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 ...
A. S. Spirin +11 more
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Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding [PDF]
Physical Biology, 8 (2011) 026005, 2011 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 ...
Ajeet K Sharma +10 more
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Ribosome recycling, diffusion, and mRNA loop formation in translational regulation [PDF]
Biophysical Journal, 85, 755-773, (2003), 2003 We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to the ...
Arfken +51 more
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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.
Mitarai, Namiko, Pedersen, Steen
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Gene length as a regulator for ribosome recruitment and protein synthesis : theoretical insights [PDF]
Scientific Reports 7, Article number: 17409 (2017), 2017 The authors would like to acknowledge the funding provided by the European Union Seventh Framework Programme [FP7/2007–2013] (NICHE; grant agreement 289384) (LDF).
Ciandrini, Luca +2 more
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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.
Agirrezabala +52 more
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Ribosomal proteins: functions beyond the ribosome [PDF]
Journal of Molecular Cell Biology, 2015 Although ribosomal proteins are known for playing an essential role in ribosome assembly and protein translation, their ribosome-independent functions have also been greatly appreciated. Over the past decade, more than a dozen of ribosomal proteins have been found to activate the tumor suppressor p53 pathway in response to ribosomal stress. In addition,
Peng Liao +4 more
openaire +4 more sources
Cotranslational folding of proteins on the ribosome.
Biomolecules, 2020 Many proteins in the cell fold cotranslationally within the restricted space of the polypeptide exit tunnel or at the surface of the ribosome. A growing body of evidence suggests that the ribosome can alter the folding trajectory in many different ways ...
Liutkute, M., Rodnina, M., Samatova, E.
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Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization [PDF]
J. Mol. Biol. 382, 236-245 (2008), 2008 Individual mRNAs are translated by multiple ribosomes that initiate translation with a few seconds interval. The ribosome speed is codon dependant, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By
Mitarai, Namiko +2 more
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Ribosome Flow Model with Extended Objects [PDF]
arXiv, 2017 We study a deterministic mechanistic model for the flow of ribosomes along the mRNA molecule, called the ribosome flow model with extended objects (RFMEO).
Margaliot, Michael +2 more
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