AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS

2007 ◽  
Vol 17 (02) ◽  
pp. 225-237 ◽  
Author(s):  
ALEXEI BYKHOVSKI ◽  
TATIANA GLOBUS ◽  
TATYANA KHROMOVA ◽  
BORIS GELMONT ◽  
DWIGHT WOOLARD
Keyword(s):  
Molecular Structure ◽  
Structural Similarity ◽  
Md Simulations ◽  
Detection Capability ◽  
Dna Structures ◽  
E Coli ◽  
Cellular Components ◽  
First Time ◽  
Insight Into ◽  
Specific Contribution

The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.

scholarly journals The impact of radical loading and oxidation on the conformation of organic radical polymers by small angle neutron scattering

2018 ◽  
Vol 6 (32) ◽  
pp. 15659-15667 ◽  
Author(s):  
Halie J. Martin ◽  
Barbara K. Hughes ◽  
Wade A. Braunecker ◽  
Thomas Gennett ◽  
Mark D. Dadmun
Keyword(s):  
Molecular Structure ◽  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Organic Radical ◽  
The Impact ◽  
First Time ◽  
Insight Into

SANS provides, for the first time, unique insight into the correlation between organic radical polymer molecular structure and their assembly.

scholarly journals Cell extract gels as an example of active matter

2020 ◽  
Vol 59 (8) ◽  
pp. 575-582
Author(s):  
Agnieszka Wisniewska ◽  
Tomasz Kalwarczyk ◽  
Jedrzej Szymanski ◽  
Katarzyna Kryszczuk ◽  
Kinga Matula ◽  
...  
Keyword(s):  
Storage Modulus ◽  
Cellular Response ◽  
Cell Extract ◽  
Bacterial Lysate ◽  
Initial State ◽  
E Coli ◽  
Cellular Environment ◽  
External Stimuli ◽  
First Time ◽  
Insight Into

Abstract Cell lysates (cellular extracts) constitute a perfect imitation of the intracellular environment that can provide insight into cellular response to external stimuli. However, most of the presented results are performed for diluted lysates that do not reflect the actual properties of a crowded cellular environment. Here, we report for the first time the measurement of the viscosity and shear storage modulus of highly concentrated Escherichia coli (E. coli) lysates with and without adenosine triphosphate (ATP). By cleavage of DNA content, we showed the value of shear storage modulus $G^{\prime }$ G ′ decreases by 19–31% in comparison to control samples. The addition of molecules that provides energy (ATP) allowed to rebuild the structure of the lysate by reversibly increasing viscous properties over elastic ones. When the energy delivered in the form of ATP is consumed by the unliving bacterial lysate, the system returns to its initial state.

scholarly journals Crystal structure of the multiple antibiotic resistance regulator MarR fromClostridium difficile

2017 ◽  
Vol 73 (6) ◽  
pp. 363-368
Author(s):  
J. W. Peng ◽  
H. Yuan ◽  
X. S. Tan
Keyword(s):  
Antibiotic Resistance ◽  
Structural Similarity ◽  
Soluble Form ◽  
Monoclinic Space Group ◽  
Multiple Antibiotic Resistance ◽  
Cell Parameters ◽  
E Coli ◽  
Archaeal Species ◽  
High Structural Similarity ◽  
First Time

Regulators of multiple antibiotic resistance (MarRs) are key players against toxins in prokaryotes. MarR homologues have been identified in many bacterial and archaeal species which pose daunting antibiotic resistance issues that threaten public health. The continuous prevalence ofClostridium difficileinfection (CDI) throughout the world is associated with the abuse of antibiotics, and antibiotic treatments of CDI have limited effect. In the genome ofC. difficilestrain 630, themarRgene (ID 4913953) encodes a MarR protein. Here, MarR fromC. difficile(MarRC.difficile) was subcloned and crystallized for the first time. MarRC.difficilewas successfully expressed inEscherichia coliin a soluble form and was purified to near-homogeneity (>95%) by a two-step purification protocol. The structure of MarRC.difficilehas been solved at 2.3 Å resolution. The crystal belonged to the monoclinic space groupP43212, with unit-cell parametersa=b= 66.569,c= 83.654 Å. The structure reported reveals MarRC.difficileto be a dimer, with each subunit consisting of six α-helices and three antiparallel β-hairpins. MarRC.difficileshows high structural similarity to the MarR proteins fromE. coliandStaphylococcus aureus, indicating that MarRC.difficilemight be a DNA-binding protein.

