PubMed · 15809641
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2005. Get the party started.. https://doi.org/10.1038/nsmb0405-279
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The contribution of hydrogen bonds and the burial of polar groups to protein stability is a controversial subject. Theoretical studies suggest that burying polar groups in the protein interior makes an unfavorable contribution to the stability, but experimental studies show that burying polar groups, especially those that are hydrogen bonded, contributes favorably to protein stability. Understanding the factors that are not properly accounted for by the theoretical models would improve the models so that they more accurately describe experimental results. It has been suggested that hydrogen bonds may contribute to protein stability, in part, by increasing packing density in the protein interior, and thereby increasing the contribution of van der Waals interactions to protein stability. To investigate the influence of hydrogen bonds on packing density, we analyzed 687 crystal structures and determined the volume of buried polar groups as a function of their extent of hydrogen bonding. Our findings show that peptide groups and polar side chains that form hydrogen bonds occupy a smaller volume than the same groups when they do not form hydrogen bonds. For example, peptide groups in which both polar groups are hydrogen bonded occupy a volume, on average, 5.2 A3 less than a peptide group that is not hydrogen bonded.
A large number of complexes of the first-row transition metals with non-innocent ligands has been characterized in the last few years. The localization of the oxidation site in such complexes can lead to discrepancies when electrons can be removed either from the metal center (leading to an M((n+1)+) closed-shell ligand) or from the ligand (leading to an M(n+) open-shell ligand). The influence of the ligand field on the oxidation site in square-planar nickel complexes of redox-active ligands is explored herein. The tetradentate ligands employed herein incorporate two di-tert-butylphenolate (pro-phenoxyl) moieties and one orthophenylenediamine spacer. The links between the spacer and both phenolates are either two imines ([Ni(L1)]), two amidates ([Ni(L3)]2-), or one amidate and one imine ([Ni(L2)]-). The structure of each nickel(II) complex is presented. In the noncoordinating solvent CH2Cl2, the one-electron-oxidized forms are ligand-radical species with a contribution from a singly occupied d orbital of the nickel. In the presence of an exogenous ligand, such as pyridine, a Ni(III) closed-shell ligand form is favored: axial ligation, which stabilizes the trivalent nickel in its octahedral geometry, induces an electron transfer from the metal(II) center to the radical ligand. The affinity of pyridine for the phenoxylnickel(II) species is correlated to the N-donor ability of the linkers.
Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures.