Li Binsen, Shahid Ramza, Peshkepija Paola, Zimmer Marc
Chemistry Department, Connecticut College, New London, CT06320.
Chem Phys. 2012 Jan 1;392(1):143-148. doi: 10.1016/j.chemphys.2011.11.001. Epub 2011 Nov 19.
The chromophore of fluorescent proteins is formed by an internal cyclization of the tripeptide 65SYG67 fragment and a subsequent oxidation. The oxidation is slow - the kinetics of this step is presumably improved in fast maturing GFPs. Water molecules can aid in the chromophore formation. We have used 50ns molecular dynamics simulations of the mature and immature forms of avGFP and TurboGFP to examine the diffusion of water molecules in-and-out of the protein β-barrel. Most crystal structures of GFPs have well-structured waters within hydrogen-bonding distance of Glu222 and Arg96. It has been proposed that they have an important role in chromophore formation. Stable waters are found in similar positions in all simulations conducted. The simulations confirm the existence of a pore that leads to the chromophore in the rapidly maturing TurboGFP; decreased water diffusion upon chromophore formation; and increased water diffusion due to the pore formation.
荧光蛋白的发色团由三肽65SYG67片段的内部环化及随后的氧化作用形成。氧化过程缓慢——这一步骤的动力学在快速成熟的绿色荧光蛋白（GFP）中可能有所改善。水分子有助于发色团的形成。我们利用对avGFP和TurboGFP成熟和未成熟形式进行的50纳秒分子动力学模拟，来研究水分子在蛋白质β桶内外的扩散情况。GFP的大多数晶体结构在距Glu222和Arg96氢键距离范围内有结构良好的水分子。有人提出它们在发色团形成中起重要作用。在所有进行的模拟中，均在相似位置发现了稳定的水分子。模拟结果证实，在快速成熟的TurboGFP中存在一个通向发色团的孔；发色团形成时水扩散减少；以及由于孔的形成导致水扩散增加。
