Living organisms regularly need to cope with fluctuating environments during their life cycle, including changes in temperature, pH, the accumulation of reactive oxygen species, and more. These fluctuations can lead to a widespread protein unfolding, aggregation, and cell death. Therefore, cells have evolved a dynamic and stress-specific network of molecular chaperones, which maintain a "healthy" proteome during stress conditions. ATP-independent chaperones constitute one major class of molecular chaperones, which serve as first-line defense molecules, protecting against protein aggregation in a stress-dependent manner. One feature these chaperones have in common is their ability to utilize structural plasticity for their stress-specific activation, recognition, and release of the misfolded client. In this paper, we focus on the functional and structural analysis of one such intrinsically disordered chaperone, the bacterial redox-regulated Hsp33, which protects proteins against aggregation during oxidative stress. Here, we present a toolbox of diverse techniques for studying redox-regulated chaperone activity, as well as for mapping conformational changes of the chaperone, underlying its activity. Specifically, we describe a workflow which includes the preparation of fully reduced and fully oxidized proteins, followed by an analysis of the chaperone anti-aggregation activity in vitro using light-scattering, focusing on the degree of the anti-aggregation activity and its kinetics. To overcome frequent outliers accumulated during aggregation assays, we describe the usage of Kfits, a novel graphical tool which allows easy processing of kinetic measurements. This tool can be easily applied to other types of kinetic measurements for removing outliers and fitting kinetic parameters. To correlate the function with the protein structure, we describe the setup and workflow of a structural mass spectrometry technique, hydrogen-deuterium exchange mass spectrometry, that allows the mapping of conformational changes on the chaperone and substrate during different stages of Hsp33 activity. The same methodology can be applied to other protein-protein and protein-ligand interactions.
Bibliographical noteFunding Information:
The authors are thankful to Meytal Radzinski for her helpful discussions and critical reading of the article, and to Patrick Griffin and his lab members for their unlimited assistance while establishing the HDX analysis platform. The authors are grateful to the German-Israel Foundation (I-2332-1149.9/2012), the Binational Science Foundation (2015056), the Marie-Curie integration grant (618806), the Israel Science Foundation (1765/13 and 2629/16), and the Human Frontier Science Program (CDA00064/2014) for their financial support.
© 2018, Journal of Visualized Experiments. All rights reserved.
- ATP-independent chaperone
- Hydrogen-deuterium exchange
- Issue 136
- Protein aggregation
- Protein aggregation kinetics and analysis
- Protein oxidation and reduction
- Redox-regulated chaperone