Related papers: Bacterial pathways for the biosynthesis of ubiquin…
This article presents the results of a study concerning interstellar molecules which are useful for the bookkeeping of the organic content of the universe and for providing a glimpse into prebiotic conditions on Earth and in other…
The mating pathway in \emph{Saccharomyces cerevisiae} is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and…
MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused…
Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of…
The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
Biomolecular condensates govern essential cellular processes yet elude description by traditional equilibrium models. This roadmap, distilled from structured discussions at a workshop and reflecting the consensus of its participants,…
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the…
Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum…
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than…
The emerging field of immunometabolism has underscored the central role of metabolic pathways in orchestrating immune cell function. Far from being passive background processes, metabolic activities actively regulate key immune responses.…
Motile cilia are a striking example of functional cellular organelle, conserved across all the eukaryotic species. Motile cilia allow swimming of cells and small organisms and transport of liquids across epithelial tissues. Whilst the…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no…
Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…
All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and…
Phagocytosis is the process by which cells, which are 5 to 10 times larger than the particle size, engulf particles, holding substantial importance in various biological contexts ranging from the nutrient uptake of unicellular organisms to…
Ubiquitin tags diseased proteins and initiates an enzyme conjugation cascade, which has three stages. The first-stage enzyme Uba1 (E1) has evolved only modestly from slime mold to humans, and is > 14 times larger than Ub. Here we use…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…