Michael Schauperl

New High-Pressure Gallium Borate Ga2B3O7(OH) with Photocatalytic Activity

The new high-pressure gallium borate Ga2B3O7(OH) was synthesized in a Walker-type multianvil apparatus under high-pressure/high-temperature conditions of 10.5 GPa and 700 °C. For the system Ga-B-O-H, it is only the second known compound next to Ga9B18O33(OH)15·H3B3O6·H3BO3. The crystal structure of Ga2B3O7(OH) was determined by single-crystal X-ray diffraction data collected at room temperature. Ga2B3O7(OH) crystallizes in the orthorhombic space group Cmce (Z = 8) with the lattice parameters a = 1050.7(2) pm, b = 743.6(2) pm, c = 1077.3(2) pm, and V = 0.8417(3) nm(3). Vibrational spectroscopic methods (Raman and IR) were performed to confirm the presence of the hydroxyl group. Furthermore, the band gap of Ga2B3O7(OH) was estimated via quantum-mechanical density functional theory calculations. These results led to the assumption that our gallium borate could be a suitable substance to split water photocatalytically, which was tested experimentally.

High-Pressure Synthesis of Cd(NH3)2[B3O5(NH3)]2: Pioneering the Way to the Substance Class of Ammine Borates†

To date, the access to the substance class of borates containing nitrogen, for example, nitridoborates, oxonitridoborates, or amine borates, was an extreme effort owing to the difficult starting materials and reaction conditions. Although a number of compounds containing boron and nitrogen are known, no adduct of ammonia to an inorganic borate has been observed so far. A new synthetic approach starting from the simple educts CdO, B2O3, and aqueous ammonia under conditions of 4.7 GPa and 800 °C led to the synthesis of Cd(NH3)2[B3O5(NH3)]2 as the first ammine borate. We thoroughly characterized this compound on the basis of low-temperature single-crystal and powder X-ray diffraction data, IR and Raman spectroscopy, and by quantum theoretical calculations. This contribution shows that the adduct of NH3 to the BO3 group of a complex B-O network can be stabilized, opening up a fundamentally new synthetic route to nitrogen-containing borates.

Enthalpic and Entropic Contributions to Hydrophobicity.

Hydrophobic hydration plays a key role in a vast variety of biological processes, ranging from the formation of cells to protein folding and ligand binding. Hydrophobicity scales simplify the complex process of hydration by assigning a value describing the averaged hydrophobic character to each amino acid. Previously published scales were not able to calculate the enthalpic and entropic contributions to the hydrophobicity directly. We present a new method, based on Molecular Dynamics simulations and Grid Inhomogeneous Solvation Theory, that calculates hydrophobicity from enthalpic and entropic contributions. Instead of deriving these quantities from the temperature dependence of the free energy of hydration or as residual of the free energy and the enthalpy, we directly obtain these values from the phase space occupied by water molecules. Additionally, our method is able to identify regions with specific enthalpic and entropic properties, allowing to identify so-called “unhappy water” molecules, which are characterized by weak enthalpic interactions and unfavorable entropic constraints.

Probing the structural and binding mechanism heterogeneity of molecularly imprinted polymers.

We devised a strategy, using a de novo building approach, to construct model molecularly imprinted polymers (MIPs) and assess their ability at binding various target molecules. While our models successfully reproduce the gross experimental selectivities for two xanthines, our atomistic models reveal in detail the considerable heterogeneity of the structure and binding mechanisms of different imprints within such a material. We also demonstrate how nonimprinted regions of a MIP are also responsible for much of binding of target molecules. High levels of cross-linking are shown to produce less specific imprints.

CaB2S4O16: A Borosulfate Exhibiting a New Structure Type with Phyllosilicate Analogue Topology

The reaction of Ca(CO3 ) with H3 BO3 in oleum (20 % SO3 ) yielded colorless single-crystals of CaB2 S4 O16 (monoclinic, P21 /c, a=5.5188(2), b=15.1288(6), c=13.2660(6) Å, β=92.88(1)°, V=1106.22(8) Å3 ). X-ray single-crystal structure analysis revealed a phyllosilicate-analogue anionic sub-structure, forming 2D infinite anionic layers, which exhibit an unprecedented arrangement of condensed twelve-membered (zwölfer) and four-membered (vierer) rings of corner-shared (SO4 ) and (BO4 ) tetrahedra. Charge compensation is achieved by Ca2+ cations, residing exclusively above the centers of the twelve-membered rings. DFT investigations on the solid-state structure corroborate the experimental findings and allow for a detailed valuation of charge distribution within the anionic network and an assignment of vibrational frequencies.

