Lee Soyoung, Tikhomirova Anna, Shalvardjian Napol, Chalikian Tigran V
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario, Canada M5S 3M2.
Biophys Chem. 2008 May;134(3):185-99. doi: 10.1016/j.bpc.2008.02.009. Epub 2008 Mar 4.
We determined the partial molar volumes, V degrees , and adiabatic compressibilities, K degrees (S), of N-acetyl amino acids with neutralized carboxyl termini, N-acetyl amino acid amides, and N-acetyl amino acid methylamides between 18 and 55 degrees C. The individual compounds in the three classes have been selected so as to collectively cover the 20 naturally occurring amino acid side chains. We interpret our experimental results in terms of the volumetric contributions and hydration properties of individual amino acid side chains and their constituent atomic groups. We also conducted pH-dependent densimetric and acoustic measurements to determine changes in volume and compressibility accompanying protonation of the aspartic acid, glutamic acid, histidine, lysine, and arginine side chains. We use our resulting data to develop an additive scheme for calculating the partial molar (specific) volume and adiabatic compressibility of fully extended polypeptide chains as a function of pH and temperature. We discuss the differences and similarities between our proposed scheme and the reported additive approaches. We compare our calculated volumetric characteristics of the fully extended conformations of apocytochrome c and apomyoglobin with the experimental values measured in water (for apocytochrome c) or acidic pH (for apomyoglobin). At these respective experimental conditions, the two proteins are unfolded. However, the comparison between the calculated and experimental volumetric characteristics suggests that neither apocytochrome c nor apomyoglobin are fully unfolded and retain a sizeable core of solvent-inaccessible groups.
我们测定了18至55摄氏度之间具有中和羧基末端的N-乙酰氨基酸、N-乙酰氨基酸酰胺和N-乙酰氨基酸甲基酰胺的偏摩尔体积（V°）和绝热压缩系数（K°(S)）。选择了这三类中的各个化合物，以便共同涵盖20种天然存在的氨基酸侧链。我们根据单个氨基酸侧链及其组成原子基团的体积贡献和水合性质来解释我们的实验结果。我们还进行了pH依赖性密度和声学测量，以确定天冬氨酸、谷氨酸、组氨酸、赖氨酸和精氨酸侧链质子化时伴随的体积和压缩性变化。我们利用所得数据开发了一种加和方案，用于计算完全伸展的多肽链的偏摩尔（比）体积和绝热压缩系数作为pH和温度的函数。我们讨论了我们提出的方案与已报道的加和方法之间的异同。我们将计算得到的脱辅基细胞色素c和脱辅基肌红蛋白完全伸展构象的体积特征与在水中（对于脱辅基细胞色素c）或酸性pH（对于脱辅基肌红蛋白）下测量的实验值进行了比较。在这些各自的实验条件下，这两种蛋白质是未折叠的。然而，计算得到的和实验测得的体积特征之间的比较表明，脱辅基细胞色素c和脱辅基肌红蛋白都没有完全展开，并且保留了相当大的一部分溶剂不可及基团的核心。
