scholarly journals Conformational Changes of Anoplin, W-MreB1–9, and (KFF)3K Peptides near the Membranes

2020 ◽  
Vol 21 (24) ◽  
pp. 9672
Author(s):  
Monika Wojciechowska ◽  
Joanna Miszkiewicz ◽  
Joanna Trylska
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Biological Activities ◽  
Membrane Disruption ◽  
Cell Penetrating Peptide ◽  
Active Peptides ◽  
E Coli ◽  
Membrane Active Peptides ◽  
Calcein Leakage ◽  
Bacterial Growth Inhibition

Many peptides interact with biological membranes, but elucidating these interactions is challenging because cellular membranes are complex and peptides are structurally flexible. To contribute to understanding how the membrane-active peptides behave near the membranes, we investigated peptide structural changes in different lipid surroundings. We focused on two antimicrobial peptides, anoplin and W-MreB1–9, and one cell-penetrating peptide, (KFF)3K. Firstly, by using circular dichroism spectroscopy, we determined the secondary structures of these peptides when interacting with micelles, liposomes, E. coli lipopolysaccharides, and live E. coli bacteria. The peptides were disordered in the buffer, but anoplin and W-MreB1–9 displayed lipid-induced helicity. Yet, structural changes of the peptide depended on the composition and concentration of the membranes. Secondly, we quantified the destructive activity of peptides against liposomes by monitoring the release of a fluorescent dye (calcein) from the liposomes treated with peptides. We observed that only for anoplin and W-MreB1–9 calcein leakage from liposomes depended on the peptide concentration. Thirdly, bacterial growth inhibition assays showed that peptide conformational changes, evoked by the lipid environments, do not directly correlate with the antimicrobial activity of the peptides. However, understanding the relation between peptide structural properties, mechanisms of membrane disruption, and their biological activities can guide the design of membrane-active peptides.

Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

1987 ◽  
Vol 45 ◽  
pp. 910-911
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
16S Rrna ◽  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Structural Changes ◽  
Ribosomal Subunit ◽  
Compact Structure ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

scholarly journals E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation and dynamics

2019 ◽  
Author(s):  
James Chen ◽  
Saumya Gopalkrishnan ◽  
Courtney Chiu ◽  
Albert Y. Chen ◽  
Elizabeth A. Campbell ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Conformational Changes ◽  
Transcription Initiation ◽  
Structural Changes ◽  
E Coli ◽  
Bacterial Proteins ◽  
Cryo Electron Microscopy ◽  
Promoter Complex ◽  
Promoter Dna ◽  
Induced Changes

AbstractTraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp. How TraR and its homologs regulate transcription is unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis of RNAP conformational heterogeneity revealed TraR-induced changes in RNAP dynamics. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.

scholarly journals E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
James Chen ◽  
Saumya Gopalkrishnan ◽  
Courtney Chiu ◽  
Albert Y Chen ◽  
Elizabeth A Campbell ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Conformational Changes ◽  
Transcription Initiation ◽  
Structural Changes ◽  
Structural Basis ◽  
E Coli ◽  
Bacterial Proteins ◽  
Promoter Complex ◽  
Promoter Dna ◽  
Induced Changes

TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.

scholarly journals Visualization of two architectures in class-II CAP-dependent transcription activation

2019 ◽  
Author(s):  
Wei Shi ◽  
Yanan Jiang ◽  
Yibin Deng ◽  
Zigang Dong ◽  
Bin Liu
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
De Novo ◽  
Transcription Activation ◽  
Class Ii ◽  
Activation Mechanism ◽  
Receptor Protein ◽  
E Coli ◽  
Isomerization Mechanism ◽  
Rna Transcript

AbstractTranscription activation by cyclic AMP receptor protein (CAP) is the classic paradigm of transcription regulation in bacteria. CAP was suggested to activate transcription on class-II promoters via a recruitment and isomerization mechanism. However, whether and how it modifies RNA polymerase (RNAP) to initiate transcription remains unclear. Here we report cryo-EM structures of an intact E. coli class-II CAP-dependent transcription activation complex (TAC) with and without de novo RNA transcript. The structures reveal two distinct architectures of TAC and show that CAP-binding induces substantial conformational changes in all the subunits of RNAP and consequently widens the main cleft of RNAP considerably to facilitate DNA promoter entering and formation of initiation open complex. These structural changes vanish during further RNA transcript synthesis. The observations in this study suggest a unique activation mechanism on class-II promoters that CAP activates transcription by first remodeling RNAP conformation and then stabilizing initiation complex.

scholarly journals Stress-Dependent Conformational Changes of Artemin: Effects of Heat and Oxidant

2020 ◽  
Author(s):  
Z. Takalloo ◽  
Z. Afshar Ardakani ◽  
B. Maroufi ◽  
S. Shirin Shahangian ◽  
R. H. Sajedi
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Hydrophobic Interactions ◽  
Biological Activities ◽  
Critical Role ◽  
Stress Conditions ◽  
Functional Changes ◽  
Fluorescence Measurements ◽  
Conformational Properties ◽  
Stress Dependent

