An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins’ first spectral absorption band maxima

• DOI: 10.1039/d0cp02638g
• Publication Date: 2020-07-17T07:03:54Z
• Authors: Dmitrii M. Nikolaev; Andrey A. Shtyrov; Andrey S. Mereshc...; Maxim S. Panov; Yuri S. Tveryanovich; Mikhail N. Ryazan...
• Keywords: Molecular mechanics; Maxima

Quantum mechanics/molecular mechanics (QM/MM) models are a widely used tool to obtain detailed insight into the properties and functioning of proteins. The outcome QM/MM studies heavily depends on quality applied model. Prediction right placement internal water molecules in protein cavities is one critical parts any model construction. Herein, we performed systematic study four hydration algorithms. We tested these algorithms for their ability predict X-ray-resolved set membrane photosensitive rhodopsin proteins, as well influence calculated absorption maxima (λmax) 49 rhodopsins intermediates with available X-ray structures test set. found that proper choice setups needed functionally important chromophore-binding cavity rhodopsins, such cluster N-H region bacteriorhodopsin or two binding pocket bovine visual rhodopsin. λmax also quite sensitive protocols. best methodology allows obtaining an 18.0 nm average value absolute deviation from experimental λmax. Although major effect originates located pocket, outside affect mainly by causing reorganization structure. results reported this can be evaluation further development methodologies, general, models, particular.