Metal ligand aromatic cation-pi interactions in metalloproteins: ligands coordinated to metal interact with aromatic residues

Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

Electron delocalization mediates the metal-dependent capacity for CH/pi interactions of acetylacetonato chelates

CH/pi interactions between the coordinated acetylacetonato ligand and phenyl rings were analyzed in the crystal structures from the Cambridge Structural Database and by quantum chemical calculations. The acetylacetonato ligand may engage in two types of interactions: it can be hydrogen atom donor or acceptor. The analysis of crystal structures and calculations show that interactions with the acetylacetonato ligand acting as hydrogen atom donor depend on the metal in an acetylacetonato chelate ring; the chelate rings with soft metals make stronger interactions. The same trend was not observed in the interactions where the acetylacetonato chelate ring acts as the hydrogen atom acceptor.

Adsorption of mycotoxins by organozeolites

Adsorption of zearalenone (ZEN), ochratoxin A (OCHRA) and aflatoxin B1 (AFB1) on natural zeolite, clinoptilolite, modified with different amounts of octadecyldimethylbenzyl ammonium (ODMBA) ions was investigated. Results showed that adsorption of hydrophobic ionizable ZEN on unmodified zeolite tuff was very low and that adsorption on organozeolites increased with increasing hydrophobicity of the zeolitic surface. The adsorption was independent of the form of ZEN in solution and the solution pH, indicating that hydrophobic interactions with ODMBA are responsible for ZEN adsorption. Adsorption of low polar ionizable OCHRA on organozeolites also increased with increasing hydrophobicity of the zeolitic surface, however, OCHRA showed moderate adsorption on unmodified zeolitic tuff at pH 3. OCHRA adsorption on unmodified zeolite as well as on lower surface coverage of organozeolite was dependent on the form of OCHRA in solution; there was a decrease of adsorption at high pH, where OCHRA is in the anionic form. It indicated that at acidic pH, low surface coverage allows some combination of hydrophobic interaction with ODMBA and interactions with the surface of the zeolite. At higher surface coverage, the OCHRA adsorption was higher and practically independent of pH, indicating that the hydrophobic interactions of OCHRA with ODMBA are responsible for its adsorption. Nonionizable low polar AFB1 had a high affinity for the unmodified zeolitic tuff and the adsorption of AFB1 was greatly reduced for organozeolites, indicating that AFB1 does not have high tendency for hydrophobic interactions with ODMBA. pH dependence of AFB1 adsorption, while AFB1 has the same form at all pHs, demonstrated that the surface modification of the zeolite depends on pH and that these modifications have influence on its adsorption. The calculated dipole moments of neutral mycotoxin molecules: AFB1-9.5D, OCHRA-6.9D and ZEN-2.2D are in qualitative agreement with adsorption experimental data.

Are Chelate Rings Aromatic? Calculations of Magnetic Properties of Acetylacetonato and o-Benzoquinonediimine Chelate Rings

The aromaticity of the chelate rings of acetylacetonato (acac) and o-benzoquinonediimine (bqdi) ligands was investigated theoretically by calculating nucleus-independent chemical shifts (NICS). The calculations were done for the complexes with various metals and various other ligands. The results show that acac chelate rings in none of the complexes satisfy this magnetic criterion for aromaticity. According to the results for bqdi chelate rings, there is only the Ru2+-bqdi chelate ring with large negative NICS values, indicating possible aromaticity by magnetic criterion.

Factors determining the orientation of axially coordinated imidazoles in heme proteins

