Leiden University Scholarly Publications

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Di Savino, A. (2021)

Understanding protein complex formation: the role of charge distribution in the encounter complex

Doctoral Thesis
Protein–protein complexes are formed via transient states called encounter complexes that greatly influence the formation of the stereospecific complex. Electrostatic charges on the protein surfaces play a major role in encounter complexes of electron transfer proteins. The complex formed by cytochrome c (Cc) and cytochrome c peroxidase (CcP) has been studied intensively because it is an excellent model to explore the properties of transient protein-protein interactions. PRE experiments previously described the encounter complex formed by the two proteins in detail. In this thesis we tested to what degree the electrostatic patch on CcP is optimized to enhance the rate of the formation of the stereospecific complex. Using paramagnetic NMR in combination with Monte Carlo simulations and stopped flow spectrophotometry, we investigate several CcP mutants with reengineered charged patches to create new encounter complexes and measure their effects on electron transfer from Cc to CcP....Show moreProtein–protein complexes are formed via transient states called encounter complexes that greatly influence the formation of the stereospecific complex. Electrostatic charges on the protein surfaces play a major role in encounter complexes of electron transfer proteins. The complex formed by cytochrome c (Cc) and cytochrome c peroxidase (CcP) has been studied intensively because it is an excellent model to explore the properties of transient protein-protein interactions. PRE experiments previously described the encounter complex formed by the two proteins in detail. In this thesis we tested to what degree the electrostatic patch on CcP is optimized to enhance the rate of the formation of the stereospecific complex. Using paramagnetic NMR in combination with Monte Carlo simulations and stopped flow spectrophotometry, we investigate several CcP mutants with reengineered charged patches to create new encounter complexes and measure their effects on electron transfer from Cc to CcP. The results indicate that the interactions with Cc are affected more by the total charge of CcP surface than the specific distribution of the charges, bringing into question the concept of electrostatic patches being highly optimized by evolution.
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Protein–protein interaction
Encounter complex
Paramagnetic nuclear magnetic resonance (NMR)
All authors
Di Savino, A.
Supervisor
Ubbink, M.; Aerts, J.M.F.G.
Committee
Overkleeft, H.S.; Dame, R.T.; Schreiber, G.; Pauleta, S.; Huber, M.I.
Qualification
Doctor (dr.)
Awarding Institution
Leiden Institute of Chemistry (LIC), Faculty of Science, Leiden University
Date
2021-06-15

Funding

Sponsorship
This work was financially supported by the Netherlands Organisation for Scientific Research (NWO-CW grant 711.013.007).