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1. The role of energy cost on accuracy, sensitivity, specificity, speed and adaptation of T cell foreign and self recognition

   https://doi.org/10.1039/d0cp02422h  

   Shin, Gyubaek; Wang, Jin (February 2021, Physical Chemistry Chemical Physics)

   null (Ed.)

   The critical role of energy consumption in biological systems including T cell discrimination process has been investigated in various ways. The kinetic proofreading (KPR) in T cell recognition involving different levels of energy dissipation influences functional outcomes such as error rates and specificity. In this work, we study quantitatively how the energy cost influences error fractions, sensitivity, specificity, kinetic speed in terms of Mean First Passage Time (MFPT) and adaption errors. These provide the background to adequately understand T cell dynamics. It is found that energy plays a central role in the system that aims to achieve minimum error fractions and maximum sensitivity and specificity with the fastest speed under our kinetic scheme for which numerical values of kinetic parameters are specially chosen, but such a condition can be broken with varying data. Starting with the application of steady state approximation (SSA) to the evaluation of the concentration of each complex produced associated with KPR, which is used to quantify various observables, we present both analytical and numerical results in detail. 

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2. Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path

   https://doi.org/10.1038/s41467-020-19165-2  

   Dodd, Thomas; Botto, Margherita; Paul, Fabian; Fernandez-Leiro, Rafael; Lamers, Meindert H.; Ivanov, Ivaylo (October 2020, Nature Communications)

   Abstract Proofreading by replicative DNA polymerases is a fundamental mechanism ensuring DNA replication fidelity. In proofreading, mis-incorporated nucleotides are excised through the 3′-5′ exonuclease activity of the DNA polymerase holoenzyme. The exonuclease site is distal from the polymerization site, imposing stringent structural and kinetic requirements for efficient primer strand transfer. Yet, the molecular mechanism of this transfer is not known. Here we employ molecular simulations using recent cryo-EM structures and biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonuclease states ofE. colireplicative DNA polymerase Pol III. We identify structures for all intermediates, in which the transitioning primer strand is stabilized by conserved Pol III residues along the fingers, thumb and exonuclease domains. We demonstrate switching kinetics on a tens of milliseconds timescale and unveil a complete pol-to-exo switching mechanism, validated by targeted mutational experiments. 

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3. Size limits the sensitivity of kinetic schemes

   https://doi.org/10.1038/s41467-023-36705-8  

   Owen, Jeremy A.; Horowitz, Jordan M. (March 2023, Nature Communications)

   Abstract Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical mechanism for sensitivity is cooperative binding, for which it can be shown that the Hill coefficient, a sensitivity measure, cannot exceed the number of binding sites. Generalizing this fact, we find that for any kinetic scheme, at or away from thermodynamic equilibrium, a very simple structural quantity, the size of the support of a perturbation, always limits the effective Hill coefficient. We show how this bound sheds light on and unifies diverse sensitivity mechanisms, including kinetic proofreading and a nonequilibrium Monod-Wyman-Changeux (MWC) model proposed for theE. coliflagellar motor switch, representing in each case a simple, precise bridge between experimental observations and the models we write down. In pursuit of mechanisms that saturate the support bound, we find a nonequilibrium binding mechanism, nested hysteresis, with sensitivity exponential in the number of binding sites, with implications for our understanding of models of gene regulation and the function of biomolecular condensates. 

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4. Diffusion control in biochemical specificity

   https://doi.org/10.1016/j.bpj.2022.03.005  

   Alejo, Jose L.; Kempes, Christopher P.; Adamala, Katarzyna P. (April 2022, Biophysical Journal)

   Biochemical specificity is critical in enzyme function, evolution, and engineering. Here we employ an established kinetic model to dissect the effects of reactant geometry and diffusion on product formation speed and accuracy in the presence of cognate (correct) and near-cognate (incorrect) substrates. Using this steady-state model for spherical geometries, we find that, for distinct kinetic regimes, the speed and accuracy of the reactions are optimized on different regions of the geometric landscape. From this model we deduce that accuracy can be strongly dependent on reactant geometric properties even for chemically limited reactions. Notably, substrates with a specific geometry and reactivity can be discriminated by the enzyme with higher efficacy than others through purely diffusive effects. For similar cognate and near-cognate substrate geometries (as is the case for polymerases or the ribosome), we observe that speed and accuracy are maximized in opposing regions of the geometric landscape. We also show that, in relevant environments, diffusive effects on accuracy can be substantial even far from extreme kinetic conditions. Finally, we find how reactant chemical discrimination and diffusion can be related to simultaneously optimize steady-state flux and accuracy. These results highlight how diffusion and geometry can be employed to enhance reaction speed and discrimination, and similarly how they impose fundamental restraints on these quantities. 

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5. Fine-Tuning of Alanyl-tRNA Synthetase Quality Control Alleviates Global Dysregulation of the Proteome

   https://doi.org/10.3390/genes11101222  

   Kelly, Paul; Kavoor, Arundhati; Ibba, Michael (October 2020, Genes)

   null (Ed.)

   One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have evolved mechanisms to prevent erroneous aa-tRNA formation with non-cognate amino acid substrates. Of particular interest is the post-transfer proofreading activity of alanyl-tRNA synthetase (AlaRS) which prevents the accumulation of Ser-tRNAAla and Gly-tRNAAla in the cell. We have previously shown that defects in AlaRS proofreading of Ser-tRNAAla lead to global dysregulation of the E. coli proteome, subsequently causing defects in growth, motility, and antibiotic sensitivity. Here we report second-site AlaRS suppressor mutations that alleviate the aforementioned phenotypes, revealing previously uncharacterized residues within the AlaRS proofreading domain that function in quality control. 

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