title: A Generalized Michaelis-Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon.
abstract: The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a 'biologically motivated' generalization of the Michaelis-Menten formula for the average rate of enzymatic reactions. This generalized Michaelis-Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.
authors.affiliation: Department of Physics, Indian Institute of Technology, Kanpur, 208016, India.
authors.forename: Annwesha
authors.initials: A
authors.lastname: Dutta
authors.affiliation: Department of Physics, Indian Institute of Technology, Kanpur, 208016, India. debch@iitk.ac.in.
authors.forename: Debashish
authors.initials: D
authors.lastname: Chowdhury
mesh_terms: D003062:Codon / Q000235:genetics; D007700:Kinetics; D055641:Mathematical Concepts; D008954:Models, Biological; D010441:Peptide Chain Elongation, Translational / Q000235:genetics; D014176:Protein Biosynthesis / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism; D013269:Stochastic Processes
chemical_list: D003062:Codon; D012333:RNA, Messenger; D012343:RNA, Transfer
keywords: Dwell time; Master equation; Michaelis–Menten equation; Ribosome; Translation