Structure prediction of physiological bis(amino acidato)copper(II) species in aqueous solution: The copper(II) compounds with l-glutamine and l-histidine.

Neutral (l-histidinato)(l-glutaminato)copper(II) [Cu(His)(Gln)] has been established as the most abundant ternary copper(II) amino acid compound of the exchangeable copper(II) pool in blood plasma. The experimental studies of Cu(His)(Gln) and bis(glutaminato)copper(II) [Cu(Gln)2] in solutions did not specify their complete geometries. To determine the geometries, this paper investigates the conformers, energy landscapes, and a structure-magnetic parameters relation of Cu(Gln)2 and Cu(His)(Gln) by the density functional theory (DFT) calculations. We assume a glycine-like coordination of Gln (other coordination patterns are dismissed because of steric reasons), and three His in-plane copper(II) binding modes. The conformational analyses are performed in the gas phase and implicitly modeled aqueous solution. The reliability of the DFT relative electronic and Gibbs free energies of the Cu(His)(Gln) conformers is confirmed by benchmarking against the corresponding energies obtained by the domain-based local pair natural orbital coupled-cluster method with singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. Several cis- and trans-Cu(His)(Gln) conformers with His in the histaminate-like and glycine-like modes have low Gibbs free energies, and the greatest estimated metal-binding affinities. The DFT-calculated magnetic parameters of the low-energy conformers reproduce best the experimental electron paramagnetic resonance parameters measured in aqueous solutions for trans- and cis-Cu(Gln)2 conformers having two oxygen atoms (either from Gln or water molecules) at the apical positions, and Cu(His)(Gln) conformers having His in the histaminate-like mode with an apically placed carboxylato oxygen atom. The predicted conformational flexibility of His­copper(II)-amino acid compounds may be connected with their physiological abundance, and the role in copper(II) exchange reactions in blood plasma.

Structure prediction of neutral physiological copper(II) compounds with l-cysteine and l-histidine.

Bis(aminoacidato)copper(II) [CuII(aa)2] coordination compounds are the physiological species of copper(II) amino acid compounds in blood plasma. Since there are no experimental data in the literature about the geometries that physiological CuII(aa)2 could form with l-cysteine (Cys), that is, for bis(l-cysteinato)copper(II) [Cu(Cys)2] and the ternary (l-histidinato)(l-cysteinato)copper(II) [Cu(His)(Cys)], this paper computationally examines the possible conformations that the two compounds could form with the Cys ligand having a protonated sulfur, as in the conventional zwitterion, which was determined to be prevailing in aqueous solution. These two amino acids can bind metals in a tridentate fashion and thus form many possible coordination patterns. Density functional calculations were performed for the conformational analyses in the gas phase and in implicitly modeled aqueous solution using a polarizable continuum model. Additionally, we examine which coordination mode, with thiol or thiolate group, is more stable. The Cys coordination via the amino N and carboxylato O atoms (a glycinato mode) is obtained as the most stable one in aqueous Cu(Cys)2, and also in Cu(His)(Cys) when the His glycinato or histaminato mode combines with the intact thiol group. Whereas the conformers with N and thiol S as the copper(II) donor atoms are predicted to be the least stable, those with the Cu-N and Cu-S(thiolate) bonding (and protonated carboxylato group) are the most stable. The differences are explained by different covalent and ionic contributions of Cu-S(thiol) vs. Cu-S(thiolate). The study can contribute to the insight into formation and reactivity of the copper(II) cysteinato complexes in solution.

Conformational Analyses of Physiological Binary and Ternary Copper(II) Complexes with l-Asparagine and l-Histidine; Study of Tridentate Binding of Copper(II) in Aqueous Solution.

This study explores the structural properties and energy landscapes of the physiologically important bis(l-asparaginato)copper(II) [Cu(l-Asn)2] and (l-histidinato)(l-asparaginato)copper(II) [Cu(l-His)(l-Asn)]. The conformational analyses in the gas phase and implicitly modeled water medium, and magnetic parameters of electron paramagnetic resonance spectra were attained using density functional theory calculations. The apical CuII coordination and hydrogen bonding were analyzed. Predicted lower-energy structures enabled the confirmation and, for apical bonding, also the refinement of structural proposals from literature. Available experimental results were indecisive regarding the amido-group binding in the CuII equatorial plane in solutions, but the examination of the relative stability of Cu(l-Asn)2 conformers in 30 binding modes confirms the glycine-like mode as the most stable one. Previously reported experimental results for Cu(l-His)(l-Asn) were interpreted for l-His to have a tridentate histamine-like mode. However, the aqueous conformers with l-His in the glycinato mode are also predicted to have low energies, which does not contradict the tridentate l-His binding. The predicted magnetic parameters of conformers with an apical oxygen atom (intramolecular or from a water molecule) can reproduce the experimental data. An extent of conformational flexibility and abundance of l-His-containing ternary copper(II) amino acid complexes under physiological conditions may be related.

New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases.

