Csontos József, Palermo Nicholas Y, Murphy Richard F, Lovas Sándor
Department of Biomedical Sciences, Creighton University Medical Center, 2500 California Plaza, Omaha, Nebraska 68178, USA.
J Comput Chem. 2008 Jun;29(8):1344-52. doi: 10.1002/jcc.20898.
The interaction energies of ubiquitous weakly polar interactions in proteins are comparable with those of hydrogen bonds, consequently, they stabilize local, secondary, and tertiary structures. However, the most widely-used density functionals fail to describe the weakly polar interactions. Thus, it is important to find and test functionals which adequately describe and quantify the energetics of such interactions. For this purpose, interaction energies in the hydrophobic core of rubredoxin (PDB id: 1rb9) and in the S22 subset of the JSCH-2005 benchmark database were computed with the BHandHLYP and PWPW91 functionals and with the pseudospectral implementation of the local MP2 (PS-LMP2) method. The cc-pVDZ, cc-pVTZ(-f), cc-pVTZ, cc-pVQZ(-g), aug-cc-pVDZ, aug-cc-VTZ(-f), and aug-cc-pVTZ basis sets were used for the calculations. In the S22 subset the PS-LMP2 results were extrapolated to the complete basis set limit. Furthermore, the a posteriori counterpoise method of Boys and Bernardi was used to correct the basis set superposition errors in the calculation of interaction energies. Calculations using the BHandHLYP functional, both for the various weakly polar interactions in rubredoxin and for the dispersion interactions in the S22 subset, were in good agreement with those using the coupled cluster (CCSD(T)) and the resolution of identity MP2 (RIMP2) methods and clearly outperformed both the PWPW91 functional and the PS-LMP2 method. The results for the S22 hydrogen bonded subset, obtained with PWPW91 calculations, were closest to those of the reference high level calculations. For the "mixed" (hydrogen bonded and dispersive) interactions in the S22 subset, results obtained with the BHandHLYP and PS-LMP2 calculations agreed well with the reference calculations.
蛋白质中普遍存在的弱极性相互作用的相互作用能与氢键的相互作用能相当，因此，它们稳定了局部、二级和三级结构。然而，最广泛使用的密度泛函无法描述弱极性相互作用。因此，找到并测试能够充分描述和量化此类相互作用能量学的泛函非常重要。为此，使用BHandHLYP和PWPW91泛函以及局部MP2（PS-LMP2）方法的伪谱实现，计算了红氧还蛋白疏水核心（PDB编号：1rb9）和JSCH-2005基准数据库的S22子集中的相互作用能。计算使用了cc-pVDZ、cc-pVTZ(-f)、cc-pVTZ、cc-pVQZ(-g)、aug-cc-pVDZ、aug-cc-VTZ(-f)和aug-cc-pVTZ基组。在S22子集中，PS-LMP2结果外推到完整基组极限。此外，使用Boys和Bernardi的后验抵消方法来校正相互作用能计算中的基组叠加误差。使用BHandHLYP泛函对红氧还蛋白中各种弱极性相互作用以及S22子集中色散相互作用的计算结果，与使用耦合簇（CCSD(T)）和单位分辨MP2（RIMP2）方法的计算结果高度一致，并且明显优于PWPW91泛函和PS-LMP2方法。用PWPW91计算得到的S22氢键子集中的结果与参考高水平计算结果最为接近。对于S22子集中的“混合”（氢键和色散）相互作用，用BHandHLYP和PS-LMP2计算得到的结果与参考计算结果吻合良好。
