Newly identified C-H⋯O hydrogen bond in histidine.

New Cδ-H⋯O histidine hydrogen bonding interactions in various proteins are identified by neutron diffraction and computationally characterized. Neutron diffraction data shows several H-bond motifs with the Cδ-H moiety in histidine side chains, including interactions in ß-sheets and with coordinated waters, mostly with histidinium and τ-tautomers. In yellow protein, an active site histidine H-bonds via Cδ-H to a main chain carbonyl while the Cε-H bond coordinates a water molecule. Although the H-bonding ability of Cε-H bonds in histidine have been previously identified, analysis of neutron diffraction structures reveals Cε-H H-bonds in notable active site interactions: for the proximal histidine in myoglobin; a zinc-bound histidine in human carbonic anhydrase II; within the Ser-Asp-His catalytic triad of the trypsin active site; and a histidine in the proton shuttle mechanism of RNase A, in addition to more general roles of coordinating water and forming H-bonds with carbonyl groups in ß-sheets within a number of proteins. Properties of these H-bonds were computationally investigated using 5-methylimidazole and 5-methylimidazolium as models for histidine and histidinium. The π- and τ-tautomeric states of 5-methylimidazole were investigated, as both histidine tautomers are observed in the crystal structures. The newly characterized Cε-H⋯O and Cδ-H⋯O model complexes with water and acetone meet the overwhelming majority of IUPAC H-bonding criteria. 5-Methylimidazolium forms complexes that are nearly twice as strong as the respective neutral τ-5-methylimidazole and π-5-methylimidazole complexes. While the τ- and π-tautomers form Cε-H⋯O complexes of similar strength, the τ-Cδ-H⋯O interaction is approximately twice as strong as the π-Cδ-H⋯O interaction. Calculated charges on C-H (and N-H) hydrogens not participating in the H-bond are only slightly perturbed upon complex formation, implying that formation of one H-bond does not diminish the molecule's capacity for further H-bond formation at other sites in the imidazole ring. Overall, findings indicate that the Cδ-H⋯O interaction may be important for ß-sheet stability, conformation, interactions with solvent, and mechanisms in the active site. Recognition of C-H bond polarity and hydrogen bonding ability in histidine may improve molecular modeling and provide further insight into the diverse roles of histidine in protein structure-function-dynamics.

Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics.

The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.