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SFB 1078:  Protonation Dynamics in Protein Function

Subject Area Biology
Term from 2013 to 2024
Website Homepage
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 221545957
 
Central mechanistic principles of protein function, such as the lock-and-key principle in substrate binding, have been identified over the past decades. CRC1078 has proposed to put a further key principle into place, namely the control and coordination of complex protein functions by protonation dynamics. Spatio-temporal fluctuations of the functionally relevant hydrogen-bonded networks result from protonation dynamics, that is, the movement of protons on various time and length scales – from femtoseconds to seconds and from less than 0.1 to more than 10 nm. The experimental works are actively linked to theory and simulations to achieve a profound understanding of protonation-dependent mechanisms in the selected proteins. Different facets of protonation dynamics have been and will be studied in two central proteins involved in biological energy conversion: Oxygen reduction coupled to proton pumping in cytochrome c oxidase and water oxidation in photosystem II. The latter will be amended by a new project on protonation dynamics in photosystem I. Whereas larger structural changes are supposed to slow down or even obstruct electron transfer in proteins, light-induced conformational changes play vital roles in phytochromes and channelrhodopsins. These structural changes are associated with or even driven by protonation events. Based on the expertise of CRC1078 and the inclusion of new projects, we will extend the scope of research by investigating pH-gated proton channels that are involved in viral infection (viroporins). Therefore, we will transfer the developed methodologies and acquired knowledge on protonation dynamics to study this new class of ion channels in the next funding period. The development and adaption of various advanced methods to the requirements of the specific protein systems was and will be a major asset of this CRC1078, including the incorporation of non-canonical amino acids into proteins, time-resolved serial femtosecond X-ray crystallography using free electron lasers, nuclear magnetic resonance spectroscopy at high magnetic fields, time-resolved electronic and vibrational spectroscopies in a wide dynamic range, and multiscale computational approaches such as quantum-mechanics, molecular dynamics simulations and their hybrids. The application of such sophisticated techniques to the research agenda of the CRC is challenging as most of the proteins are integral membrane proteins.In conclusion, CRC1078 aims at the comprehensive understanding of protonation dynamics and their role in the function of the five selected proteins and to establish this process as a generic principle in protein function. Beyond the anticipated scientific success of CRC1078, the training of graduate students in this truly interdisciplinary field is particularly rewarding as a basis is generated for career development not only in academia but also for the employability in industry.
DFG Programme Collaborative Research Centres
International Connection Israel

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Applicant Institution Freie Universität Berlin
Spokespersons Professor Dr. Holger Dau, until 3/2017; Professor Dr. Joachim Heberle, since 3/2017
 
 

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