scholarly journals Encrypting messages with artificial bacterial receptors

2020 ◽  
Vol 16 ◽  
pp. 2749-2756
Author(s):  
Pragati Kishore Prasad ◽  
Naama Lahav-Mankovski ◽  
Leila Motiei ◽  
David Margulies
Keyword(s):  
Protein C ◽  
Molecular Level ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Potential Contribution ◽  
Information Protection ◽  
Emission Pattern ◽  
E Coli ◽  
Artificial Receptors ◽  
Engineered Bacteria

A method for encrypting messages using engineered bacteria and different fluorescently labeled synthetic receptors is described. We show that the binding of DNA-based artificial receptors to E. coli expressing His-tagged outer membrane protein C (His-OmpC) induces a Förster resonance energy transfer (FRET) between the dyes, which results in the generation of a unique fluorescence fingerprint. Because the bacteria continuously divide, the emission pattern generated by the modified bacteria dynamically changes, enabling the system to produce encryption keys that change with time. Thus, this development indicates the potential contribution of live-cell-based encryption systems to the emerging area of information protection at the molecular level.

Comparative Performance Evaluation of Real-Time PCR and Dual-Labeled Fluorescence Resonance Energy Transfer Probe-Based Melt Peak Analysis for the Detection of Escherichia coli O157:H7 in Beef Products

2019 ◽  
Vol 82 (3) ◽  
pp. 507-512
Author(s):  
JOSEPH M. BOSILEVAC ◽  
HARI P. DWIVEDI ◽  
PATRICE CHABLAIN ◽  
MICHAEL ULLERY ◽  
JOSEPH S. BAILEY ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Performance Evaluation ◽  
Energy Transfer ◽  
Real Time Pcr ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Escherichia Coli O157 ◽  
Comparative Performance ◽  
E Coli ◽  
Beef Products

ABSTRACT Contaminated beef and beef products remain a frequent vehicle for the transmission of Escherichia coli O157:H7. The current U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) regulatory testing for E. coli O157:H7 uses the method described in the USDA-FSIS Microbiology Laboratory Guidebook (MLG), chapter 5. At times, described presumptive test results are nonconfirmable, suggesting that recent PCR technological advancements and presumed enhanced sensitivity and specificity may offer beneficial changes. Here, we have evaluated the precision and sensitivity of a fluorescence resonance energy transfer–based real-time PCR assay called ECO for the detection of E. coli O157:H7. ECO detects the gene target specific to both E. coli O157:H7 and E. coli O157:non-H7 but distinguishes the two by using a melt curve analysis. A total of 3,113 O157:H7 and O157:non-H7 isolates were used to define this melting temperature–based criteria. The simulated comparative performance evaluation in the spiked beef samples indicated detection of 3 of 3 samples by ECO at <3.3 log CFU/mL, whereas MLG only detected 1 of 3 (<3.3 log CFU/mL). Using modified tryptic soy broth–enriched natural beef and veal product samples (n = 452), the comparative sensitivity, specificity, false-positive rate, and false-negative rate against culture between MLG and ECO were 75 versus 92%, 91 versus 99%, 8.9 versus 0.77%, and 25 versus 8.3%, respectively. Positive predictive value, negative predictive value, and the overall accuracy were found to be 56 versus 94%, 96 versus 98%, and 88 versus 98%, for MLG and ECO, respectively. These data demonstrate that the ECO assay is comparable to MLG detection of E. coli O157:H7 and offers improved sensitivity.

scholarly journals Quality control for unfolded proteins at the plasma membrane

2010 ◽  
Vol 191 (3) ◽  
pp. 553-570 ◽  
Author(s):  
Pirjo M. Apaja ◽  
Haijin Xu ◽  
Gergely L. Lukacs
Keyword(s):  
Quality Control ◽  
Plasma Membrane ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Cellular Protein ◽  
Temperature Sensitive ◽  
Potential Contribution ◽  
Unfolded Proteins ◽  
Endosomal Sorting ◽  
V2 Receptor

