Publications by authors named "Collin Marshall"

2 Publications

  • Page 1 of 1

Quantitative analysis of mitochondrial ATP synthesis.

Math Biosci 2021 Jun 17:108646. Epub 2021 Jun 17.

Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, 48109, MI, USA. Electronic address:

We present a computational framework for analyzing and simulating mitochondrial ATP synthesis using basic thermodynamic and kinetic principles. The framework invokes detailed descriptions of the thermodynamic driving forces associated with the processes of the electron transport chain, mitochondrial ATP synthetase, and phosphate and adenine nucleotide transporters. Assembling models of these discrete processes into an integrated model of mitochondrial ATP synthesis, we illustrate how to analyze and simulate in vitro respirometry experiments and how models identified from in vitro experimental data effectively explain cardiac respiratory control in vivo. Computer codes for these analyses are embedded as Python scripts in a Jupyter Book to facilitate easy adoption and modification of the concepts developed here. This accessible framework may also prove useful in supporting educational applications. All source codes are available on at https://beards-lab.github.io/QAMAS_book/.
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http://dx.doi.org/10.1016/j.mbs.2021.108646DOI Listing
June 2021

Hierarchical mechanism of amino acid sensing by the T-box riboswitch.

Nat Commun 2018 05 14;9(1):1896. Epub 2018 May 14.

Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.

In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5' half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification. Using single-molecule fluorescence microscopy, we have probed the kinetic and structural underpinnings of tRNA binding to a glycyl T-box riboswitch. We observe a two-step mechanism where fast, dynamic recruitment of tRNA by Stem-I is followed by ultra-stable anchoring by the downstream antiterminator, but only without aminoacylation. Our results support a hierarchical sensing mechanism wherein dynamic global binding of the tRNA body is followed by localized readout of its aminoacylation status by snap-lock-based trapping.
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http://dx.doi.org/10.1038/s41467-018-04305-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5951919PMC
May 2018
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