Bachler Zachary T, Brown Michael F
Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona.
Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona.
Biophys J. 2024 Dec 17;123(24):4167-4179. doi: 10.1016/j.bpj.2024.11.012. Epub 2024 Nov 16.
Structural biology relies on several powerful techniques, but these tend to be limited in their ability to characterize protein fluctuations and mobility. Overreliance on structural approaches can lead to omission of critical information regarding biological function. Currently there is a need for complementary biophysical methods to visualize these mobile aspects of protein function. Here, we review hydrostatic and osmotic pressure-based techniques to address this shortcoming for the paradigm of rhodopsin. Hydrostatic and osmotic pressure data contribute important examples, which are interpreted in terms of an energy landscape for hydration-mediated protein dynamics. We find that perturbations of rhodopsin conformational equilibria by force-based methods are not unrelated phenomena; rather they probe various hydration states involving functional proton reactions. Hydrostatic pressure acts on small numbers of strongly interacting structural or solvent-shell water molecules with relatively high energies, while osmotic pressure acts on large numbers of weakly interacting bulk-like water molecules with low energies. Local solvent fluctuations due to the hydration shell and collective water interactions affect hydrogen-bonded networks and domain motions that are explained by a hierarchical energy landscape model for protein dynamics.
结构生物学依赖于多种强大的技术，但这些技术在表征蛋白质波动和流动性方面的能力往往有限。过度依赖结构方法可能会导致遗漏有关生物学功能的关键信息。目前，需要互补的生物物理方法来可视化蛋白质功能的这些动态方面。在这里，我们回顾基于静水压力和渗透压的技术，以解决视紫红质范例中的这一缺点。静水压力和渗透压数据提供了重要的示例，这些示例根据水合介导的蛋白质动力学的能量景观来解释。我们发现，基于力的方法对视紫红质构象平衡的扰动并非无关现象；相反，它们探测涉及功能性质子反应的各种水合状态。静水压力作用于少量具有相对较高能量的强相互作用结构或溶剂壳水分子，而渗透压作用于大量具有低能量的弱相互作用类本体水分子。由水合壳和集体水相互作用引起的局部溶剂波动会影响氢键网络和结构域运动，这可以通过蛋白质动力学的层次能量景观模型来解释。