Factors determining conformations of imidazole axially coordinated to heme in heme proteins were investigated by analyzing 693 hemes in 432 different crystal structures of heme proteins from the Protein Data Bank (PDB), where at least one histidine is ligated to heme. The results from a search of the PDB for protein structures were interpreted with molecular force field computations. Analysis of data from these crystal structures indicated that there are two main factors that determine the orientations of imidazole ligated to heme. These are the interactions of imidazole with the propionic acid side chains of heme and with the histidine backbone. From the analysis of the crystal structures of heme proteins, it turned out that the hydrogen bonding pattern is often not decisive, though it is probably used by nature to fine-tune the orientation of imidazole axially ligated to heme. We found that in many heme proteins the NdeltaH group of imidazole ligated to heme can assume a number of different hydrogen bonds and that in mutant structures the orientation of the ligated imidazole often does not change significantly, although the mutant altered the hydrogen bonding scheme involving the imidazole. Data from crystal structures of heme proteins show that there are preferred orientations of imidazoles with respect to heme. Generally, the NdeltaH group of imidazole is oriented toward the propionic acid groups of the heme. In some cases, the NdeltaH group of imidazole is close to only one of the propionic acid groups, but it is practically never oriented in the opposite direction. The imidazole also adopts a preferred orientation with respect to its histidine backbone such that the plane of the imidazole ring is practically never parallel to the Calpha-Cbeta bond of its histidine backbone. For a given conformation of histidine backbone with respect to heme, as well as imidazole with respect to histidine backbone, the orientation of the imidazole with respect to heme is uniquely determined, since the three orientations depend on each other. Hence, the interaction of the imidazole with the backbone also influences the orientation of the imidazole with respect to the heme. Force field computations are in agreement with experimental data. With this method, we showed that there is an energy minimum when the NdeltaH group of the imidazole is oriented toward the propionic acid groups and that there are minima of energy for orientations where the imidazole ring is orthogonal to the plane defined by the Calpha-Cbeta and Cbeta-Cgamma bonds of the histidine. The computations also demonstrated that these interactions are mainly of electrostatic origin. By taking into account these two major factors, we were able to understand the orientations of axially coordinated imidazoles for all groups of heme proteins, except for the group of cytochrome c peroxidase. In this group, the orientation of the imidazole is determined by a strong hydrogen bond of the NdeltaH group with Asp235.

C-H. . .pi interactions in the metal-porphyrin complexes with chelate ring as the H acceptor

Specific C-H. . .pi interactions with the pi-system of porphyrinato chelate ring were found in crystal structures of transition metal complexes from the Cambridge Structural Database and statistical analysis of geometrical parameters for intramolecular and intermolecular interactions was done. By density functional theory calculations on a model system it was evaluated that an interaction energy is above 1.5 kcal/mol and that the strongest interaction occurs when the distance between hydrogen atom and the center of the chelate ring is 2.6 A. This prediction is in good agreement with the distances for intermolecular interactions found in the crystal structures. In many cases the intramolecular interaction distances are much shorter than 2.6 A, and these short distances are caused by geometrical constrains. The C-H. . .pi interactions with chelate ring of porphyrinato ligand can influence the structure, contribute to its stability, and play some role in the function of biomolecules with metalo porphyrins.

A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure

The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cbeta and Cgamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on Cbeta and Cgamma atoms, nor branching or aromatic group on the Cbeta atom. All strand preferrers have aromatic groups or branching groups on the Cbeta atom. All turn and bend preferrers have a polar heteroatom on the Cbeta or Cgamma atoms or do not have a Cbeta atom at all. These new rules could be helpful in making predictions about non-natural amino acids.

Mechanistic Investigation of the Oxygen-Atom-Transfer Reactivity of Dioxo-molybdenum(VI) Complexes

