SFB 1078: Protonation Dynamics in Protein Function

蛋白质功能的中心机制原理，例如底物结合中的锁和钥匙原理，在过去的几十年里已经被识别出来。CRC1078已经提出了进一步的关键原则，即通过质子化动力学来控制和协调复杂的蛋白质功能。功能上相关的氢键网络的时空涨落源于质子化动力学，即质子在不同的时间和长度尺度上的运动--从飞秒到秒，从小于0.1到超过10纳米。实验工作积极地与理论和模拟相联系，以实现对所选蛋白质中质子化依赖机制的深刻理解。在参与生物能量转换的两种核心蛋白质中，质子化动力学的不同方面已经并将被研究：氧还原与细胞色素C氧化酶中的质子泵入和光系统II中的水氧化。后者将被一个新的光系统I中的质子化动力学项目所修正。虽然较大的结构变化被认为会减缓甚至阻碍蛋白质中的电子传递，但光诱导的构象变化在光致变色素和通道视紫红质中起着至关重要的作用。这些结构变化与质子化事件有关，甚至受到质子化事件的驱动。基于CRC1078的专业知识和新项目的纳入，我们将通过研究与病毒感染有关的pH门控质子通道(病毒孔蛋白)来扩大研究范围。因此，我们将在下一个资金阶段将已开发的质子化动力学方法和已获得的知识用于研究这类新的离子通道。各种先进方法的开发和适应特定蛋白质系统的需求曾经是并将成为CRC1078的一项主要资产，包括将非规范氨基酸纳入蛋白质中，使用自由电子激光的时间分辨连续飞秒X射线结晶学，高磁场下的核磁共振光谱，宽动态范围的时间分辨电子和振动光谱，以及量子力学、分子动力学模拟及其混合的多尺度计算方法。CRC1078的目的是全面理解质子化动力学及其在所选五种蛋白质功能中的作用，并将这一过程确立为蛋白质功能的一般原理。除了CRC1078预期的科学成就之外，这一真正跨学科领域的研究生培训尤其值得，因为这不仅为学术界的职业发展奠定了基础，也为行业的就业能力奠定了基础。

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.