Global phylogenetic analysis of the RNA-dependent RNA polymerase with OrViT (OrthornaVirae Tree)
Frontiers in Virology, 2022 Viruses of the kingdom Orthornavirae are the causative agents of many diseases in humans, animals and plants and play an important role in the ecology of the biosphere.
Dong-Qiang Cheng +3 more
doaj +1 more source
Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis [PDF]
Physical Review E 77, 011921 (2008), 2007 RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input to move along the track formed by a DNA. In many circumstances, which are described in this paper, a large number
arxiv +1 more source
Bayesian inference of polymerase dynamics over the exclusion process [PDF]
arXiv, 2021 Transcription is a complex phenomenon that permits the conversion of genetic information into phenotype by means of an enzyme called RNA polymerase, which erratically moves along and scans the DNA template. We perform Bayesian inference over a paradigmatic mechanistic model of non-equilibrium statistical physics, i.e., the asymmetric exclusion ...
arxiv
Molecular Biomedicine, 2021 Repurposing of existing drugs and drug candidates is an ideal approach to identify new potential therapies for SARS-CoV-2 that can be tested without delay in human trials of infected patients.
Sakshi Piplani +3 more
doaj +1 more source
Transcription-translation machinery -- an autocatalytic network coupling all cellular cycles and generating a plethora of growth laws [PDF]
arXiv, 2021 Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known relations, as well as new relations that we derive, stems from a universal autocatalytic network common to all bacteria,
arxiv
Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir
Viruses, 2019 Remdesivir (GS-5734) is a 1′-cyano-substituted adenosine nucleotide analogue prodrug that shows broad-spectrum antiviral activity against several RNA viruses.
Egor P. Tchesnokov +3 more
doaj +1 more source
How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene Expression [PDF]
, 2019 Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad of sequenced regulatory architectures as well as to design novel synthetic circuits.
arxiv +1 more source
Glutathionylation of dengue and Zika NS5 proteins affects guanylyltransferase and RNA dependent RNA polymerase activities. [PDF]
PLoS ONE, 2018 It has been estimated for dengue infection that the global population at risk is 3.5 billion people, which makes dengue an important public health problem. The causative agents of dengue are dengue viruses.
Chonticha Saisawang +4 more
doaj +1 more source
Stochastic Models of Regulation of Transcription in Biological Cells [PDF]
arXiv, 2022 In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment of the cell is not favorable.
arxiv
Theoretical model of transcription based on torsional mechanics of DNA template [PDF]
Journal of Statistical Physics 174 (2019) 1316, 2018 Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed experimentally, much of physical behavior of transcription remains largely unknown.
arxiv +1 more source