The oxygen-atom-transfer (OAT) reactivity of [LiPrMoO2(OPh)] (1, LiPr=hydrotris(3-isopropylpyrazol-1-yl)borate) with the tertiary phosphines PEt3 and PPh2Me in acetonitrile was investigated. The first step, [LiPrMoO2(OPh)]+PR3-->[LiPrMoO(OPh)(OPR3)], follows a second-order rate law with an associative transition state (PEt3, DeltaH not equal=48.4 (+/-1.9) kJ mol-1, DeltaS not equal=-149.2 (+/-6.4) J mol-1 K-1, DeltaG not equal=92.9 kJ mol-1; PPh2Me, DeltaH not equal=73.4 (+/-3.7) kJ mol-1, DeltaS not equal=-71.9 (+/-2.3) J mol-1 K-1, DeltaG not equal=94.8 kJ mol-1). With PMe3 as a model substrate, the geometry and the free energy of the transition state (TS) for the formation of the phosphine oxide-coordinated intermediate were calculated. The latter, 95 kJ mol-1, is in good agreement with the experimental values. An unexpectedly large O-P-C angle calculated for the TS suggests that there is significant O-nucleophilic attack on the P--C sigma* in addition to the expected nucleophilic attack of the P on the Mo==O pi*. The second step of the reaction, that is, the exchange of the coordinated phosphine oxide with acetonitrile, [LiPrMoO(OPh)(OPR3)]+MeCN-->[LiPrMoO(OPh)(MeCN)]+OPR3, follows a first-order rate law in MeCN. A dissociative interchange (Id) mechanism, with activation parameters of DeltaH not equal=93.5 (+/-0.9) kJ mol-1, DeltaS not equal=18.2 (+/-3.3) J mol-1 K-1, DeltaG not equal=88.1 kJ mol-1 and DeltaH not equal=97.9 (+/-3.4) kJ mol-1, DeltaS not equal=47.3 (+/-11.8) J mol-1 K-1, DeltaG not equal=83.8 kJ mol-1, for [LiPrMoO(OPh)(OPEt3)] (2 a) and [LiPrMoO(OPh)(OPPh2Me)] (2 b), respectively, is consistent with the experimental data. Although gas-phase calculations indicate that the Mo--OPMe3 bond is stronger than the Mo--NCMe bond, solvation provides the driving force for the release of the phosphine oxide and formation of [LiPrMoO(OPh)(MeCN)] (3).

Energetics of radical transfer in DNA photolyase

Charge separation and radical transfer in DNA photolyase from Escherichia coli is investigated by computing electrostatic free energies from a solution of the Poisson-Boltzmann equation. For the initial charge separation 450 meV are available. According to recent experiments [Aubert et al. Nature 2000, 405, 586-590] the flavin receives an electron from the proximal tryptophan W382, which consequently forms a cationic radical WH(*)(+)382. The radical state is subsequently transferred along the triad W382-W359-W306 of conserved tryptophans. The radical transfer to the intermediate tryptophan W359 is nearly isoenergetic (58 meV uphill); the radical transfer from the intermediate W359 to the distal W306 is 200 meV downhill in energy, funneling and stabilizing the radical state at W306. The resulting cationic radical WH(*)(+)306 is further stabilized by deprotonation, yielding the neutral radical W(*)306, which is 214 meV below WH(*)(+)306. The time scale of the charge recombination process yielding back the resting enzyme with FADH(*) is governed by reprotonation of W306, with a calculated lifetime of 1.2 ms that correlates well with the measured lifetime of 17 ms. In photolyase from Anacystis nidulans the radical state is partially transferred to a tyrosine [Aubert et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 5423-5427]. In photolyase from Escherichia coli, there is a tyrosine (Y464) close to the distal tryptophan W306 that could play this role. We show that this tyrosine cannot be involved in radical transfer, because the electron transfer from tyrosine to W306 is much too endergonic (750 meV) and a direct hydrogen transfer is likely too slow. Coupling of specific charge states of the tryptophan triad with protonation patterns of titratable residues of photolyase is small.

Artificial cytochrome b: computer modeling and evaluation of redox potentials

We generated atomic coordinates of an artificial protein that was recently synthesized to model the central part of the native cytochrome b (Cb) subunit consisting of a four-helix bundle with two hemes. Since no X-ray structure is available, the structural elements of the artificial Cb were assembled from scratch using all known chemical and structural information available and avoiding strain as much as possible. Molecular dynamics (MD) simulations applied to this model protein exhibited root-mean-square deviations as small as those obtained from MD simulations starting with the crystal structure of the native Cb subunit. This demonstrates that the modeled structure of the artificial Cb is relatively rigid and strain-free. The model structure of the artificial Cb was used to determine the redox potentials of the two hemes by calculating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation (LPBE). The calculated redox potentials agree within 20 meV with the experimentally measured values. The dependence of the redox potentials of the hemes on the protein environment was analyzed. Accordingly, the total shift in the redox potentials is mainly due to the low dielectric medium of the protein, the protein backbone charges, and the salt bridges formed between the arginines and the propionic acid groups of the hemes. The difference in the shift of the redox potentials is due to the interactions with the hydrophilic side chains and the salt bridges formed with the propionic acids of the hemes. For comparison and to test the computational procedure, the redox potentials of the two hemes in the native Cb from the cytochrome bc(1) (Cbc(1)) complex were also calculated. Also in this case the computed redox potentials agree well with experiments.

