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World Journal of Microbiology &... Jun 2024The analysis of transcriptional activity of the bacteriophage T5 hol/endo operon conducted in the paper revealed a strong constitutive promoter recognized by E. coli RNA...
The analysis of transcriptional activity of the bacteriophage T5 hol/endo operon conducted in the paper revealed a strong constitutive promoter recognized by E. coli RNA polymerase and a transcription initiation point of the operon. It was also shown that the only translational start codon for holin was a non-canonical TTG. Translation initiation regions (TIRs) of both genes of the operon (hol and endo) were further analyzed using chimeric constructs, in which parts of the hol/endo regulatory regions were fused with the gene of a reporter protein (EGFP). It was found that TIR of hol was 20 times less effective than that of endo. As it turned out, the level of EGFP production was influenced by the composition of the constructs and the type of the hol start codon. Apparently, the translational suppression of holin's accumulation and posttranslational activation of endolysin by Ca are the main factors ensuring the proper timing of the host cell lysis by bacteriophage T5. The approach based on the use of chimeric constructs proposed in the paper can be recommended for studying other native or artificial operons of any complexity: analyzing the impacts of separate DNA regions, as well as their coupled effect, on the processes of transcription and translation of recombinant protein(s).
Topics: Operon; Endopeptidases; Viral Proteins; Transcription, Genetic; Promoter Regions, Genetic; Escherichia coli; Protein Biosynthesis; Gene Expression Regulation, Viral; Green Fluorescent Proteins; Codon, Initiator; DNA-Directed RNA Polymerases; DNA, Viral; Bacteriophages
PubMed: 38926173
DOI: 10.1007/s11274-024-04063-2 -
Transfusion Medicine (Oxford, England) Jun 2024Having faster plasma thawing devices could be beneficial for transfusion services, as it may improve the rapid availability of thawed plasma for bleeding patients, and...
BACKGROUND
Having faster plasma thawing devices could be beneficial for transfusion services, as it may improve the rapid availability of thawed plasma for bleeding patients, and it might remove the need to have extended pre-thawed plasma: thus, reducing unnecessary plasma wastage.
STUDY DESIGN AND METHODS
The aims of this study were to assess (a) the thawing times and (b) in vitro haemostatic quality of thawed plasma using Barkey Plasmatherm V (PTV) at 37 and 45°C versus Barkey Plasmatherm Classic (PTC) at 37 and 45°C, Sarstedt Sahara-III Maxitherm (SS-III) at 37°C and Helmer Scientific Thermogenesis Thermoline (TT) at 37°C. Haemostatic quality was assessed using LG-Octaplas at three different time points: baseline (5 min), 24 and 120 h after thawing.
RESULTS
The thawing time (SD) of 2 and 4 units was significantly different between different thawers. PTV at 45°C was the fastest method for both 2 and 4 units (7.06 min [0.68], 9.6 min [0.87], respectively). SS-III at 37°C being the slowest method (24.69 min [2.09] and 27.18 min [4.4], respectively) (p = < 0.05). Baseline measurements for all assays showed no significant difference in the prothrombin time, fibrinogen, FII, FV, protein C activity or free protein S antigen between all methods tested. However, at baseline PTV (both 37°C and 45°C) had significantly higher levels of FVII, FVIII and FXI and shortened activated partial thromboplastin time.
DISCUSSION
PTV was the quickest method at thawing plasma at both 37 and at 45°C. The haemostatic quality of plasma thawed at 45 versus 37°C was not impaired. Thawing frozen plasma at 45°C should be considered.
PubMed: 38923078
DOI: 10.1111/tme.13061 -
Photochemistry and Photobiology Jun 2024Studies focusing on how photobiomodulation (PBM) can affect the structure and function of proteins are scarce in the literature. Few previous studies have shown that the...
Studies focusing on how photobiomodulation (PBM) can affect the structure and function of proteins are scarce in the literature. Few previous studies have shown that the enzymatic activity of Na,K-ATPAse (NKA) can be photo-modulated. However, the variability of sample preparation and light irradiation wavelengths have not allowed for an unequivocal conclusion about the PBM of NKA. Here, we investigate minimal membrane models containing NKA, namely, native membrane fraction and DPPC:DPPE proteoliposome upon laser irradiation at wavelengths 532, 650, and 780 nm. Interestingly, we show that the PBM on the NKA enzymatic activity has a bell-shaped profile with a stimulation peak (~15% increase) at around 20 J.cm and 6 J.cm for the membrane-bound and the proteoliposome samples, respectively, and are practically wavelength independent. Further, by normalizing the enzymatic activity by the NKA enzyme concentration, we show that the PBM response is related to the protein amount with small influence due to protein's environment. The stimulation decays over time reaching the basal level around 6 h after the irradiation for the three lasers and both NKA samples. Our results demonstrate the potential of using low-level laser therapy to modulate NKA activity, which may have therapeutic implications and benefits.