scholarly journals An Update of the Virion Proteome of Kaposi Sarcoma-Associated Herpesvirus

Viruses ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 1382
Author(s):  
Ramina Nabiee ◽  
Basir Syed ◽  
Jesus Ramirez Castano ◽  
Rukhsana Lalani ◽  
Jennifer E. Totonchy
Keyword(s):  
Mass Spectrometry ◽  
Kaposi Sarcoma ◽  
Protein Composition ◽  
Viral Proteins ◽  
Novel Proteins ◽  
Flight Mass Spectrometry ◽  
Associated Proteins ◽  
Cellular Components ◽  
First Time ◽  
Insight Into

The virion proteins of Kaposi sarcoma-associated herpesvirus (KSHV) were initially characterized in 2005 in two separate studies that combined the detection of 24 viral proteins and a few cellular components via LC-MS/MS or MALDI-TOF. Despite considerable advances in the sensitivity and specificity of mass spectrometry instrumentation in recent years, leading to significantly higher yields in detections, the KSHV virion proteome has not been revisited. In this study, we have re-examined the protein composition of purified KSHV virions via ultra-high resolution Qq time-of-flight mass spectrometry (UHR-QqTOF). Our results confirm the detection of all previously reported virion proteins, in addition to 17 other viral proteins, some of which have been characterized as virion-associated using other methods, and 10 novel proteins identified as virion-associated for the first time in this study. These results add KSHV ORF9, ORF23, ORF35, ORF48, ORF58, ORF72/vCyclin, K3, K9/vIRF1, K10/vIRF4, and K10.5/vIRF3 to the list of KSHV proteins that can be incorporated into virions. The addition of these proteins to the KSHV virion proteome provides novel and important insight into early events in KSHV infection mediated by virion-associated proteins. Data are available via ProteomeXchange with identifier PXD022626.

scholarly journals Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

2020 ◽  
Vol 8 (6) ◽  
pp. 943 ◽  
Author(s):  
Rachel M. Johnson ◽  
Chiara Fais ◽  
Mayuriben Parmar ◽  
Harish Cheruvara ◽  
Robert L. Marshall ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Clinical Importance ◽  
Resistant Mutant ◽  
Md Simulations ◽  
Drug Efflux ◽  
E Coli ◽  
Novel Structure ◽  
Experimental Structure ◽  
Insight Into

Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.

scholarly journals Ultrafast Laser-Probing Spectrocopy for Studying Molecular Structure of Polymeric Proteins

2016 ◽  
Author(s):  
Huihun Jung ◽  
Chester J. Szwejkowski ◽  
Abdon Pena-Francesch ◽  
Benjamin Allen ◽  
Şahin Kaya Özdemir ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Refractive Index ◽  
Recombinant Protein ◽  
Time Domain ◽  
Ultrafast Laser ◽  
E Coli ◽  
Laser Probing ◽  
A New Technique ◽  
First Time

AbstractWe report the development of a new technique to screen protein crystallinity quantitatively based on laser-probing spectroscopy with sub-picosecond resolution. First, we show theoretically that the temperature dependence of the refractive index of a polymeric protein is correlated to its crystallinity. Then, we performed time-domain thermo-transmission experiments on purified semi-crystalline proteins, both native and recombinant (i.e., silk and squid ring teeth), and also on intactE. colicells bearing overexpressed recombinant protein. Our results demonstrate, for the first time, quantification of crystallinity in real time for polymeric proteins. Our approach can potentially be used for screening an ultra-large number of polymeric proteinsin vivo.