The main aim of this work was to find parameters for the zinc ion in human dipeptidyl peptidase III (DPP III) active site that would enable its reliable modeling. Since the parameters publicly available failed to reproduce the zinc ion coordination in the enzyme, we developed a new set of the hybrid bonded/nonbonded parameters for the zinc ion suitable for molecular modeling of the human DPP III, dynamics, and ligand binding. The parameters allowed exchange of the water molecules coordinating the zinc ion and proved to be robust enough to enable reliable modeling not only of human DPP III and its orthologues but also of the other zinc-dependent peptidases with the zinc ion coordination similar to that in dipeptidyl peptidases III, i.e., peptidases with the zinc ion coordinated with two histidines and one glutamate. The new parameters were tested on a set of 21 different systems comprising 8 different peptidases, 5 DPP III orthologues, thermolysin, neprilysin, and aminopeptidase N, and the results are summarized in the second part of the article.

Calculating the geometry and Raman spectrum of physiological bis(L-histidinato)copper(II): an assessment of DFT functionals for aqueous and isolated systems.

Reliable density functional theory (DFT) calculations can be performed in conjuction with spectroscopic measurements to elucidate the structural properties of physiologically important bis(amino acidato)copper(II) compounds in solutions. They can provide insight into the influence of intermolecular interactions on the molecular geometry in the crystal lattice or solution when compared with a DFT gas-phase minimum. Our previous paper [Markovic et al. (2014) Eur J Inorg Chem 198] reported the DFT-determined geometries and Raman spectra for different conformers of physiological bis(L-histidinato)copper(II) with 20 explicit water molecules, as calculated using the B3LYP functional. The present study examined the reliability of those B3LYP results by applying the M06 functional instead, as it should better account for noncovalent interactions. The water molecules were positioned more compactly around the complex by M06 than by B3LYP. The accuracies of the two functionals when compared to relevant experimental data showed that M06 was better at reproducing in-plane Cu-N bond lengths but B3LYP gave more accurate axial Cu-O distances. Both functionals reproduced the experimental Raman spectrum at pH 8 to similar levels of accuracy and provided precise information on the Cu(II) coordination mode and conformation in aqueous solution. Additionally, we assessed several DFT and DFT-D functionals (BP86, B3LYP, B3LYP-D, M06, M06 L, wB97XD, mPW2PLYPD) by using them to model the geometries of experimental bis(L-histidinato)copper(II) crystalline conformations as isolated systems, and then benchmarking the results against those from high-level second-order pertubation Møller-Plesset (MP2) calculations. Although this assessment resulted in an equivocal conclusion because the MP2 results for the isolated complex were inconsistent with the corresponding DFT outcomes, it does provide new information on future benchmark options.

The Important Role of the Hydroxyl Group on the Conformational Adaptability in Bis(l-threoninato)copper(II) Compared to Bis(l-allo-threoninato)copper(II): Quantum Chemical Study.

Detailed structural properties of physiological bis(amino acidato)copper(II) complexes are generally unknown in solutions. This paper examines how stereochemical differences between the essential amino acid l-threonine and its diastereomer l-allo-threonine, which is rarely present in nature, may affect relative stabilities of bis(l-threoninato)copper(II) and bis(l-allo-threoninato)copper(II) in the gas phase and aqueous solution. These amino acids can bind to Cu(II) via the nitrogen and carboxylato oxygen atoms, the nitrogen and hydroxyl oxygen atoms, and the carboxylato and hydroxyl oxygen atoms. We term these coordination modes G, No, and Oo, respectively. The density functional theory (DFT) calculations with the B3LYP functional of the conformational landscapes for all possible coordination modes of both complexes revealed their very similar stability in the gas phase and in aqueous solution. The conformational analyses resulted in 196 and 267 conformers of isolated copper(II) chelates with l-threonine and l-allo-threonine, respectively. The G-G coordination mode is the most stable, both in the gas phase and aqueous solution. Very similar energy values of the lowest-energy solvated cis and trans G-G conformers in implicitly accounted water medium are in accord with the experimental results that these isomers are present in aqueous solution at physiological pH values. The transition-state structures, activation Gibbs free energies, and reaction rates calculated using DFT/B3LYP and MP2 for the transformations from the most stable cis G-G and trans Oo-G conformers to trans G-G ones for the first time reveal several alternate coordination-mode transformation mechanisms in the copper(II) complexes with amino acids other than glycine. The trans Oo-G conformers are kinetically more stable than cis G-G ones in the gas phase. The only significant difference found between the two complexes is a more suitable position of the hydroxyl group in physiological bis(l-threoninato)copper(II) to form intramolecular hydrogen bonds, which may restrain its conformational space.

Dke1--structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis.

This study elucidates the role of the protein structure in the catalysis of ß-diketone cleavage at the three-histidine metal center of diketone cleaving enzyme (Dke1) by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor, were performed and showed a distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. It is shown that in the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination. The substrate binding modes and channels for the traffic of water and ligands (2,4-pentandionyl anion, methylglyoxal, and acetate) were identified. To characterize the impact of the hydrophobic protein environment around the metal center on catalysis, a set of hydrophobic residues close to the active site were targeted. The variations resulted in an up to tenfold decrease of the O(2) reduction rates for the mutants. Molecular dynamics studies revealed an impact of the hydrophobic residues on the substrate stabilization in the active site as well as on the orientations of Glu98 and Arg80, which have previously been shown to be crucial for catalysis. Consequently, the Glu98-His104 interaction in the variants is weaker than in the wild-type complex. The role of protein structure in stabilizing the primary O(2) reduction step in Dke1 is discussed on the basis of our results.

A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins.

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach.