Review of: "Impact of crowded environments on binding between protein and single-stranded DNA"
Year: 2021
Type: peer-review
Abstract: BackgroundCells retain large amounts of macromolecules within their plasma membranes, up to 400 g/L depending on their physiologic state. [1]Mutual exclusion is a fundamental property of polymers in solution. [2][3] Classically, this excluded volume effect is treated as hard-core repulsion: an entropic depletion force that drives folding and interactions towards more compact states. [4][5] More recent studies show that depletion forces are supplemented by lower-potential "soft" interactions which may even be attractive. [6][7][8][9][10] While the impact of crowders on protein stability and dynamics in solution has been recognized since the early works of Ogston [11] and Laurent [12] , their theoretical treatment continues to be debated. [13][14][15][16][17][18] Experimental measurements remain a mainstay of studying biological interactions in a crowded environment.In their study, Köhn et al. characterize the impact of macromolecular crowding on the binding of singlestranded DNA, specifically oligothymidines (dTn, n = 5 to 7 nucleotides) by cold shock protein B from Bacillus subtilis (BsCspB, 67 residues), using polyethylene glycol (PEG1 and PEG8, 1k and 8k), ethylene glycol (EG), dextran (Dex20, 20k), and glucose as cosolutes.Monomer-polymer pairs enable a comparison of both chemical composition and size.On the one hand, PEG and EG act more like an organic solvent, which displays hydrophobic tendencies.On the other hand, Dex and glucose are more polar.The authors hypothesize that weak chemical interactions dominate excluded volume effects in crowding protein/DNA binding. Technical reviewBsCspB structure is conserved under crowding.High concentrations of any cosolute always raises a concern of specific interactions that would obscure the intended interpretation of the data.To assess this possibility, the authors used heteronuclear NMR spectroscopy to probe the equilibrium structures of free BsCspB and dTn-bound complexes.An extensive series of 1D ( 1 H and 31 P) and 2D( 1 H-15 N HSQC and 1 H-13 C HSQC) experiments showed substantially similar chemical shift perturbations (CSP) or intensity in both the protein and DNA upon binding whether in dilute solution or up to 300 g/L of crowding agent.While the CSP data is presented as overlays of the free and bound states under identical Qeios, CC-BY 4.0
DOI: 10.32388/1pziy1
Authors: Gregory Poon, Tyler Vernon
Institution: Georgia State University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W3215112750