Impact of crowded environments on binding between protein and single-stranded DNA
Journal article, 2021

The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA–protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein’s hydration shell via soft interactions that, in turn, tune protein–ligand binding dynamics and affinity.

Author

Birgit Köhn

University of Konstanz

Patricia Schwarz

University of Konstanz

Pernilla Wittung Stafshede

Chalmers, Biology and Biological Engineering, Chemical Biology

M. Kovermann

University of Konstanz

Scientific Reports

2045-2322 (ISSN)

Vol. 11 1 17682

Subject Categories

Physical Chemistry

Biophysics

Structural Biology

DOI

10.1038/s41598-021-97219-1

PubMed

34480058

More information

Latest update

9/22/2021