic from prokaryotic microbes, with the preferred method depending on the type and relative abundance of organisms to be separated. Minicells were separated from mother cells in transformed Escherichia coli cultures, heterotrophic flagellates (e.g., Diplonema papillatum …
Primary Microrna Processing Assay Reconstituted Using Recombinant Drosha And Dgcr8., Ian Barr, Feng Guo
Primary Microrna Processing Assay Reconstituted Using Recombinant Drosha And Dgcr8., Ian Barr, Feng Guo
Natural Sciences and Mathematics | Faculty Scholarship
In animals, the Microprocessor complex cleaves primary transcripts of microRNAs (pri-miRNAs) to produce precursor microRNAs in the nucleus. The core components of Microprocessor include the Drosha ribonuclease and its RNA-binding partner protein DiGeorge critical region 8 (DGCR8). DGCR8 has been shown to tightly bind an Fe(III) heme cofactor, which activates its pri-miRNA processing activity. Here we describe how to reconstitute pri-miRNA processing using recombinant human Drosha and DGCR8 proteins. In particular, we present the procedures for expressing and purifying DGCR8 as an Fe(III) heme-bound dimer, the most active form of this protein, and for estimating its heme content.
Mscs-Like Mechanosensitive Channels In Plants And Microbes, Margaret E. Wilson, Grigory Maksaev, Elizabeth S. Haswell
Mscs-Like Mechanosensitive Channels In Plants And Microbes, Margaret E. Wilson, Grigory Maksaev, Elizabeth S. Haswell
Biology Faculty Research
The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. …
Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Elastic Deformations Of The Rotary Double Motor Of Single F(O)F(1)-Atp Synthases Detected In Real Time By Förster Resonance Energy Transfer., Stefan Ernst, Monika G Düser, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Biochemistry Publications
Elastic conformational changes of the protein backbone are essential for catalytic activities of enzymes. To follow relative movements within the protein, Förster-type resonance energy transfer (FRET) between two specifically attached fluorophores can be applied. FRET provides a precise ruler between 3 and 8nm with subnanometer resolution. Corresponding submillisecond time resolution is sufficient to identify conformational changes in FRET time trajectories. Analyzing single enzymes circumvents the need for synchronization of various conformations. F(O)F(1)-ATP synthase is a rotary double motor which catalyzes the synthesis of adenosine triphosphate (ATP). A proton-driven 10-stepped rotary F(O) motor in the Escherichia coli enzyme is connected to …
Two Rotary Motors In F-Atp Synthase Are Elastically Coupled By A Flexible Rotor And A Stiff Stator Stalk., André Wächter, Yumin Bi, Stanley D Dunn, Brian D Cain, Hendrik Sielaff, Frank Wintermann, Siegfried Engelbrecht, Wolfgang Junge
Two Rotary Motors In F-Atp Synthase Are Elastically Coupled By A Flexible Rotor And A Stiff Stator Stalk., André Wächter, Yumin Bi, Stanley D Dunn, Brian D Cain, Hendrik Sielaff, Frank Wintermann, Siegfried Engelbrecht, Wolfgang Junge
Biochemistry Publications
ATP is synthesized by ATP synthase (F(O)F(1)-ATPase). Its rotary electromotor (F(O)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (F(1)). Elastic power transmission between F(O) and F(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. A particularly compliant elastic domain is located on the central rotor (c(10-15)/ε/γ), right between the two sites of torque generation and consumption. The hinge on the active lever on subunit β adds further compliance. It is under contention whether or not the peripheral stalk (and the "stator" as a whole) …
Genetic And Molecular Characterization Of A Cryptochrome From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Chen-Hui Chen, William J. Belden, Cornelia Madeti
Genetic And Molecular Characterization Of A Cryptochrome From The Filamentous Fungus Neurospora Crassa, Allan C. Froehlich, Chen-Hui Chen, William J. Belden, Cornelia Madeti
Dartmouth Scholarship
In plants and animals, cryptochromes function as either photoreceptors or circadian clock components. We have examined the cryptochrome from the filamentous fungus Neurospora crassa and demonstrate that Neurospora cry encodes a DASH-type cryptochrome that appears capable of binding flavin adenine dinucleotide (FAD) and methenyltetrahydrofolate (MTHF). The cry transcript and CRY protein levels are strongly induced by blue light in a wc-1-dependent manner, and cry transcript is circadianly regulated, with a peak abundance opposite in phase to frq. Neither deletion nor overexpression of cry appears to perturb the free-running circadian clock. However, cry disruption knockout mutants show a small phase delay …
