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@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},
}