Green fluorescent proteins: Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamics simulation's of the wild type and S65T mutant
Green fluorescent proteins: Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamics simulation's of the wild type and S65T mutant
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DOI：
10.1021/jp014476w
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发表时间：
2002-06-20
影响因子：
3.3
通讯作者：
Thiel, W
中科院分区：
文献类型：
--
作者：
Reuter, N;Lin, H;Thiel, W
报道了绿色荧光蛋白(GFP)的中性和阴离子形式的绿色荧光蛋白(GFP)的中性和阴离子形式的CHARMM力场参数。根据从头算(RHF/6-31G*)和密度泛函(B3LYP/6-31G*)的参考数据，对分离的生色团模型化合物及其与水的络合物进行了拟合。更具体地说，键合相互作用的参数根据模型化合物的B3LYP几何构型和转动势垒进行了校正，非键库仑相互作用的原子电荷根据RHF几何构型和络合物的结合能进行了拟合，van der Waals参数来自相关的CHARMM残基。优化后的参数较好地再现了参考数据。为了进一步验证，对具有中性生色团的野生型GFP和具有阴离子生色团的S65T突变体进行了分子动力学(MD)模拟。400ps生产运行的平均MD结构与可用的X射线结构通常是合理一致的，例如，关于蛋白质中生色团的几何形状和生色团周围的氢键网络。然而，在某些方面，目前的MD模拟与已发表的X射线结果不同：特别是，它们提出了一个问题，即S65T突变体中的Glu222残基是否可能被去质子化，这与X射线工作的结论相反。
CHARMM force field parameters are reported for the neutral and anionic form of the p-hydroxybenzylidene-imidazolinone chromophore of green fluorescent protein (GFP). They were derived by fitting against ab initio (RHF/6-31G*) and density functional (B3LYP/6-31G*) reference data for the isolated chromophore model compounds and their complexes with water. More specifically, the parameters for the bonded interactions were calibrated against B3LYP geometries and rotational barriers of the model compounds, the atomic charges for the nonbonded Coulomb interactions were fitted against RHF geometries and binding energies of the complexes, and the van der Waals parameters were taken from related CHARMM residues. The optimized parameters reproduce the reference data well. For further validation, molecular dynamics (MD) simulations were carried out for wild-type GFP with a neutral chromophore and for the S65T mutant with an anionic chromophore. The average MD structures from 400 ps production runs are generally in reasonable agreement with the available X-ray structures, e.g., concerning the geometry of the chromophore in the protein and the hydrogen bonding network around the chromophore. In some aspects, however, the present MD simulations differ from the published X-ray results: in particular, they raise the issue whether the residue Glu222 might be deprotonated in the S65T mutant, contrary to the conclusions from the X-ray work.