Water, protons, and ions biomolecular systems

水在生物分子的稳定性、动力学和功能中起着中心作用(悍马，摩尔。太棒了。2007)。通过疏水效应和氢键相互作用，水是蛋白质折叠的主要因素。在许多酶中，它直接参与催化功能。具体地说，蛋白质内部的水经常调节质子在溶剂介质和活性中心之间的转移。这种水通常被限制在相对非极性的纳米尺度的孔和腔中，表现出非常不寻常的性质，如高水流动性、高质子传导性，或者在填充状态和空状态之间的急剧转变。蛋白质在生物功能中利用承压水的这些不同寻常的特性，例如，确保水在水通道中的快速流动，或在质子泵和酶中开启质子流动。 在与Sol Gruner教授(康奈尔大学)和Brian Matthews教授(俄勒冈大学和HHMI)的实验小组合作下，我们已经表明T4溶菌酶突变体中大空腔的水填充对溶剂条件高度敏感(Collins等人，J.Mol)。比奥尔。2007)。通过结合高压X射线结晶学和分子动力学模拟，我们发现适度的压力会导致大约四个水分子进入空腔，而蛋白质本身基本上保持不变。在压力下，空腔保持坚硬，而蛋白质的其他区域则发生显著变形。蛋白质内部的合成图像是构象波动的侧基提供了类似液体的环境，这使得水在动力学和热力学上都是可行的。 我们与缅因州大学的Jay Rasaiah教授合作，研究了深海生物表层的一种超稳定蛋白质--四臂藻的内部水化作用(Yen等人，J.Am化学。SoC。2007)。这种极不寻常的蛋白质展示了很可能是迄今为止发现的所有蛋白质中最大的非极性内部洞。我们发现，在这个空腔中，由7到9个水分子组成的氢键水团簇在环境温度和最适生长温度365K下都是热力学稳定的。由最佳尺寸团簇的转移自由能衡量的稳定性随着温度的升高而降低。因此，充水是由转移能驱动的，而不是由转移熵驱动的，两者都只弱地依赖于温度。我们的计算表明，仅略高于生物体最适生长的温度，星团的形成就变得不利。因此，空腔的干燥先于蛋白质变性。这一观察结果导致了我们的假设，即四臂藻中异常大的空腔可能作为两种蛋白酶的结合部位，显示出恰好在大空腔上方结合，这可能解释了所产生的蛋白酶-茎复合体(高达390K，120℃)的异常热稳定性。 在与克里斯托夫·德拉戈教授(维也纳大学)的合作下，我们探索了质子在水分子有序链(Dellago和Hummer，Phys)介导的低介电性膜之间的转移。莱特牧师。2006)。自由能和速率常数计算表明，质子沿着氢键水分子的单分子链扩散穿过膜。质子通过膜受到有效电势的高势垒的反对，反映了巨大的静电惩罚，使人想起生物水通道中的电荷排斥。我们的观察结果不仅解释了水通道中质子转移率低的原因，而且对燃料电池中新型质子膜的设计也有一定的指导意义。

Water plays a central role in the stability, dynamics, and function of biomolecules (Hummer, Mol. Phys. 2007). Through the hydrophobic effect and hydrogen bond interactions, water is a major factor in the folding of proteins. In many enzymes, it participates directly in the catalytic function. In particular, water in the protein interior often mediates the transfer of protons between the solvent medium and the active site. Such water, often confined into relatively nonpolar pores and cavities of nanoscopic dimensions, exhibits highly unusual properties, such as high water mobility, high proton conductivity, or sharp transitions between filled and empty states. Proteins exploit these unusual properties of confined water in their biological function, e.g., to ensure rapid water flow in aquaporins, or to gate proton flow in proton pumps and enzymes. In collaboration with the experimental groups of Prof Sol Gruner (Cornell) and Prof Brian Matthews (University of Oregon and HHMI), we have shown that water filling of a large cavity in a T4 lysozyme mutant is highly sensitive to the solvent conditions (Collins et al., J. Mol. Biol. 2007). By combining high-pressure X-ray crystallography and molecular dynamics simulations, we found that application of modest pressure causes approximately four water molecules to enter the cavity while the protein itself remains essentially unchanged. Under pressure, the cavity remained rigid, while other regions of the protein deform substantially. The resultant picture of the protein interior is one in which conformationally fluctuating side groups provide a liquid-like environment, that makes water penetration feasible both kinetically and thermodynamically. In collaboration with Prof Jay Rasaiah (University of Maine), we studied the interior hydration in tetrabrachion, a hyperstable protein of the surface layer of a deep-sea organism (Yin et al., J. Am. Chem. Soc. 2007). This highly unusual protein exhibits what may well be the largest nonpolar interior hole of any protein found so far. We showed that hydrogen-bonded water clusters of seven to nine water molecules are thermodynamically stable in this cavity at both ambient temperature and 365 K, the temperature of optimal growth. The stability, as measured by the transfer free energy of the optimal size cluster, decreases with increasing temperature. Water filling is thus driven by the energy of transfer and opposed by the transfer entropy, both depending only weakly on temperature. Our calculations suggest that cluster formation becomes unfavorable just slightly above the temperature of optimal growth of the organism. Drying of the cavity thus precedes protein denaturation. This observation led us to the hypothesis that the unusually large cavity in tetrabrachion may act as binding site for two proteases, shown to bind just above the large cavity, possibly explaining the unusual thermostability of the resulting protease-stalk complexes (up to 390 K, 120 deg-C). In collaboration with Prof Christoph Dellago (University of Vienna), we explored the transfer of protons across low-dielectric membranes, mediated by ordered chains of water molecules (Dellago and Hummer, Phys. Rev. Lett. 2006). Free energy and rate constant calculations show that protons move across the membrane diffusively along single-file chains of hydrogen-bonded water molecules. Proton passage through the membrane is opposed by a high barrier in the effective potential, reflecting the large electrostatic penalty for desolvation and reminiscent of charge exclusion in biological water channels. Our observations not only provide an explanation for the low rate of proton transfer trough aquaporin-type channels, but are also relevant for the design of novel proton membranes in fuel cells.