Mechanochemistry: pre-stress for tuning biochemical reactions in proteins
Final Report Abstract
Disulfides are the most wide spread type of protein crosslinks. They are essential for the structure, regulation and function of proteins. If a pair of two cysteine aminoacids is in the oxidized, i.e. disulfide bonded, form or not is largely determined by its redox potential. Predicting redox potentials is thus of very high interest but has yet remained a challenge. More recently, it has been proposed that disulfide bonds can be subject to strain as present in the surrounding protein scaffold they crosslink, and that the strain level is pivotal for the disulfide’s function. In this project, we developed and employed computational structure-based methods to analyze protein disulfide bonds in terms of their structures, prestress and redox potentials, in order to reveal general principles of disulfide properties in proteins. For the calculation of redox potentials, we have successfully developed a new and relatively efficient free energy perturbation method. For a set of 12 proteins from the thioredoxin superfamily, we obtained satisfying agreement with experiment, with a residual error of 40mV. Our new method is more approximate, but significantly more efficient and straightforward to use compared to the combined quantum and classical mechanical approach we have devised previously. It therefore opens up the possibility to compare redox potentials within large protein structure data sets. Secondly, we systematically analyzed the prestress in disulfide bonds as a potential hint towards a regulatory function within the protein. To this end, we employed Force Distribution Analysis (FDA), as previously developed in our group, to the available set of unique disulfide-bonded protein structures. We identified two particularly prestressed disulfide configurations, both of which turn out to be primarily located in beta-sheet regions. This is in line with the high proportion of these configurations in regulatory or ‘allosteric’ disulfide bonds, which serve as redox switches. Finally, we extended our stress analysis to allosteric proteins in order to reveal basic mechanisms of allosteric communication. More specifically, within this project, we detected specific force propagation pathways, using extensive MD simulations and FDA, upon ligand binding for two case studies, the catabolite activator protein (CAP) and Focal Adhesion Kinase (FAK). We detect significant long-range stress propagation pathways from the site of ligand binding to the regulatory or active sites of these two allosteric proteins. Taken together, this project has taken important steps forward in the field of protein mechanics in general and disulfide mechanochemistry in particular, with regard to both methods development and advances in our understanding. Most importantly, our study put forward molecular stress as a useful measure of biochemical function, with implications for protein regulation and signaling.
Publications
- (2014). Graphene mechanics: I. Efficient first principles based Morse potential. Phys Chem Chem Phys., 16(24):12591-8
B. I. Costescu, I. B. Baldus, F. Grater
(See online at https://doi.org/10.1039/c3cp55340j) - (2014). Identification of allosteric disulfides from prestress analysis. Biophys J., 107(3):672-81
B. Zhou, I. B. Baldus, W. Li, S. A. Edwards, F. Grater
(See online at https://doi.org/10.1016/j.bpj.2014.06.025) - (2015). Allosteric regulation of focal adhesion kinase by PIP2 and ATP. Biophys. J. 108(3):698-705
J. Zhou, A. K. Bronowska, J. Le Coq, D. Lietha, F. Grater
(See online at https://doi.org/10.1016/j.bpj.2014.11.3454) - (2015). Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces. PLoS Comput. Biol. 11(8):e1004358
M. Louet, C. Seifert, U. Hensen, F. Grater
(See online at https://doi.org/10.1371/journal.pcbi.1004358) - (2015). Mechanism of focal adhesion mechanosensing. PLoS Comput. Biol. 11(11):e1004593
J. Zhou, C. Aponte-Santamaria, S. Sturm, J. T. Bullerjahn, A. Bronowska, F. Grater
(See online at https://doi.org/10.1371/journal.pcbi.1004593) - (2015). Redox potentials of protein disulfide bonds from free-energy calculations. J. Phys. Chem. B. 119(17):5386-5391
W. Li, I. B. Baldus, F. Grater
(See online at https://doi.org/10.1021/acs.jpcb.5b01051)
