Previous work has established that soluble, long-lived, non-functional protein misfolded states can arise from alteration of translation-elongation kinetics. Here, we estimate the extent of this phenomenon across the nascent proteome of an organism and examine the structural and kinetic properties of t...
The geometric transformer operation is translation-invariant, rotation-equivariant and independent of the order of the atoms and order of the interactions. In order to retain the rotation equivariance of the vector states (see Supplementary Methods), the transformer attention linearly combines the scaled...
FIGURE 1.1.Prokaryotic translation initiation region. A mRNA can be functionally divided into three regions: 5 ‘UTR (untranslated region), ORF (open reading frame), and 3 ‘UTR. The first nucleotide A of the initiator codon AUG is conventionally numbered as +1. The region comprising approximate...
Therefore, the average translation rate of high expression proteins was significantly greater than that of the low expression proteins. Additionally, the correlation coefficients between the codon usage vector of the endogenous genes in the E. coli and the genes for the high or low expressed ...
One of the most prevalent domains in constitutively-expressed transcripts in both species is ubiquitin-associated/translation elongation factor (IPR015940). Figure 2 Transcript expression in different developmental stages. This figure represents the number of transcripts expressed in each stage and the ...
“PRevention Of Malnutrition In Senior Subjects in the EU”) and the informed consent; this was followed by a screening for sample selection based on gender, age, region and current living condition. The core questions consisted of eight sections: appetite, dietary habits, physical activity, food...
In orthodox seeds, the embryo is metabolically quiescent, this is why the resumption of essential processes, including transcription, translation, and DNA repair, is the first sign of germination [99,100]. There are diverse changes in protein accumulation between TI and T2 stages, the seed and ...
Clearly, there will not be one answer for all purposes, but the recent reports on climate change strongly suggest to begin considering such questions. Quantitative metrics for hypothetical improvements over MSA-based methods? If methods using single sequences without MSAs perform as well as, or ...
The UPRmt is a vigorous transcriptional reaction that has been proposed to alleviate the proteostatic stress in mitochondria by promoting folding, restricting import, and diminishing the translation of mitochondrial proteins [17]. In addition, a related basic pathway of mitochondrial damage in many ...
A new alternative to SILAC mice is the use of noncanonical amino acids (ncAAs) which can be incorporated into proteins using native or engineered protein translation machinery (Fig. 1C). ncAAs are often used to introduce bioorthogonal tags that can be labeled or enriched using click chemistry....