ABSTRACTArtemin is an abundant thermostable protein in Artemia embryos and considered as a highly efficient molecular chaperone against extreme environmental stress conditions. The dynamic conformational properties of artemin appear to play a critical role in its biological activities. In this study, we have investigated the conformational transitions and functional changes of artemin under heat and oxidative stress to find some evidence of the relationship between the structure and function of artemin. The tertiary and quaternary structures of artemin have been evaluated by fluorescence measurements, protein cross-linking analysis, and dynamic light scattering. Based on the structural analysis, artemin showed irreversible substantial conformational lability in response to heat and oxidant which mainly mediated through the hydrophobic interactions and dimerization of the chaperone. In addition, the chaperone-like activity of the heated and oxidized artemin was examined using lysozyme refolding assay and the experiments showed that although both factors, i.e. heat and oxidant, at specific levels improved artemin potency, simultaneous incubation with both stressors significantly triggered the activation of artemin. Moreover, the heat-induced dimerization of artemin was found to be the most critical factor for its activation. It was suggested that oxidation presumably acts through stabilizing the dimer structures of artemin through formation of disulfide bridges between the subunits and strengthens its chaperoning efficacy. Accordingly, it was proposed that artemin probably exists in a monomer–oligomer equilibrium in Artemia cysts and environmental stresses and intracellular portion of protein substrates may shift the equilibrium towards the active dimer forms of the chaperone.STATEMENT OF SIGNIFICANCEThere are a number of reports in which the chaperone-like activity of artemin, as a stress protein, has been confirmed in vivo and in vitro. Nonetheless, the details of structural changes of the protein have not been fully discovered yet. In the present work, we focused on conformational properties of artemin from A. urmiana upon exposing to heat and oxidation, by using various structural and functional analysis in order to predict the mechanisms of artemin’s activation. Notably, this is the first document on reporting the structural transitions of the chaperone in stress conditions.

Influence of Ascorbic Acid on the Structure and Function of Alpha-2- macroglobulin: Investigations using Spectroscopic and Thermodynamic Techniques

2020 ◽  
Vol 27 (3) ◽  
pp. 201-209
Author(s):  
Syed Saqib Ali ◽  
Mohammad Khalid Zia ◽  
Tooba Siddiqui ◽  
Haseeb Ahsan ◽  
Fahim Halim Khan
Keyword(s):  
Ascorbic Acid ◽  
Conformational Changes ◽  
Structural Changes ◽  
The Body ◽  
Titration Calorimetry ◽  
Spectroscopic Techniques ◽  
Human Beings ◽  
Plasma Ascorbic Acid ◽  
Dietary Antioxidant ◽  
And Function

Background: Ascorbic acid is a classic dietary antioxidant which plays an important role in the body of human beings. It is commonly found in various foods as well as taken as dietary supplement. Objective: The plasma ascorbic acid concentration may range from low, as in chronic or acute oxidative stress to high if delivered intravenously during cancer treatment. Sheep alpha-2- macroglobulin (α2M), a human α2M homologue is a large tetrameric glycoprotein of 630 kDa with antiproteinase activity, found in sheep’s blood. Methods: In the present study, the interaction of ascorbic acid with alpha-2-macroglobulin was explored in the presence of visible light by utilizing various spectroscopic techniques and isothermal titration calorimetry (ITC). Results: UV-vis and fluorescence spectroscopy suggests the formation of a complex between ascorbic acid and α2M apparent by increased absorbance and decreased fluorescence. Secondary structural changes in the α2M were investigated by CD and FT-IR spectroscopy. Our findings suggest the induction of subtle conformational changes in α2M induced by ascorbic acid. Thermodynamics signatures of ascorbic acid and α2M interaction indicate that the binding is an enthalpy-driven process. Conclusion: It is possible that ascorbic acid binds and compromises antiproteinase activity of α2M by inducing changes in the secondary structure of the protein.

scholarly journals KUALITAS AIR SUNGAI DI KAWASAN WISATA PANTAI PETITENGET, KEROBOKAN KABUPATEN BADUNG BALI

2018 ◽  
Vol 12 (2) ◽  
pp. 226
Author(s):  
Wayan Budiarsa Suyasa ◽  
Sri Kunti Pancadewi G. A ◽  
Iryanti E. Suprihatin ◽  
Dwi Adi Suastuti G. A.
Keyword(s):  
Water Quality ◽  
Structural Changes ◽  
Pollution Index ◽  
Basic Structure ◽  
Physical Damage ◽  
E Coli ◽  
Pollutant Source ◽  
Quality Category ◽  
Index Value ◽  
The Impact

