Definition Of The Minimal Contents For The Molecular Simulation Of The Yeast Cytoplasm

Vijay Phanindra Srikanth Kompella, Ian Stansfield, Maria Carmen Romano, Ricardo L. Mancera* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

The cytoplasm is a densely packed environment filled with macromolecules with hindered diffusion. Molecular simulation of the diffusion of biomolecules under such macromolecular crowding conditions requires the definition of a simulation cell with a cytoplasmic-like composition. This has been previously done for prokaryote cells (E. coli) but not for eukaryote cells such as yeast as a model organism. Yeast proteomics datasets vary widely in terms of cell growth conditions, the technique used to determine protein composition, the reported relative abundance of proteins, and the units in which abundances are reported. We determined that the gene ontology profiles of the most abundant proteins across these datasets are similar, but their abundances vary greatly. To overcome this problem, we chose five mass spectrometry proteomics datasets that fulfilled the following criteria: high internal consistency, consistency with published experimental data, and freedom from GFP-tagging artefacts. Using these datasets, the contents of a simulation cell containing a single 80S ribosome were defined, such that the macromolecular density and the mass ratio of ribosomal-to-cytoplasmic proteins were consistent with experiment and chosen datasets. Finally, multiple tRNAs were added, consistent with their experimentally-determined number in the yeast cell. The resulting composition can be readily used in molecular simulations representative of yeast cytoplasmic macromolecular crowding conditions to characterise a variety of phenomena, such as protein diffusion, protein-protein interactions and biological processes such as protein translation.
Original languageEnglish
Article number97
Number of pages9
JournalFrontiers in Molecular Biosciences
Volume6
Early online date2 Oct 2019
DOIs
Publication statusPublished - Oct 2019

Fingerprint

Yeast
Proteins
Chemical analysis
Cell growth
Biomolecules
Transfer RNA
Macromolecules
Escherichia coli
Mass spectrometry
Ontology
Genes
Cells
Experiments

Keywords

  • macromolecular crowding
  • proteomics
  • protein translation
  • yeast
  • molecular dynamics

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Biochemistry

Cite this

Definition Of The Minimal Contents For The Molecular Simulation Of The Yeast Cytoplasm. / Kompella, Vijay Phanindra Srikanth; Stansfield, Ian; Romano, Maria Carmen; Mancera, Ricardo L. (Corresponding Author).

In: Frontiers in Molecular Biosciences, Vol. 6, 97, 10.2019.

Research output: Contribution to journalArticle

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