PubMed: 38922888
DOI: 10.1111/php.13987 -
Analytical Methods : Advancing Methods... Jun 2024Protein -acylation is an important lipid modification and plays a series of biological functions. As a classic proteomic method for -acylated proteome analysis, the...
Protein -acylation is an important lipid modification and plays a series of biological functions. As a classic proteomic method for -acylated proteome analysis, the acyl-biotin exchange and its derivative methods are known to be very labour-intensive and time-consuming all the time, and will result in significant sample loss. Multiple methanol-chloroform precipitations are involved in order to remove the substances that would interfere with enrichment and identification including detergents, the residual reduction and alkylation reagents. Here, we developed a rapid and convenient method for -acylation proteomics by combining a dissolvable tube gel and the classic ABE method, a Dissolvable Gel based One-Tube sample Treatment method (DGOTT) method. The protein fixation rate, impact of the gel size on analysis performance and feasibility for analyzing complex samples were evaluated. This method enabled the alkylation and chemical substitution reactions to be conducted in a single EP tube, and convenient removal of interferents through gel washing, which could obviously simplify operations and shorten the sample treatment duration. Finally, we identified a total of 1625 potential -acylated proteins from 800 μg of mouse brain cerebral cortex proteins. We believe that our method could offer potential for high-throughput analysis of protein -acylation.
PubMed: 38920099
DOI: 10.1039/d4ay00937a -
ACS Applied Bio Materials Jun 2024β-Thalassemia especially transfusion-dependent thalassemia (TDT) associates with a hypercoagulable state, which is the main cause of thromboembolic events (TEE). Plasma...
A Compact Differential Dynamic Microscopy-based Device (cDDM): An Approach Tool for Early Detection of Hypercoagulable State in Transfusion-Dependent-β-Thalassemia Patients.
β-Thalassemia especially transfusion-dependent thalassemia (TDT) associates with a hypercoagulable state, which is the main cause of thromboembolic events (TEE). Plasma viscosity and rheological parameters could be essential markers for determining hypercoagulable state in β-thalassemia patients. The traditional methods for measuring viscosity are often limited by large sample volumes and are impractical for routine clinical monitoring. The compact differential dynamic microscopy-based device (cDDM), an optical microscopy for quantitative rheological assessment, was developed and applied for prognosis of the hypercoagulable state in β-TDT with and without splenectomy. The device was performed plasma viscosity measurement using low plasma volume (8 μL) and revealed a value as modulus of complex viscosity |η(ω)| in 7 min. We also parallelly demonstrated the correlation of the viscosity and related-coagulable parameters: complete blood count, prothrombin time (PT), activated partial thromboplastin time (APTT), protein C (PC), protein S (PS), CD62P and CD63 expression, and platelet aggregation test. The thalassemia plasma exhibited a higher value of |η(ω)| than healthy plasma, which can represent a different viscoelastic property among the groups. Even all related-coagulable parameters indicated hypercoagulable state in both nonsplenectomies and splenectomies β-TDT patients when compared to control, only high platelet numbers significantly correlated to high plasma viscosity in the splenectomy group. However, the other coagulable parameters have shown a trend of positive relationship with high plasma viscosity in all β-1thalassemia TDT patients. The relative results suggested that our device would be an approach tool for early detection of hypercoagulable state in transfusion-dependent-β-thalassemia patients, which can help to prevent TEE and the critical consequent-complications.
PubMed: 38920024
DOI: 10.1021/acsabm.4c00516 -
Annals of Vascular Diseases Jun 2024Inherited Protein S (PS) deficiency is an autosomal dominant thrombotic disorder. We encountered a case of inherited type I PS deficiency following a close examination...
Inherited Protein S (PS) deficiency is an autosomal dominant thrombotic disorder. We encountered a case of inherited type I PS deficiency following a close examination for recurrent pregnancy loss and identified the mutation responsible; a novel splice donor site mutation in intron 13 of the gene appeared to have caused a frameshift with premature termination at amino acid +551. These results will contribute to the creation of an accurate database and define the molecular basis for PS deficiency.
PubMed: 38919323
DOI: 10.3400/avd.cr.23-00076 -
AlphaFold2 as a replacement for solution NMR structure determination of small proteins: Not so fast!Journal of Magnetic Resonance (San... Jun 2024The determination of a protein's structure is often a first step towards the development of a mechanistic understanding of its function. Considerable advances in...
