Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
J Phys Chem B. 2010 Sep 2;114(34):11323-37. doi: 10.1021/jp104425t.
How a biological system responds to a charge shift is a challenging question directly relevant to biological function. Time-resolved fluorescence of a tryptophan residue reflects protein and solvent response to the difference in pi-electron density between the excited and the ground state. In this study we use molecular dynamics to calculate the time-dependent spectral shift (TDSS) in the fluorescence of Trp-43 in GB1 protein. A new computational method for separating solvent, protein, and fluorophore contributions to TDSS is applied to 100 nonequilibrium trajectories for GB1 in TIP3P water. The results support several nontrivial conclusions. Both longitudinal and transverse relaxation modes of bulk solvent contribute to the TDSS in proteins. All relaxation components slower than the transverse relaxation of bulk solvent have significant contributions from both protein and solvent, with a negative correlation between them. Five exponential terms in the TDSS of GB1 are well separated by their relaxation times. A 0.036 ps term is due to both solvent (60%) and protein (40%). Two exponential terms represent longitudinal (tau(L) approximately = 0.4 ps) and transverse (tau(D) approximately = 5.6 ps) relaxation modes of TIP3P water. A 131 ps term is attributable to a small change in the tertiary structure, with the alpha-helix moving 0.2 A away from the beta-strand containing Trp-43. A 2580 ps term is due to the change in the conformation of the Glu-42 side chain that brings its carboxyl group close to the positively charged end of the excited fluorophore. Interestingly, water cancels 60% of the TDSS resulting from this conformational change.
生物体系如何响应电荷转移是一个具有挑战性的问题，直接关系到生物功能。色氨酸残基的时间分辨荧光反映了蛋白质和溶剂对激发态和基态之间π电子密度差的响应。在这项研究中，我们使用分子动力学计算 GB1 蛋白中色氨酸 43 残基的荧光的时变光谱位移（TDSS）。一种新的计算方法用于分离溶剂、蛋白质和荧光团对 TDSS 的贡献，应用于 TIP3P 水中 100 个非平衡 GB1 轨迹。结果支持了几个重要结论。溶剂的纵向和横向弛豫模式都对蛋白质中的 TDSS 有贡献。所有比溶剂横向弛豫慢的弛豫成分都来自蛋白质和溶剂，它们之间存在负相关。GB1 的 TDSS 中有五个指数项可以通过它们的弛豫时间很好地区分。0.036 ps 的项是由溶剂（60%）和蛋白质（40%）共同贡献的。两个指数项代表 TIP3P 水的纵向（tau(L)约为 0.4 ps）和横向（tau(D)约为 5.6 ps）弛豫模式。131 ps 的项归因于三级结构的微小变化，其中α螺旋从含有色氨酸 43 的β链上移动了 0.2 A。2580 ps 的项是由于 Glu-42 侧链的构象变化，使其羧基基团靠近激发态荧光团的正电荷端。有趣的是，水抵消了由这种构象变化引起的 TDSS 的 60%。