Balance between hydration enthalpy and entropy is important for ice binding surfaces in Antifreeze Proteins

Antifreeze Proteins (AFPs) inhibit the growth of an ice crystal by binding to it. The detailed binding mechanism is, however, still not fully understood. We investigated three AFPs using Molecular Dynamics simulations in combination with Grid Inhomogeneous Solvation Theory, exploring their hydration thermodynamics. The observed enthalpic and entropic differences between the ice-binding sites and the inactive surface reveal key properties essential for proteins in order to bind ice: While entropic contributions are similar for all sites, the enthalpic gain for all ice-binding sites is lower than for the rest of the protein surface. In contrast to most of the recently published studies, our analyses show that enthalpic interactions are as important as an ice-like pre-ordering. Based on these observations, we propose a new, thermodynamically more refined mechanism of the ice recognition process showing that the appropriate balance between entropy and enthalpy facilitates ice-binding of proteins. Especially, high enthalpic interactions between the protein surface and water can hinder the ice-binding activity.

Characterizing Protease Specificity: How Many Substrates Do We Need?

Calculation of cleavage entropies allows to quantify, map and compare protease substrate specificity by an information entropy based approach. The metric intrinsically depends on the number of experimentally determined substrates (data points). Thus a statistical analysis of its numerical stability is crucial to estimate the systematic error made by estimating specificity based on a limited number of substrates. In this contribution, we show the mathematical basis for estimating the uncertainty in cleavage entropies. Sets of cleavage entropies are calculated using experimental cleavage data and modeled extreme cases. By analyzing the underlying mathematics and applying statistical tools, a linear dependence of the metric in respect to 1/n was found. This allows us to extrapolate the values to an infinite number of samples and to estimate the errors. Analyzing the errors, a minimum number of 30 substrates was found to be necessary to characterize substrate specificity, in terms of amino acid variability, for a protease (S4-S4’) with an uncertainty of 5 percent. Therefore, we encourage experimental researchers in the protease field to record specificity profiles of novel proteases aiming to identify at least 30 peptide substrates of maximum sequence diversity. We expect a full characterization of protease specificity helpful to rationalize biological functions of proteases and to assist rational drug design.

Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases

Members of the same protease family show different substrate specificity, even if they share identical folds, depending on the physiological processes they are part of. Here, we investigate the key factors for subpocket and global specificity of factor Xa, elastase, and granzyme B which despite all being serine proteases and sharing the chymotrypsin-fold show distinct substrate specificity profiles. We determined subpocket interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket interaction potentials determined for static X-ray structures turned out to be insufficient to explain serine protease specificity for all subpockets. Therefore, we generated conformational ensembles using molecular dynamics simulations. We identified representative binding site conformations using distance-based hierarchical agglomerative clustering and determined subpocket interaction potentials for each representative conformation of the binding site. Considering the differences in subpocket interaction potentials for these representative conformations as well as their abundance allowed us to quantitatively explain subpocket specificity for the nonprime side for all three example proteases on a molecular level. The methods to identify key regions determining subpocket specificity introduced in this study are directly applicable to other serine proteases, and the results provide starting points for new strategies in rational drug design.

Protease Inhibitors in View of Peptide Substrate Databases

Protease substrate profiling has nowadays almost become a routine task for experimentalists, and the knowledge on protease peptide substrates is easily accessible via the MEROPS database. We present a shape-based virtual screening workflow using vROCS that applies the information about the specificity of the proteases to find new small-molecule inhibitors. Peptide substrate sequences for three to four substrate positions of each substrate from the MEROPS database were used to build the training set. Two-dimensional substrate sequences were converted to three-dimensional conformations through mutation of a template peptide substrate. The vROCS query was built from single amino acid queries for each substrate position considering the relative frequencies of the amino acids. The peptide-substrate-based shape-based virtual screening approach gives good performance for the four proteases thrombin, factor Xa, factor VIIa, and caspase-3 with the DUD-E data set. The results show that the method works for protease targets with different specificity profiles as well as for targets with different active-site mechanisms. As no structure of the target and no information on small-molecule inhibitors are required to use our approach, the method has significant advantages in comparison with conventional structure- and ligand-based methods.

Binding Pose Flip Explained via Enthalpic and Entropic Contributions

The anomalous binding modes of five highly similar fragments of TIE2 inhibitors, showing three distinct binding poses, are investigated. We report a quantitative rationalization for the changes in binding pose based on molecular dynamics simulations. We investigated five fragments in complex with the transforming growth factor β receptor type 1 kinase domain. Analyses of these simulations using Grid Inhomogeneous Solvation Theory (GIST), pKA calculations, and a tool to investigate enthalpic differences upon binding unraveled the various thermodynamic contributions to the different binding modes. While one binding mode flip can be rationalized by steric repulsion, the second binding pose flip revealed a different protonation state for one of the ligands, leading to different enthalpic and entropic contributions to the binding free energy. One binding pose is stabilized by the displacement of entropically unfavored water molecules (binding pose determined by solvation entropy), ligands in the other binding pose are stabilized by strong enthalpic interactions, overcompensating the unfavorable water entropy in this pose (binding pose determined by enthalpic interactions). This analysis elucidates unprecedented details determining the flipping of the binding modes, which can elegantly explain the experimental findings for this system.