Cellular protein homeostasis profoundly depends on the disposal of terminally damaged polypeptides. To demonstrate the operation and elucidate the molecular basis of quality control of conformationally impaired plasma membrane (PM) proteins, we constructed CD4 chimeras containing the wild type or a temperature-sensitive bacteriophage λ domain in their cytoplasmic region. Using proteomic, biochemical, and genetic approaches, we showed that thermal unfolding of the λ domain at the PM provoked the recruitment of Hsp40/Hsc70/Hsp90 chaperones and the E2–E3 complex. Mixed-chain polyubiquitination, monitored by bioluminescence resonance energy transfer and immunoblotting, is responsible for the nonnative chimera–accelerated internalization, impaired recycling, and endosomal sorting complex required for transport–dependent lysosomal degradation. A similar paradigm prevails for mutant dopamine D4.4 and vasopressin V2 receptor removal from the PM. These results outline a peripheral proteostatic mechanism in higher eukaryotes and its potential contribution to the pathogenesis of a subset of conformational diseases.

scholarly journals MreC and MreD balance the interaction between the elongasome proteins PBP2 and RodA

2019 ◽  
Author(s):  
Xiaolong Liu ◽  
Jacob Biboy ◽  
Waldemar Vollmer ◽  
Tanneke den Blaauwen
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Cell Envelope ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Cylindrical Part ◽  
E Coli ◽  
Length Growth ◽  
Antibiotic Drug

AbstractRod-shape of most bacteria is maintained by the elongasome, which mediates the synthesis and insertion of peptidoglycan into the cylindrical part of the cell wall. The elongasome contains several essential proteins, such as RodA, PBP2, and the MreBCD proteins, but how its activities are regulated remains poorly understood. Using E. coli as a model system, we investigated the interactions between core elongasome proteins in vivo. Our results show that PBP2 and RodA form a complex mediated by their transmembrane and periplasmic parts and independent of their catalytic activity. MreC and MreD also interact directly with PBP2. MreC elicits a chance in the interaction between PBP2 and RodA, which is suppressed by MreD. The cytoplasmic domain of PBP2 is required for this suppression. We hypothesize that the in vivo measured PBP2-RodA interaction change induced by MreC corresponds to the conformational change in PBP2 as observed in the MreC-PBP2 crystal structure, which was suggested to be the “on state” of PBP2. Our results indicate that the balance between MreC and MreD determines the activity of PBP2, which could open new strategies for antibiotic drug development.ImportanceThe cell envelope of Escherichia coli bears the protective and shape-determining peptidoglycan layer sandwiched between the outer and inner membranes. Length growth in bacteria is accomplished by a protein complex termed elongasome. We used Förster Resonance Energy Transfer (FRET) that reports not only on whether proteins interact with each other but also on conformational changes during interactions, to investigate how the elongasome might be activated. RodA and PBP2 provide the peptidoglycan glycosyltransferase and transpeptidase activities needed to synthesize new peptidolgycan during length growth, respectively, and PBP2 activates RodA. We show that the interactions between MreC and MreD with PBP2-RodA alter the nature of the interaction between PBP2 and RodA and hypothesis that the corresponding conformational change in the PBP2-RodA complex allows switching between the ‘on’ and ‘off’ states of the elongasome.

scholarly journals Site-directed spectroscopy of cardiac myosin-binding protein C reveals effects of phosphorylation on protein structural dynamics

2016 ◽  
Vol 113 (12) ◽  
pp. 3233-3238 ◽  
Author(s):  
Brett A. Colson ◽  
Andrew R. Thompson ◽  
L. Michel Espinoza-Fonseca ◽  
David D. Thomas
Keyword(s):  
Protein C ◽  
Binding Protein ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Md Simulations ◽  
Cardiac Myosin ◽  
Myosin Binding Protein ◽  
Myosin Binding Protein C ◽  
Myosin Binding

