% IMPORTANT: The following is UTF-8 encoded. This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.
@ARTICLE{Dutta:874555,
author = {Dutta, Annwesha and Schütz, Gunter M. and Chowdhury,
Debashish},
title = {{S}tochastic thermodynamics and modes of operation of a
ribosome: {A} network theoretic perspective},
journal = {Physical review / E},
volume = {101},
number = {3},
issn = {2470-0045},
address = {Woodbury, NY},
publisher = {Inst.},
reportid = {FZJ-2020-01509},
pages = {032402},
year = {2020},
abstract = {The ribosome is one of the largest and most complex
macromolecular machines in living cells. It polymerizes a
protein in a step-by-step manner as directed by the
corresponding nucleotide sequence on the template messenger
RNA (mRNA) and this process is referred to as
“translation” of the genetic message encoded in the
sequence of mRNA transcript. In each successful
chemomechanical cycle during the (protein) elongation stage,
the ribosome elongates the protein by a single subunit,
called amino acid, and steps forward on the template mRNA by
three nucleotides called a codon. Therefore, a ribosome is
also regarded as a molecular motor for which the mRNA serves
as the track, its step size is that of a codon and two
molecules of GTP and one molecule of ATP hydrolyzed in that
cycle serve as its fuel. What adds further complexity is the
existence of competing pathways leading to distinct cycles,
branched pathways in each cycle, and futile consumption of
fuel that leads neither to elongation of the nascent protein
nor forward stepping of the ribosome on its track. We
investigate a model formulated in terms of the network of
discrete chemomechanical states of a ribosome during the
elongation stage of translation. The model is analyzed using
a combination of stochastic thermodynamic and kinetic
analysis based on a graph-theoretic approach. We derive the
exact solution of the corresponding master equations. We
represent the steady state in terms of the cycles of the
underlying network and discuss the energy transduction
processes. We identify the various possible modes of
operation of a ribosome in terms of its average velocity and
mean rate of GTP hydrolysis. We also compute entropy
production as functions of the rates of the interstate
transitions and the thermodynamic cost for accuracy of the
translation process.},
cin = {IBI-5},
ddc = {530},
cid = {I:(DE-Juel1)IBI-5-20200312},
pnm = {551 - Functional Macromolecules and Complexes (POF3-551)},
pid = {G:(DE-HGF)POF3-551},
typ = {PUB:(DE-HGF)16},
UT = {WOS:000517966800001},
doi = {10.1103/PhysRevE.101.032402},
url = {https://juser.fz-juelich.de/record/874555},
}