PubMed · 11567144
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R Kazlauskas. 2001-09-21. Tech.Sight. Modeling--a tool for experimentalists.. https://doi.org/10.1126/science.293.5538.2277
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The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.
Copper(I) and copper(II) complexes of two mononucleating and four dinucleating tetradentate ligands with a bispidine backbone (2,4-substituted (2-pyridyl or 4-methyl-2-pyridyl) 3,7-diazabicyclo[3.3.1]nonanone) have been prepared and analyzed structurally, spectroscopically, and electrochemically. The structures of the copper chromophores are square pyramidal, except for two copper(I) compounds which are four-coordinate with one noncoordinated pyridine. The other copper(I) structures have the two pyridine donors, the co-ligand (NCCH(3)), and one of the tertiary amines (N3) in-plane with the copper center and the other amine (N7) coordinated axially (Cu-N3 > Cu-N7, approximately 2.25 A vs 2.20 A). The copper(II) compounds with pyridine donors have a similar structure, but the axial amine has a weaker bond to the copper(II) center (Cu-N3 < Cu-N7, approximately 2.03 A vs 2.30 A). The structures with methylated pyridine donors are also square pyramidal with the co-ligands (Cl(-) or NCCH(3)) in-plane. With NCCH(3) the same structural type as for the other copper(II) complexes is observed, and with the bulkier Cl(-) the co-ligand is trans to N7, leading to a square pyramidal structure with the pyridine donors rotated out of the basal plane and only a small difference between axial and in-plane amines (2.15, 2.12 A). These structural differences, enforced by the rigid bispidine backbone, lead to large variations in spectroscopic and electrochemical properties and reactivities. Oxygenation of the copper(I) complexes with pyridine-substituted bispidine ligands leads to relatively stable mu-peroxo-dicopper(II) complexes; with a preorganization of the dicopper chromophores, by linking the two donor sets, these peroxo compounds are stable at room temperature for up to 1 h. The stabilization of the peroxo complexes is to a large extent attributed to the square pyramidal coordination geometry with the substrate bound in the basal plane, a structural motif enforced by the rigid bispidine backbone. The stabilities and structural properties are also seen to correlate with the spectroscopic (UV-vis and Raman) and electrochemical properties.
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