ArticleBioinformatics (Oxford, England)2012
Biologistics--diffusion coefficients for complete proteome of Escherichia coli.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 101 citations in OpenAlex.
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- Optimal density of bacterial cells.PLoS computational biology · 2023Article
- Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.The journal of physical chemistry. B · 2023Article
- Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death.ACS central science · 2023Article
- A proteome scale study reveals how plastic surfaces and agitation promote protein aggregation.Scientific reports · 2023Article
- Ultrafast and absolute quantification of SARS-CoV-2 on food using hydrogel RT-LAMP without pre-lysis.Journal of hazardous materials · 2023Article
- Dependence of diffusion ineLife · 2022Article
- Diffusion control in biochemical specificity.Biophysical journal · 2022Article
- Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification.Biosensors · 2022Article
- Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness.Science advances · 2021Article
- Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.Molecular cell · 2021Article
- Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines.The journal of physical chemistry letters · 2020Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationBiologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type.
resultsWe demonstrate a method for the determination of in vivo DCs for any molecule--regardless of its molecular weight, size and structure--in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. CONTACT: rholyst@ichf.edu.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.