In order to maintain the environmental carrying capacity of coastal tourism, this research was conducted to determine the condition of river water environmental pollution in the Petitenget beach area and pollutant source activities. Determination of water quality is carried out by analyzing the water quality taken at several sampling points in the four rivers that lead to the Petitenget beach. Determined the pollution index value (IP) of the physical chemical and biological pollution parameters. The results showed that the four rivers that flow into the Petitenget Beach area had been contaminated with indications of pH, BOD, COD, ammonia, Coliform and E. coli which exceeded water quality category III class quality (PerGub Bali No 16 Year 2016). The four rivers are included in the criteria of severe contamination. The four rivers have experienced physical damage or structural changes that have very high discharge fluctuations both in quantity and quality. Slimy basic structure, smelly and slum aesthetic waters. While the indication of the impact of pollution is waste water which is directly discharged into the river from hotels, restaurants, homestays, commercial centers and settlements.

scholarly journals Chemical Composition and Antibacterial and Antioxidant Activity of a Citrus Essential Oil and Its Fractions

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2888
Author(s):  
Carmen M. S. Ambrosio ◽  
Gloria L. Diaz-Arenas ◽  
Leidy P. A. Agudelo ◽  
Elena Stashenko ◽  
Carmen J. Contreras-Castillo ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Antibacterial Activity ◽  
Chemical Composition ◽  
Essential Oil ◽  
Biological Activities ◽  
E Coli ◽  
Beneficial Bacterium ◽  
Minor Compounds ◽  
Antibacterial And Antioxidant Activity ◽  
High Relative Amount

Essential oils (EOs) from Citrus are the main by-product of Citrus-processing industries. In addition to food/beverage and cosmetic applications, citrus EOs could also potentially be used as an alternative to antibiotics in food-producing animals. A commercial citrus EO—Brazilian Orange Terpenes (BOT)—was fractionated by vacuum fractional distillation to separate BOT into various fractions: F1, F2, F3, and F4. Next, the chemical composition and biological activities of BOT and its fractions were characterized. Results showed the three first fractions had a high relative amount of limonene (≥10.86), even higher than the whole BOT. Conversely, F4 presented a larger relative amount of BOT’s minor compounds (carvone, cis-carveol, trans-carveol, cis-p-Mentha-2,8-dien-1-ol, and trans-p-Mentha-2,8-dien-1-ol) and a very low relative amount of limonene (0.08–0.13). Antibacterial activity results showed F4 was the only fraction exhibiting this activity, which was selective and higher activity on a pathogenic bacterium (E. coli) than on a beneficial bacterium (Lactobacillus sp.). However, F4 activity was lower than BOT. Similarly, F4 displayed the highest antioxidant activity among fractions (equivalent to BOT). These results indicated that probably those minor compounds that detected in F4 would be more involved in conferring the biological activities for this fraction and consequently for the whole BOT, instead of the major compound, limonene, playing this role exclusively.

scholarly journals Biosynthesis of resveratrol derivatives and evaluation of their anti-inflammatory activity

2021 ◽  
Vol 64 (1) ◽  
Author(s):  
Yoojin Chong ◽  
Hye Lim Lee ◽  
Jihyeon Song ◽  
Youngshim Lee ◽  
Bong-Gyu Kim ◽  
...  
Keyword(s):  
Biological Activities ◽  
Stilbene Synthase ◽  
Inflammatory Activity ◽  
E Coli ◽  
Prephenate Dehydrogenase ◽  
Coa Ligase ◽  
Final Yield ◽  
Resveratrol Derivatives ◽  
Anti Inflammatory ◽  
Tyrosine Biosynthesis

AbstractResveratrol is a typical plant phenolic compound whose derivatives are synthesized through hydroxylation, O-methylation, prenylation, and oligomerization. Resveratrol and its derivatives exhibit anti-neurodegenerative, anti-rheumatoid, and anti-inflammatory effects. Owing to the diverse biological activities of these compounds and their importance in human health, this study attempted to synthesize five resveratrol derivatives (isorhapontigenin, pterostilbene, 4-methoxyresveratrol, piceatannol, and rhapontigenin) using Escherichia coli. Two-culture system was used to improve the final yield of resveratrol derivatives. Resveratrol was synthesized in the first E. coli cell that harbored genes for resveratrol biosynthesis including TAL (tyrosine ammonia lyase), 4CL (4-coumaroyl CoA ligase), STS (stilbene synthase) and genes for tyrosine biosynthesis such as aroG (deoxyphosphoheptonate aldolase) and tyrA (prephenate dehydrogenase). Thereafter, culture filtrate from the first cell was used for the modification reaction carried out using the second E. coli harboring hydroxylase and/or O-methyltransferase. Approximately, 89.8 mg/L of resveratrol was synthesized and using the same, five derivatives were prepared with a conversion rate of 88.2% to 22.9%. Using these synthesized resveratrol derivatives, we evaluated their anti-inflammatory activity. 4-Methoxyresveratrol, pterostilbene and isorhapontigenin showed the anti-inflammatory effects without any toxicity. In addition, pterostilbene exhibited the enhanced anti-inflammatory effects for macrophages compared to resveratrol.

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