Kocher J P, Prévost M, Wodak S J, Lee B
Unité de Conformation de Macromolécules Biologiques, Université Libre de Bruxelles, Belgium.
Structure. 1996 Dec 15;4(12):1517-29. doi: 10.1016/s0969-2126(96)00157-8.
The classical picture of the hydrophobic stabilization of proteins invokes a resemblance between the protein interior and nonpolar solvents, but the extent to which this is the case has often been questioned. The protein interior is believed to be at least as tightly packed as organic crystals, and was shown to have very low compressibility. There is also evidence that these properties are not uniform throughout the protein, and conflicting views exist on the nature of sidechain packing and on its influence on the properties of the protein.
In order to probe the physical properties of the protein, the free energy associated with the formation of empty cavities has been evaluated for two proteins: barnase and T4 lysozyme. To this end, the likelihood of encountering such cavities was computed from room temperature molecular dynamics trajectories of these proteins in water. The free energy was evaluated in each protein taken as a whole and in submolecular regions. The computed free energies yielded information on the manner in which empty space is distributed in the system, while the latter undergoes thermal motion, a property hitherto not analyzed in heterogeneous media such as proteins. Our results showed that the free energy of cavity formation is higher in proteins than in both water and hexane, providing direct evidence that the native protein medium differs in fundamental ways from the two liquids. Furthermore, although the packing density was found to be higher in nonpolar regions of the protein than in polar ones, the free energy cost of forming atomic size cavities is significantly lower in nonpolar regions, implying that these regions contain larger chunks of empty space, thereby increasing the likelihood of containing atomic size packing defects. These larger empty spaces occur preferentially where buried hydrophobic sidechains belonging to secondary structures meet one another. These particular locations also appear to be more compressible than other parts of the core or surface of the protein.
The cavity free energy calculations described here provide a much more detailed physical picture of the protein matrix than volume and packing calculations. According to this picture, the packing of hydrophobic sidechains is tight in the interior of the protein, but far from uniform. In particular, the packing is tighter in regions where the backbone forms less regular hydrogen-bonding interactions than at interfaces between secondary structure elements, where such interactions are fully developed. This may have important implications on the role of sidechain packing in protein folding and stability.
蛋白质疏水稳定性的经典图景认为蛋白质内部与非极性溶剂有相似之处，但这种相似程度常受到质疑。蛋白质内部被认为至少与有机晶体一样紧密堆积，并且已证明其具有非常低的压缩性。也有证据表明这些性质在整个蛋白质中并不均匀，关于侧链堆积的性质及其对蛋白质性质的影响存在相互矛盾的观点。
为了探究蛋白质的物理性质，已对两种蛋白质：芽孢杆菌RNA酶和T4溶菌酶，评估了与空穴形成相关的自由能。为此，从这些蛋白质在水中的室温分子动力学轨迹计算遇到此类空穴的可能性。在将每个蛋白质作为一个整体以及在亚分子区域中评估自由能。计算得到的自由能给出了在系统进行热运动时空隙在系统中分布方式的信息，这是迄今为止在诸如蛋白质这样的非均匀介质中尚未分析过的性质。我们的结果表明，蛋白质中空穴形成的自由能高于水和己烷中的自由能，这提供了直接证据表明天然蛋白质介质在基本方面与这两种液体不同。此外，尽管发现蛋白质的非极性区域的堆积密度高于极性区域，但在非极性区域形成原子尺寸空穴的自由能成本显著更低，这意味着这些区域包含更大块的空隙，从而增加了包含原子尺寸堆积缺陷的可能性。这些更大的空隙优先出现在属于二级结构的埋藏疏水侧链相互交汇的地方。这些特定位置似乎也比蛋白质核心或表面的其他部分更具可压缩性。
此处描述的空穴自由能计算提供了比体积和堆积计算更详细的蛋白质基质物理图景。根据这一图景，疏水侧链在蛋白质内部的堆积紧密，但远非均匀。特别是，在主链形成较不规则氢键相互作用的区域比在二级结构元件之间的界面处堆积更紧密，在二级结构元件之间的界面处这种相互作用充分发展。这可能对侧链堆积在蛋白质折叠和稳定性中的作用具有重要意义。
