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000874555 1001_ $$0P:(DE-HGF)0$$aDutta, Annwesha$$b0
000874555 245__ $$aStochastic thermodynamics and modes of operation of a ribosome: A network theoretic perspective
000874555 260__ $$aWoodbury, NY$$bInst.$$c2020
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000874555 520__ $$aThe 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.
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000874555 7001_ $$0P:(DE-Juel1)130966$$aSchütz, Gunter M.$$b1
000874555 7001_ $$0P:(DE-HGF)0$$aChowdhury, Debashish$$b2$$eCorresponding author
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000874555 999C5 $$1A. S. Spirin$$2Crossref$$oA. S. Spirin Ribosomes 2002$$tRibosomes$$y2002
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1146/annurev.biophys.093008.131427
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1146/annurev-biochem-060408-173330
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1038/nsmb.3177
000874555 999C5 $$1J. Frank$$2Crossref$$9-- missing cx lookup --$$a10.1017/CBO9781139003704$$y2011
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.str.2015.04.007
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1038/nature09206
000874555 999C5 $$2Crossref$$oRibosomes: Structure, Function, and Dynamics 2011$$tRibosomes: Structure, Function, and Dynamics$$y2011
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1371/journal.pcbi.1000865
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jtbi.2005.08.007
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1007/s00249-012-0879-4
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1371/journal.pone.0134994
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.cell.2013.03.032
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1119/1.2757628
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevE.80.011908
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevE.79.011916
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.physrep.2013.03.005
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/1478-3975/8/2/026005
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevE.82.031912
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1007/s11538-017-0266-5
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.compbiolchem.2007.07.003
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.bpj.2016.04.004
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1093/nar/gku646
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/0034-4885/75/12/126001
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpclett.7b03197
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/1361-6633/aab3ed
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevE.74.011906
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/0953-8984/28/15/153004
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevX.6.041064
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.physa.2017.10.024
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1142/S1793048010001214
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.bpj.2010.02.040
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1140/epje/i2011-11026-7
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.4973544
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/RevModPhys.69.1269
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1098/rstb.2016.0182
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1038/nsmb.3193
000874555 999C5 $$1T. L. Hill$$2Crossref$$9-- missing cx lookup --$$a10.1007/978-1-4612-3558-3$$y1989
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/0022-5193(66)90137-8
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/RevModPhys.48.571
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/0953-8984/17/47/010
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1007/s10955-010-0050-5
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1209/0295-5075/77/50002
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/1742-5468/2007/07/P07020
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1038/nrm1982
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.7554/eLife.03406
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1371/journal.pcbi.1003909
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.febslet.2014.08.035
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevE.94.052117
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1088/1367-2630/aaa15f
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1103/PhysRevE.79.011917
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1126/science.1184939
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1039/b903536b
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1023/A:1004589714161
000874555 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jtbi.2018.11.025