We have used the site-directed spectroscopies of time-resolved fluorescence resonance energy transfer (TR-FRET) and double electron–electron resonance (DEER), combined with complementary molecular dynamics (MD) simulations, to resolve the structure and dynamics of cardiac myosin-binding protein C (cMyBP-C), focusing on the N-terminal region. The results have implications for the role of this protein in myocardial contraction, with particular relevance to β-adrenergic signaling, heart failure, and hypertrophic cardiomyopathy. N-terminal cMyBP-C domains C0–C2 (C0C2) contain binding regions for potential interactions with both thick and thin filaments. Phosphorylation by PKA in the MyBP-C motif regulates these binding interactions. Our spectroscopic assays detect distances between pairs of site-directed probes on cMyBP-C. We engineered intramolecular pairs of labeling sites within cMyBP-C to measure, with high resolution, the distance and disorder in the protein’s flexible regions using TR-FRET and DEER. Phosphorylation reduced the level of molecular disorder and the distribution of C0C2 intramolecular distances became more compact, with probes flanking either the motif between C1 and C2 or the Pro/Ala-rich linker (PAL) between C0 and C1. Further insight was obtained from microsecond MD simulations, which revealed a large structural change in the disordered motif region in which phosphorylation unmasks the surface of a series of residues on a stable α-helix within the motif with high potential as a protein–protein interaction site. These experimental and computational findings elucidate structural transitions in the flexible and dynamic portions of cMyBP-C, providing previously unidentified molecular insight into the modulatory role of this protein in cardiac muscle contractility.

scholarly journals mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding

2020 ◽  
Author(s):  
Chen Bao ◽  
Sarah Loerch ◽  
Clarence Ling ◽  
Andrei A. Korostelev ◽  
Nikolaus Grigorieff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Translation Elongation ◽  
Stem Loop ◽  
E Coli ◽  
Immunodeficiency Virus ◽  
A Site ◽  
Trna Binding

Although the elongating ribosome is an efficient helicase, certain mRNA stem-loop structures are known to impede ribosome movement along mRNA and stimulate programmed ribosome frameshifting via mechanisms that are not well understood. Using biochemical and single-molecule Förster resonance energy transfer (smFRET) experiments, we studied how frameshift-inducing stem-loops from E. coli dnaX mRNA and the gag-pol transcript of Human Immunodeficiency Virus (HIV) perturb translation elongation. We find that upon encountering the ribosome, the stem-loops strongly inhibit A-site tRNA binding and ribosome intersubunit rotation that accompanies translation elongation. Electron cryo-microscopy (cryo-EM) reveals that the HIV stem-loop docks into the A site of the ribosome. Our results suggest that mRNA stem-loops can transiently escape ribosome helicase by binding to the A site. Thus, the stem-loops can modulate gene expression by sterically hindering tRNA binding and inhibiting translation elongation.

scholarly journals Frustration and folding of a TIM barrel protein

2019 ◽  
Vol 116 (33) ◽  
pp. 16378-16383 ◽  
Author(s):  
Kevin T. Halloran ◽  
Yanming Wang ◽  
Karunesh Arora ◽  
Srinivas Chakravarthy ◽  
Thomas C. Irving ◽  
...  
Keyword(s):  
Triosephosphate Isomerase ◽  
Molecular Level ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Similar Rate ◽  
Coarse Grained ◽  
Free Energy Surface ◽  
Glycerol Phosphate ◽  
Time Resolved ◽  
Tim Barrel

Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture that supports a myriad of enzymatic functions, but also a conserved folding mechanism that involves on- and off-pathway intermediates. Although experiments have proven to be invaluable in defining the folding free-energy surface, they provide only a limited understanding of the structures of the partially folded states that appear during folding. Coarse-grained simulations employing native centric models are capable of sampling the entire energy landscape of TIM barrels and offer the possibility of a molecular-level understanding of the readout from sequence to structure. We have combined sequence-sensitive native centric simulations with small-angle X-ray scattering and time-resolved Förster resonance energy transfer to monitor the formation of structure in an intermediate in the Sulfolobus solfataricus indole-3-glycerol phosphate synthase TIM barrel that appears within 50 μs and must at least partially unfold to achieve productive folding. Simulations reveal the presence of a major and 2 minor folding channels not detected in experiments. Frustration in folding, i.e., backtracking in native contacts, is observed in the major channel at the initial stage of folding, as well as late in folding in a minor channel before the appearance of the native conformation. Similarities in global and pairwise dimensions of the early intermediate, the formation of structure in the central region that spreads progressively toward each terminus, and a similar rate-limiting step in the closing of the β-barrel underscore the value of combining simulation and experiment to unravel complex folding mechanisms at the molecular level.