The Proton-Translocating A Subunit Of F0f1-Atp Synthase Is Allocated Asymmetrically To The Peripheral Stalk., Monika G Düser, Yumin Bi, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
The Proton-Translocating A Subunit Of F0f1-Atp Synthase Is Allocated Asymmetrically To The Peripheral Stalk., Monika G Düser, Yumin Bi, Nawid Zarrabi, Stanley D Dunn, Michael Börsch
Biochemistry Publications
The position of the a subunit of the membrane-integral F0 sector of Escherichia coli ATP synthase was investigated by single molecule fluorescence resonance energy transfer studies utilizing a fusion of enhanced green fluorescent protein to the C terminus of the a subunit and fluorescent labels attached to specific positions of the epsilon or gamma subunits. Three fluorescence resonance energy transfer levels were observed during rotation driven by ATP hydrolysis corresponding to the three resting positions of the rotor subunits, gamma or epsilon, relative to the a subunit of the stator. Comparison of these positions of the rotor sites with those …
Domain Compliance And Elastic Power Transmission In Rotary F(O)F(1)-Atpase., Hendrik Sielaff, Henning Rennekamp, André Wächter, Hao Xie, Florian Hilbers, Katrin Feldbauer, Stanley D Dunn, Siegfried Engelbrecht, Wolfgang Junge
Domain Compliance And Elastic Power Transmission In Rotary F(O)F(1)-Atpase., Hendrik Sielaff, Henning Rennekamp, André Wächter, Hao Xie, Florian Hilbers, Katrin Feldbauer, Stanley D Dunn, Siegfried Engelbrecht, Wolfgang Junge
Biochemistry Publications
The 2 nanomotors of rotary ATP synthase, ionmotive F(O) and chemically active F(1), are mechanically coupled by a central rotor and an eccentric bearing. Both motors rotate, with 3 steps in F(1) and 10-15 in F(O). Simulation by statistical mechanics has revealed that an elastic power transmission is required for a high rate of coupled turnover. Here, we investigate the distribution in the F(O)F(1) structure of compliant and stiff domains. The compliance of certain domains was restricted by engineered disulfide bridges between rotor and stator, and the torsional stiffness (kappa) of unrestricted domains was determined by analyzing their thermal rotary …
Probing The Functional Tolerance Of The B Subunit Of Escherichia Coli Atp Synthase For Sequence Manipulation Through A Chimera Approach., Yumin Bi, Joel C Watts, Pamela Krauss Bamford, Lee-Ann K Briere, Stanley D Dunn
Probing The Functional Tolerance Of The B Subunit Of Escherichia Coli Atp Synthase For Sequence Manipulation Through A Chimera Approach., Yumin Bi, Joel C Watts, Pamela Krauss Bamford, Lee-Ann K Briere, Stanley D Dunn
Biochemistry Publications
A dimer of 156-residue b subunits forms the peripheral stator stalk of eubacterial ATP synthase. Dimerization is mediated by a sequence with an unusual 11-residue (hendecad) repeat pattern, implying a right-handed coiled coil structure. We investigated the potential for producing functional chimeras in the b subunit of Escherichia coli ATP synthase by replacing parts of its sequence with corresponding regions of the b subunits from other eubacteria, sequences from other polypeptides having similar hendecad patterns, and sequences forming left-handed coiled coils. Replacement of positions 55-110 with corresponding sequences from Bacillus subtilis and Thermotoga maritima b subunits resulted in fully functional …
The Stator Complex Of The A1a0-Atp Synthase--Structural Characterization Of The E And H Subunits., Erik Kish-Trier, Lee-Ann K Briere, Stanley D Dunn, Stephan Wilkens
The Stator Complex Of The A1a0-Atp Synthase--Structural Characterization Of The E And H Subunits., Erik Kish-Trier, Lee-Ann K Briere, Stanley D Dunn, Stephan Wilkens
Biochemistry Publications
Archaeal ATP synthase (A-ATPase) is the functional homolog to the ATP synthase found in bacteria, mitochondria and chloroplasts, but the enzyme is structurally more related to the proton-pumping vacuolar ATPase found in the endomembrane system of eukaryotes. We have cloned, overexpressed and characterized the stator-forming subunits E and H of the A-ATPase from the thermoacidophilic Archaeon, Thermoplasma acidophilum. Size exclusion chromatography, CD, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and NMR spectroscopic experiments indicate that both polypeptides have a tendency to form dimers and higher oligomers in solution. However, when expressed together or reconstituted, the two individual polypeptides interact with …