Structural similarity of ribosomes from E. coli and A. salina

1978 ◽  
Vol 36 (2) ◽  
pp. 242-243
Author(s):  
M. Boublik ◽  
R.M. Wydro ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Ribosomal Proteins ◽  
Direct Evidence ◽  
Structural Similarity ◽  
Carbon Support ◽  
Artemia Salina ◽  
Uranyl Acetate ◽  
Biological Assays ◽  
E Coli ◽  
And Function ◽  
Fine Carbon

Ribosomes are ribonucleoprotein particles necessary for processing the genetic information of mRNA into proteins. Analogy in composition and function of ribosomes from diverse species, established by biochemical and biological assays, implies their structural similarity. Direct evidence obtained by electron microscopy seems to be of increasing relevance in understanding the structure of ribosomes and the mechanism of their role in protein synthesis.The extent of the structural homology between prokaryotic and eukaryotic ribosomes has been studied on ribosomes of Escherichia coli (E.c.) and Artemia salina (A.s.). Despite the established differences in size and in the amount and proportion of ribosomal proteins and RNAs both types of ribosomes show an overall similarity. The monosomes (stained with 0.5% aqueous uranyl acetate and deposited on a fine carbon support) appear in the electron micrographs as round particles with a diameter of approximately 225Å for the 70S E.c. (Fig. 1) and 260Å for the 80S A.s. monosome (Fig. 2).

Aleksey Peshkov as an editor of Samarskaya Gazeta

2020 ◽  
pp. 128-138
Author(s):  
A. S. Bik-Bulatov
Keyword(s):  
Local History ◽  
Organizational Skills ◽  
First Time ◽  
New Evidence ◽  
Insight Into ◽  
Shed Light

The article uses little known letters of M. Gorky, many of which were published for the first time in 1997, as well as findings of Samara-based experts in local history to shed light on the writer’s work as editor-in-chief of the Samarskaya Gazeta newspaper in 1895. The researcher introduces hitherto unstudied reminiscences of the journalist D. Linyov (Dalin) about this period, which reference a letter by Gorky, now lost. The paper details a newly discovered episode of Gorky’s professional biography as a journalist: it concerns his campaign against a Samara ‘she-wolf,’ the madam of a local brothel A. Neucheva. Linyov’s reminiscences turn out to be an important and interesting source, offering an insight into the daily grind of the young editor Gorky, providing new evidence of his excellent organizational skills, and describing his moral and social stance. The author presents his work in the context of a recently initiated broader discussion about the need to map out all Russian periodicals for the period until 1917, as well as all research devoted to individual publications.

scholarly journals Comparative Study of Chemical Compositions and Antioxidant Capacities of Oils Obtained from 15 Macadamia (Macadamia integrifolia) Cultivars in China

Foods ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1031
Author(s):  
Xixiang Shuai ◽  
Taotao Dai ◽  
Mingshun Chen ◽  
Ruihong Liang ◽  
Liqing Du ◽  
...  
Keyword(s):  
Palmitoleic Acid ◽  
Linear Regression Analysis ◽  
Monounsaturated Fatty Acids ◽  
Multiple Linear Regression Analysis ◽  
Chemical Compositions ◽  
Macadamia Integrifolia ◽  
Antioxidant Capacities ◽  
Squalene Content ◽  
First Time ◽  
Insight Into

The planting area of macadamia in China accounted for more than one third of the world’s planted area. The lipid compositions, minor components, and antioxidant capacities of fifteen varieties of macadamia oil (MO) in China were comparatively investigated. All varieties of MO were rich in monounsaturated fatty acids, mainly including oleic acid (61.74–66.47%) and palmitoleic acid (13.22–17.63%). The main triacylglycerols of MO were first time reported, including 19.2–26.1% of triolein, 16.4–18.2% of 1-palmitoyl-2,3-dioleoyl-glycerol, and 11.9–13.7% of 1-palmitoleoyl-2-oleoyl-3-stearoyl-glycerol, etc. The polyphenol, α-tocotrienol and squalene content varied among the cultivars, while Fuji (791) contained the highest polyphenols and squalene content. Multiple linear regression analysis indicated the polyphenols and squalene content positively correlated with the antioxidant capacity. This study can provide a crucial directive for the breeding of macadamia and offer an insight into industrial application of MO in China.

Probing pyrolysis chemistry of 1-heptene pyrolysis with insight into fuel molecular structure effects

2021 ◽  
Vol 227 ◽  
pp. 79-94
Author(s):  
Chuangchuang Cao ◽  
Wei Li ◽  
Qiang Xu ◽  
Beibei Feng ◽  
Zhandong Wang ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Insight Into
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