Balog Erika, Smith Jeremy C, Perahia David
Institut des Hautes Etudes Scientifiques, 35 route de Chartres, 91440, Bures sur Yvette, France.
Phys Chem Chem Phys. 2006 Dec 21;8(47):5543-8. doi: 10.1039/b610075a. Epub 2006 Nov 8.
Molecular dynamics simulation and normal mode analysis are used to calculate the vibrational density of states of dihydrofolate reductase complexed with nicotinamide adenine dinucleotide phosphate at 120 K and the results are compared with the experimental spectrum derived from inelastic neutron scattering. The simulation results indicate that the experimental spectrum arises from an average over proteins trapped in different conformations with structural differences mainly in the loop regions, and that these conformations have significantly different low-frequency (<20 cm(-1)) spectra. Thus, the experimentally measured spectrum is an average over the vibrational modes of different protein conformations and is thus inhomogeneously broadened. The implications of this broadening for future neutron scattering experiments and ligand binding calculations are discussed.
分子动力学模拟和简正模式分析被用于计算在120 K下与烟酰胺腺嘌呤二核苷酸磷酸结合的二氢叶酸还原酶的振动态密度，并将结果与由非弹性中子散射得到的实验光谱进行比较。模拟结果表明，实验光谱源于被困在不同构象的蛋白质的平均值，这些构象的结构差异主要在环区域，并且这些构象具有显著不同的低频（<20 cm(-1)）光谱。因此，实验测量的光谱是不同蛋白质构象的振动模式的平均值，因此是不均匀展宽的。讨论了这种展宽对未来中子散射实验和配体结合计算的影响。
