Amin Md Asif, Halder Ritaban, Ghosh Catherine, Jana Biman, Bhattacharyya Kankan
Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
J Chem Phys. 2016 Dec 21;145(23):235102. doi: 10.1063/1.4972065.
Effect of ethanol on the size and structure of a protein cytochrome C (Cyt C) is investigated using fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations. For FCS studies, Cyt C is covalently labeled with a fluorescent probe, alexa 488. FCS studies indicate that on addition of ethanol, the size of the protein varies non-monotonically. The size of Cyt C increases (i.e., the protein unfolds) on addition of alcohol (ethanol) up to a mole fraction of 0.2 (44.75% v/v) and decreases at higher alcohol concentration. In order to provide a molecular origin of this structural transition, we explore the conformational free energy landscape of Cyt C as a function of radius of gyration (R) at different compositions of water-ethanol binary mixture using MD simulations. Cyt C exhibits a minimum at R ∼ 13 Å in bulk water (0% alcohol). Upon increasing ethanol concentration, a second minimum appears in the free energy surface with gradually larger R up to χ ∼ 0.2 (44.75% v/v). This suggests gradual unfolding of the protein. At a higher concentration of alcohol (χ > 0.2), the minimum at large R vanishes, indicating compaction. Analysis of the contact map and the solvent organization around protein indicates a preferential solvation of the hydrophobic residues by ethanol up to χ = 0.2 (44.75% v/v) and this causes the gradual unfolding of the protein. At high concentration (χ = 0.3 (58% v/v)), due to structural organization in bulk water-ethanol binary mixture, the extent of preferential solvation by ethanol decreases. This causes a structural transition of Cyt C towards a more compact state.
利用荧光相关光谱法（FCS）和分子动力学（MD）模拟研究了乙醇对蛋白质细胞色素C（Cyt C）大小和结构的影响。对于FCS研究，细胞色素C用荧光探针alexa 488进行共价标记。FCS研究表明，加入乙醇后，蛋白质的大小呈非单调变化。加入酒精（乙醇）至摩尔分数为0.2（44.75% v/v）时，细胞色素C的大小增加（即蛋白质展开），而在更高酒精浓度下则减小。为了探究这种结构转变的分子起源，我们使用MD模拟探索了在不同水 - 乙醇二元混合物组成下，细胞色素C作为回转半径（R）函数的构象自由能景观。在纯水（0%酒精）中，细胞色素C在R ∼ 13 Å处呈现最小值。随着乙醇浓度增加，在自由能表面出现第二个最小值，R逐渐增大，直至χ ∼ 0.2（44.75% v/v）。这表明蛋白质逐渐展开。在更高的酒精浓度（χ > 0.2）下，大R处的最小值消失，表明蛋白质发生压缩。对蛋白质周围的接触图和溶剂组织分析表明，直至χ = 0.2（44.75% v/v），乙醇优先溶剂化疏水残基，这导致蛋白质逐渐展开。在高浓度（χ = 0.3（58% v/v））时，由于水 - 乙醇二元混合物中的结构组织，乙醇的优先溶剂化程度降低。这导致细胞色素C向更紧凑状态的结构转变。