Parallel alignment of water and aryl rings-crystallographic and theoretical evidence for the interaction

Analysis of crystal structures from the Cambridge Structural Database (CSD) that involve close contact between water and aryl rings revealed the existance of conformations where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane at distances typical for stacking interactions; attractive interaction energies obtained from ab initio calculations performed on model systems are significant (e.g.DeltaE(CCSD(T)) = -1.60 kcal mol(-1)) and consistent with the observed structures.

Computational studies on imidazole heme conformations

Density functional theory computations of heme with ionized propionic acid groups, axially coordinated with two imidazoles, were performed for different mutual orientations of the imidazole planes. Environmental influences from water or protein were considered with a continuum dielectric medium by solving the Poisson equation. In vacuum, optimized geometries yielded imidazole-heme conformations where the NH groups of imidazoles are oriented toward the heme propionic groups in agreement with data from crystal structures of heme proteins. Conformational free-energy dependencies of the mutual orientation of axially ligated imidazoles calculated in protein (epsilon=10) and water (epsilon=80) environments confirmed the vacuum results, albeit the energy difference between the preferred and the 180 degrees opposite orientations of the imidazole ligand decreased from 3.84 kcal/mol in vacuum to 2.35 and 2.40 kcal/mol in protein and water, respectively. Two main factors determine the imidazole orientation: (1) the direct intramolecular electrostatic interactions of propionic groups with the polar NH groups of imidazole and (2) the electrostatic interaction of the total dipole moment of the imidazole-heme complex with the reaction field. In vacuum, only the first type of interaction is present, while in a dielectric medium the latter effect becomes competitive at high dielectric constant, resulting in a decrease of the orientational preference. Interestingly, the orientational preference of the imidazole axially ligated to heme becomes even more pronounced, if the negatively charged propionates are neutralized by counter charges that mimic salt bridges or protonation of the propionates.

XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins

Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the pi system of every porphyrin ring is involved in XH/pi interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered chelate rings are involved in XH/pi interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered rings. We found interactions with C-H and N-H groups as hydrogen-atom donors; however, the number of CH/pi interactions is much larger than the number of NH/pi interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin is involved in XH/pi interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/pi interactions play an important role in porphyrin-protein stability.

Influence of natural zeolitic tuff and organozeolites surface charge on sorption of ionizable fumonisin B(1)

Natural zeolitic tuff was modified with 2, 5 and 10mmol M(+)/100g of octadecyldimethylbenzyl ammonium (ODMBA) ions and the products were denoted as OZ-2, OZ-5 and OZ-10. The starting material and organozeolites were characterized by determination of the point of zero charge (pH(pzc)) and by thermal analysis. In vitro sorption of fumonisin B(1) (FB(1)) was studied for all sorbents at pH 3, 7 and 9. The pH(pzc) for the zeolitic tuff was 6.8+/-0.1, while the pH(pzc) for OZ-2, OZ-5 and OZ-10 pH(pzc) was 7.0+/-0.1. The curves pH(final)=f(pH(initial)) suggest that the surfaces of all sorbents are positively charged at pH 3 and uncharged at pH 7 and 9. High sorption of FB(1) by the zeolitic tuff in acidic solution suggests electrostatic interactions between the anionic FB(1) and the positively charged surface. At pH 7 and 9, adsorption of FB(1) is prevented because anionic FB(1) cannot be adsorbed at the uncharged surface. From the pH(pzc) for the organozeolites, it is possible that with lower amounts of ODMBA (OZ-2 and OZ-5), at pH 3, beside interactions between head groups of ODMBA and its alkyl chains and anionic FB(1), electrostatic interactions between positive uncovered surface and anionic FB(1) contribute to the sorption, while at pH 7 and 9 there is only the possibility for interactions between FB(1) and ODMBA. When the zeolitic surface was completely covered with ODMBA (OZ-10), FB(1) sorption was independent of the form of FB(1) suggesting only interactions between ODMBA and FB(1).

Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules

Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

Orientations of axially coordinated imidazoles and pyridines in crystal structures of model systems of cytochromes

Many properties of cytochromes and model systems depend on orientations of axial ligands. In this work, we elucidated the role of porphyrin substituents on orientation of axial ligands in model systems of cytochromes. The orientations of axially coordinated imidazoles and pyridines in crystal structures of model systems of cytochromes were analyzed and data were compared with previous quantum-chemical calculations. The results show that eight ethyl groups on porphyrin ring strongly favor parallel orientation, hence, in all these complexes axial ligands, pyridines or imidazoles, are mutually parallel. Four phenyl or mesityl groups at meso-carbons also favor parallel orientation but less strongly. Hence, in most of the bis-imidazole complexes the orientation is parallel, while in bis-pyridine complexes the orientation of pyridines depends on oxidation state of Fe. In bis-pyridine Fe(II) complexes orientation is parallel, in Fe(III) it is orthogonal. This analysis is in agreement with previous quantum-chemical calculations.

Prediction of strong O-H/M hydrogen bonding between water and square-planar Ir and Rh complexes

Intermolecular O-H/M interactions, between a water molecule and square-planar acac complexes ([M(acac)L₂]), with different types of L ligands (en, H₂O, CO, CN^-, and OH^-) and different types of metal atoms (Ir(i), Rh(i), Pt(ii), and Pd(ii)) were studied by high level ab initio calculations. Among the studied neutral complexes, the [Pd(acac)(CN)(CO)] complex forms the weakest interaction, -0.62 kcal mol^-1, while the [Ir(acac)(en)] complex forms the strongest interaction, -9.83 kcal mol^-1, which is remarkably stronger than the conventional hydrogen bond between two water molecules (-4.84 kcal mol^-1).

The Structural Details of Aspirin Molecules and Crystals

We revisit, in the key of structural chemistry, one of the most known and important drugs: the aspirin. Although apparently simple, the factors determining the molecular structure and supramolecular association in crystals are not trivial. We addressed the problem from experimental and theoretical sides, considering issues from X-ray measurements and results of first-principle reconstruction of molecule and lattices by ab initio calculations. Some puzzling problems can give headaches to specialists and intrigue the general public. Thus, the reported polymorphism of aspirin is disputed, a so-called form II being alleged as a result of misinterpretation. At the same time, were presented evidences that the structure of common form I can be disrupted by domains where the regular packing is changed to the pattern of form II. The problems appear even at the level of independent molecule: the most stable conformation computed by various techniques of electronic structure differs from those encountered in crystals. Because the energy difference between the related conformational isomers (computed as most stable vs. the experimental structure) is small, about 1 kcal/mol, comprised in the error bars of used methods, the unresting question is whether the modelling is imprecise, or the supramolecular factors are mutating the conformational preferences. By a detective following of the issue, the intermolecular effects were made responsible for the conformation of the molecule in crystal. The presented problems were gathered from literature results, debates, glued with modelling and analysis redone by ourselves, in order to secure the unitary view of the considered prototypic topic.

[Personal experience in the treatment of pulmonary tuberculosis in mentally retarded persons]

The results of the therapy of pulmonary tuberculosis in 90 mentally retarded patients in various forms and degrees of retardation are presented. General and clinical condition of 62 patients was very bad prior to the onset of antituberculotic therapy and most of them were immobile due to the mental retardation and dissemination of pulmonary tuberculosis. In 30 patients advanced form of tuberculosis, in 54 patients mild form and in 6 patients a minimal degree of tuberculosis were found. In hospitalized patients all clinical forms of pulmonary tuberculosis were found. The therapy started with triplicate antituberculotic therapy and the patients were also administered other drugs due to their mental retardation. During the first two months of antituberculotic therapy a high mortality rate was registered (27 or 30%) especially in younger patients. The reason for such high rate cannot be attributed only to pulmonary tuberculosis but also to the primary disease as was the main reason of patients' hospitalization at the institute for mentally retarded persons. Many complications in antituberculotic use could not be registered since many of the basic data could not be obtained from mentally retarded subjects. The complete recovery or improvement of pulmonary tuberculosis was achieved in 63 patients.