scholarly journals Probing the active site of YjeE: a vital Escherichia coli protein of unknown function

2004 ◽  
Vol 384 (3) ◽  
pp. 577-584 ◽  
Author(s):  
Abdellah ALLALI-HASSANI ◽  
Tracey L. CAMPBELL ◽  
Andy HO ◽  
Jeffrey W. SCHERTZER ◽  
Eric D. BROWN
Keyword(s):  
Escherichia Coli ◽  
Unknown Function ◽  
Equilibrium Dialysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Wild Type ◽  
E Coli ◽  
High Affinity ◽  
Hydrolysis Of

In the study described here, we have taken steps to characterize the YjeE protein, an Escherichia coli protein of unknown function that is essential for bacterial viability. YjeE represents a protein family whose members are broadly conserved in bacteria, absent from eukaryotes and contain both Walker A and B motifs, characteristic of P-loop ATPases. We have revisited the dispensability of the yjeE gene in E. coli and describe efforts to probe the function of the YjeE protein with in vitro biochemistry. We have looked critically for ATPase activity in the recombinant E. coli protein and have made vigilant use of site-directed variants in the Walker A [K41A (Lys41→Ala) and T42A] and putative Walker B (D80Q) motifs. We noted that any hydrolysis of ATP by the wild-type E. coli protein might be attributed to background ATPase, since it was not appreciably different from that of the variants. To overcome potential contaminants, we turned to crystalline pure YjeE protein from Haemophilus influenzae that was found to hydrolyse ATP at a slow rate (kcat=1 h−1). We have also shown high-affinity binding to YjeE by ADP using equilibrium dialysis (Kd=32 μM) and by fluorescence resonance energy transfer from a conserved tryptophan in YjeE to a fluorescent derivative of ADP, 2′-/3′-O-(N-methylanthraniloyl)adenosine 5′-O-diphosphate (Kd=8 μM). Walker motif variants were notably impaired for ADP binding and T42A and D80Q mutations in yjeE were incapable of complementing the yjeE deletion strain.

scholarly journals Functionalized Protein Nanotubes Based on the Bacteriophage vB_KleM-RaK2 Tail Sheath Protein

Nanomaterials ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3031
Author(s):  
Greta Labutytė ◽  
Simona Povilonienė ◽  
Eugenijus Šimoliūnas ◽  
Dovydas Gabrielaitis ◽  
Martynas Skapas ◽  
...  
Keyword(s):  
Fluorescent Proteins ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Stimulated Emission ◽  
Chimeric Proteins ◽  
Tubular Structures ◽  
E Coli ◽  
Tail Sheath ◽  
Delivery Vehicles ◽  
Hydrolysis Of

We report on the construction of functionalized nanotubes based on tail sheath protein 041 from vB_KleM-RaK2 bacteriophage. The truncated 041 protein (041Δ200) was fused with fluorescent proteins GFP and mCherry or amidohydrolase YqfB. The generated chimeric proteins were successfully synthesized in E. coli BL21 (DE3) cells and self-assembled into tubular structures. We detected the fluorescence of the structures, which was confirmed by stimulated emission depletion microscopy. When 041Δ200GFP and 041Δ200mCherry were coexpressed in E. coli BL21 (DE3) cells, the formed nanotubes generated Förster resonance energy transfer, indicating that both fluorescent proteins assemble into a single nanotube. Chimeric 041Δ200YqfB nanotubes possessed an enzymatic activity, which was confirmed by hydrolysis of N4-acetyl-2′-deoxycytidine. The enzymatic properties of 041Δ200YqfB were similar to those of a free wild-type YqfB. Hence, we conclude that 041-based chimeric nanotubes have the potential for the development of delivery vehicles and targeted imaging and are applicable as scaffolds for biocatalysts.

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