Results 1 to 10 of about 2,891 (24)

Mediating Ribosomal Competition by Splitting Pools [PDF]

LCSS Vol 5 Issue 5 (Nov 2020), 2020
Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing resources in the cell, such as ATP, RNA polymerase, amino acids, and ribosomes. Ribosomal competition among strands of
arxiv   +1 more source

Polysomally Protected Viruses [PDF]

Phys. Biol. 18 046009 (2021), 2021
It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and how its presence might be detected by ribosome profiling.
arxiv   +1 more source

Growth-laws and invariants from ribosome biogenesis in lower Eukarya [PDF]

Phys. Rev. Research 3, 013020 (2021), 2020
Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria, whereas Bacteria have none.
arxiv   +1 more source

Traffic of interacting ribosomes: effects of single-machine mechano-chemistry on protein synthesis [PDF]

Physical Review E 75, 021902 (2007), 2006
Many ribosomes simultaneously move on the same messenger RNA (mRNA), each separately synthesizing the protein coded by the mRNA. Earlier models of ribosome traffic represent each ribosome by a ``self-propelled particle'' and capture the dynamics by an extension of the totally asymmetric simple exclusion process (TASEP).
arxiv   +2 more sources

Control of ribosome traffic by position-dependent choice of synonymous codons [PDF]

Phys. Biol. 10 (2013) 056011, 2013
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein.
arxiv   +1 more source

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding [PDF]

Physical Biology, 8 (2011) 026005, 2010
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in
arxiv   +1 more source

Stochastic theory of protein synthesis and polysome: ribosome profile on a single mRNA transcript [PDF]

Journal of Theoretical Biology, vol.289, 36-46 (2011), 2011
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the track. Often several ribosomes may translate the same (mRNA) simultaneously.
arxiv   +1 more source

Dynamics of ribosomes in mRNA translation under steady and non-steady state conditions [PDF]

Phys. Rev. E 101, 062404 (2020), 2020
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally asymmetric simple exclusion process (TASEP) using realistic kinetic parameters.
arxiv   +1 more source

Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination [PDF]

Proc. Natl. Acad. Sci. USA 105, 18159-18164 (2008), 2008
In fast growing bacteria, ribosomal RNA (rRNA) is required to be transcribed at very high rates to sustain the high cellular demand on ribosome synthesis. This results in dense traffic of RNA polymerases (RNAP). We developed a stochastic model, integrating results of single-molecule and quantitative in vivo studies of E.
arxiv   +1 more source

Stochastic kinetics of ribosomes: single motor properties and collective behavior [PDF]

Physical Review E, vol.80, 011908 (2009), 2009
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein.
arxiv   +1 more source