The determination of a protein's structure is often a first step towards the development of a mechanistic understanding of its function. Considerable advances in computational protein structure prediction have been made in recent years, with AlphaFold2 (AF2) emerging as the primary tool used by researchers for this purpose. While AF2 generally predicts accurate structures of folded proteins, we present here a case where AF2 incorrectly predicts the structure of a small, folded and compact protein with high confidence. This protein, pro-interleukin-18 (pro-IL-18), is the precursor of the cytokine IL-18. Interestingly, the structure of pro-IL-18 predicted by AF2 matches that of the mature cytokine, and not the corresponding experimentally determined structure of the pro-form of the protein. Thus, while computational structure prediction holds immense promise for addressing problems in protein biophysics, there is still a need for experimental structure determination, even in the context of small well-folded, globular proteins.
PubMed: 38917639
DOI: 10.1016/j.jmr.2024.107725 -
BioRxiv : the Preprint Server For... Jun 2024Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry...
Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly used to infer the presence of protein isoforms. However, the detection and quantification processes are noisy; in particular, peptides may be erroneously detected, and most peptides, known as shared peptides, are associated to multiple protein isoforms. As a consequence, studying individual protein isoforms is challenging, and inferred protein results are often abstracted to the gene-level or to groups of protein isoforms. Here, we introduce , a novel statistical method to perform inference at the isoform level. Our method enhances the information available, by integrating mass spectrometry proteomics and transcriptomics data in a Bayesian probabilistic framework. To account for the uncertainty in the measurement process, we propose a two-layer latent variable approach: first, we sample if a peptide has been correctly detected (or, alternatively filter peptides); second, we allocate the abundance of such selected peptides across the protein(s) they are compatible with. This enables us, starting from peptide-level data, to recover protein-level data; in particular, we: i) infer the presence/absence of each protein isoform (via a posterior probability), ii) estimate its abundance (and credible interval), and iii) target isoforms where transcript and protein relative abundances significantly differ. We benchmarked our approach in simulations, and in two multi-protease real datasets: our method displays good sensitivity and specificity when detecting protein isoforms, its estimated abundances highly correlate with the ground truth, and can detect changes between protein and transcript relative abundances. is freely distributed as a Bioconductor R package, and is accompanied by an example usage vignette.
PubMed: 38915658
DOI: 10.1101/2024.06.10.598223 -
Nature Communications Jun 2024The NuA3 complex is a major regulator of gene transcription and the cell cycle in yeast. Five core subunits are required for complex assembly and function, but it...
The NuA3 complex is a major regulator of gene transcription and the cell cycle in yeast. Five core subunits are required for complex assembly and function, but it remains unclear how these subunits interact to form the complex. Here, we report that the Taf14 subunit of the NuA3 complex binds to two other subunits of the complex, Yng1 and Sas3, and describe the molecular mechanism by which the extra-terminal domain of Taf14 recognizes the conserved motif present in Yng1 and Sas3. Structural, biochemical, and mutational analyses show that two motifs are sandwiched between the two extra-terminal domains of Taf14. The head-to-toe dimeric complex enhances the DNA binding activity of Taf14, and the formation of the hetero-dimer involving the motifs of Yng1 and Sas3 is driven by sequence complementarity. In vivo assays in yeast demonstrate that the interactions of Taf14 with both Sas3 and Yng1 are required for proper function of the NuA3 complex in gene transcription and DNA repair. Our findings suggest a potential basis for the assembly of three core subunits of the NuA3 complex, Taf14, Yng1 and Sas3.
Topics: Saccharomyces cerevisiae Proteins; Saccharomyces cerevisiae; Protein Binding; Transcription Factor TFIID; Protein Subunits; TATA-Binding Protein Associated Factors; Histone Acetyltransferases; Protein Multimerization; Models, Molecular; Transcription, Genetic; Amino Acid Sequence
PubMed: 38914563
DOI: 10.1038/s41467-024-49730-y -
The Journal of Physical Chemistry. B Jun 2024Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD), a chromophore within cryptochromes,...
Cryptochromes are essential flavoproteins for circadian rhythms and avian magnetoreception. Flavin adenine dinucleotide (FAD), a chromophore within cryptochromes, absorbs blue light, initiating electron transfer processes that lead to a biological signaling cascade. A key step in this cascade is the formation of the FAD semiquinone radical (FADH), characterized through a specific red-light absorption. The absorption spectra of FADH in cryptochromes are, however, significantly different from those recorded for the cofactor in solution, primarily due to protein-induced shifts in the absorption peaks. This study employs a multiscale approach, combining molecular dynamics (MD) simulations with quantum mechanical/molecular mechanical (QM/MM) methodologies, to investigate the influence of protein dynamics on embedded FADH absorption. We emphasize the role of the protein's polarizable environment in the shaping of the absorption spectrum, crucial for accurate spectral predictions in cryptochromes. Our findings provide valuable insights into the absorption process, advancing our understanding of cryptochrome functioning.
PubMed: 38913544
DOI: 10.1021/acs.jpcb.4c02168