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Physiology and Growth
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Concluding the negative effects of rifamycin on phage replication, the direct influence of the drug on phage replication was excluded since this effect was absent in a mutant host with the drug-resistant DNA-dependent RNA polymerase (Marino et al. 1968, Passent and Kaesberg 1971; Igarashi 1972). Generally, it was assumed that RNA phage replication required participation of a short-lived host protein which became deficient within 25–30 min postinfection in the presence of rifamycin. Such a hypothetical protein was suggested to be involved in either phage RNA synthesis (Engelberg 1972; Engelberg et al. 1975), or both RNA and protein syntheses (Meier and Hofschneider 1972; Rothwell and Yamazaki 1972), or in assembly (Passent and Kaesberg 1971), or in the phage release (Engelberg and Soudry 1971a). Remarkably, direct treatment of the phage f2 with rifamycin in vitro led to a dramatic loss of infectivity by the drug binding to phage RNA at a few specific sites (Naimski and Chroboczek 1977). By this interaction, the phage capsid acted as a protective barrier, since inhibition of phage RNA infectivity occurred at 10–100 times lower molar excess of rifamycin than inhibition of infectivity of the intact phage particles.
Linezolid
Published in M. Lindsay Grayson, Sara E. Cosgrove, Suzanne M. Crowe, M. Lindsay Grayson, William Hope, James S. McCarthy, John Mills, Johan W. Mouton, David L. Paterson, Kucers’ The Use of Antibiotics, 2017
In addition, with use of laboratory-derived linezolid-resistant mutants of S. pneumoniae, mutations in a hypothetical protein predicted to encode a ribosomal methyltransferase (spr033) were found to increase linezolid resistance (Feng et al., 2009). A deletion in an S. aureus homolog of this gene (SAV1444) has also been found in a clinical linezolid-resistant isolate (in addition to a G2576T ribosomal mutation) (Feng et al., 2009).
Pindborg Tumor-Associated Amyloid Proteins
Published in Gilles Grateau, Robert A. Kyle, Martha Skinner, Amyloid and Amyloidosis, 2004
C. L. Murphy, S. Wang, D.P. Kestler, S.D. Macy, T.K. Williams, E.R. Carlson, D.T. Weiss, A. Solomon
From our studies of 3 additional CEOT amyloid-associated cases, we have confirmed that the FLJ20513-related protein was present and, further, that all the samples contained a heretofore unrecognized product of the FLJ40850 gene. In two cases, other components derived from different mRNA transcripts arising from this ORF also were detected. Notably, the N-termini of #3 and #2, located 8 and 29 residues proximal to the translated portion of cDNA FLJ20513, respectively, seemingly were not derived from either the FLJ20513 or FLJ40850 gene. Conceivably, these molecules could have resulted from degradation of the hypothetical protein arising from the entire ORF transcript contained in THC 1981099. Although the function of this gene (or products) is as yet unknown, it is of interest that it is located on chromosome 4 adjacent to those specifying salivary proteins.
Reverse phase protein arrays in acute leukemia: investigative and methodological challenges
Published in Expert Review of Proteomics, 2021
Fieke W. Hoff, Terzah M. Horton, Steven M. Kornblau
A potential application of proteomics may be to guide therapy selection. Given that the majority of drugs currently being tested in clinical trials target proteins, we hypothesize that abnormal protein expression could identify a critical dependency in leukemia and could pinpoint a targeted therapy across leukemia subgroups. High-protein expression that results in chemotherapy resistance could result in the identification of a patient targeted for protein inhibition, while proteins with lower expression could act as target for replacement or re-activation. This would result in rational selection of therapeutic agents, either as single agent or in combination, rather than ‘randomly’ selecting drugs in the absence of clinical features previously identified as conferring sensitivity/ resistance. Hypothetical protein targets can be identified from either a CON (and can thus also be a target across other subgroups) or a SIG. Because we are identifying aberrant protein expression patterns and not at genetic events, there is a limited number of protein expression patterns that tell us in which direction we should target.
Sounds interesting: can sonification help us design new proteins?
Published in Expert Review of Proteomics, 2019
Sebastian L. Franjou, Mario Milazzo, Chi-Hua Yu, Markus J. Buehler
Sonification is often used as a way to make new sounds or musical compositions based on scientific data. By introducing a reverse mapping, we can do the opposite, and use music as a design tool for making proteins. Any piece of music following the conventions of our ‘protein music’ contains the sequence of a hypothetical protein, with its secondary structure and folding – the latter encoded in the form of a contact map of geometrically close amino acids by multiple musical voices. Empowered by the emergent discipline of machine learning (ML), one can adopt a ML model to study the embedded patterns in this sonified protein data and use them to generate new proteins. Moreover, we could design de novo proteins by using tools previously reserved to music, such as interpolating between two proteins. The representation of proteins as music encodes the amino acid sequence as well as secondary structure and folding, and allows us to conveniently embed all of this information into a type of data that can be well processed by a neural network. This makes this representation especially well-suited to machine-learning-powered applications: for example, by training a neural network on specific types of protein, we could design new proteins that share characteristics with the proteins of the dataset. Some of these concepts have been explored in [9], where a ML approach was used to compose new music from musical data derived from proteins that was translated back into proteins (for audio examples, please see [13]).
Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola
Published in Journal of Oral Microbiology, 2020
Lin Xin Kin, Catherine A. Butler, Nada Slakeski, Brigitte Hoffmann, Stuart G. Dashper, Eric C. Reynolds
Of the identified putative proteases (Supplementary Table S5), microarray data from co-culture of P. gingivalis with T. denticola in a continuous culture system showed increased gene expression of PG0753 and PG0383, in comparison to monoculture [22]. Therefore, the putative PrtQ collagenase (PG0753) that belongs to the U32 peptidase family was also selected for further analysis. PG0383, annotated as a regulated intramembrane proteolytic (RIP) metalloprotease RseP, was considered unlikely to be involved in free glycine release and was therefore not selected for further analysis. Although PG0753 was predicted to be located in the cytoplasm by PSORTb, it was selected for further investigation as the possibility of glycine-containing peptides being hydrolyzed intracellularly and the resultant free glycine being released into the environment could not be ruled out. Therefore, genes encoding PG0753, PG1605, and PG1788 were selected for inactivation. The resulting mutant strains were confirmed by PCR and whole-genome sequencing was performed to confirm the veracity of the mutants. All sequenced mutants had the appropriate target genes deleted from their genomes and strains ∆PG0753 and ∆PG1605 had no additional SNPs or mutations when compared to the laboratory wild type strain. However, two gene loci in ∆PG1788 each had a single nucleotide polymorphism that resulted in substitution of a highly conserved amino acid, as determined using COBALT (data not shown), which should not affect the resulting protein structure or function (Supplementary Table S6). The affected proteins were PG0867, a hypothetical protein, and PG1864, a TIR-domain containing protein.