Crowding and confinement effects on protein diffusion in vivo

MC Konopka, IA Shkel, S Cayley, MT Record… - Journal of …, 2006 - Am Soc Microbiol
The first in vivo measurements of a protein diffusion coefficient versus cytoplasmic biopolymer
volume fraction are presented. Fluorescence recovery after photobleaching yields the …

Diffusion dependent cell behavior in microenvironments

H Yu, I Meyvantsson, IA Shkel, DJ Beebe - Lab on a Chip, 2005 - pubs.rsc.org
Understanding the interaction between soluble factors and cells in the cellular microenvironment
is critical to understanding a wide range of diseases. Microchannel culture systems …

Cytoplasmic Protein Mobility in Osmotically Stressed Escherichia coli

…, KA Sochacki, BP Bratton, IA Shkel… - Journal of …, 2009 - Am Soc Microbiol
Facile diffusion of globular proteins within a cytoplasm that is dense with biopolymers is
essential to normal cellular biochemical activity and growth. Remarkably, Escherichia coli grows …

Chemical interactions of polyethylene glycols (PEGs) and glycerol with protein functional groups: Applications to effects of PEG and glycerol on protein processes

DB Knowles, IA Shkel, NM Phan, M Sternke… - Biochemistry, 2015 - ACS Publications
In this work, we obtain the data needed to predict chemical interactions of polyethylene glycols
(PEGs) and glycerol with proteins and related organic compounds and thereby interpret …

[PDF][PDF] Protein diffusion in the periplasm of E. coli under osmotic stress

KA Sochacki, IA Shkel, MT Record, JC Weisshaar - Biophysical journal, 2011 - cell.com
The physical and mechanical properties of the cell envelope of Escherichia coli are poorly
understood. We use fluorescence recovery after photobleaching to measure diffusion of …

How glutamate promotes liquid-liquid phase separation and DNA binding cooperativity of E. coli SSB protein

…, MK Shinn, E Weiland, B Nguyen, IA Shkel… - Journal of molecular …, 2022 - Elsevier
E. coli single-stranded-DNA binding protein (EcSSB) displays nearest-neighbor (NN) and
non-nearest-neighbor (NNN)) cooperativity in binding ssDNA during genome maintenance. …

Separating chemical and excluded volume interactions of polyethylene glycols with native proteins: Comparison with PEG effects on DNA helix formation

IA Shkel, DB Knowles, MT Record Jr - Biopolymers, 2015 - Wiley Online Library
Small and large PEGs greatly increase chemical potentials of globular proteins (μ 2 ), thereby
favoring precipitation, crystallization, and protein–protein interactions that reduce water‐…

[HTML][HTML] Analytic binding isotherms describing competitive interactions of a protein ligand with specific and nonspecific sites on the same DNA oligomer

OV Tsodikov, JA Holbrook, IA Shkel, MT Record - Biophysical journal, 2001 - cell.com
Many studies of specific protein-nucleic acid binding use short oligonucleotides or restriction
fragments, in part to minimize the potential for nonspecific binding of the protein. However, …

Temperature effects on RNA polymerase initiation kinetics reveal which open complex initiates and that bubble collapse is stepwise

…, C Evensen, S Dyke, IA Shkel… - Proceedings of the …, 2021 - National Acad Sciences
Transcription initiation is highly regulated by promoter sequence, transcription factors, and
ligands. All known transcription inhibitors, an important class of antibiotics, act in initiation. To …

[PDF][PDF] Basis of protein stabilization by K glutamate: Unfavorable interactions with carbon, oxygen groups

…, EJ Guinn, E Buechel, R Wong, R Sengupta, IA Shkel… - Biophysical journal, 2016 - cell.com
Potassium glutamate (KGlu) is the primary Escherichia coli cytoplasmic salt. After sudden
osmotic upshift, cytoplasmic KGlu concentration increases, initially because of water efflux and …