Imidazole Binding Research Articles

Self-Assembly of Russian Doll Concentric Porphyrin Nanorings.

Electronic communication between concentric macrocycles with wave functions that extend around their circumferences can lead to remarkable behavior, as illustrated by multiwalled carbon nanotubes and photosynthetic chlorophyll arrays. However, it is difficult to hold one π-conjugated molecular ring inside another. Here, we show that ring-in-ring complexes, consisting of a 6-porphyrin ring locked inside a 12-porphyrin ring, can be assembled by placing different metals in the two rings (zinc and aluminum). A bridging ligand with carboxylate and imidazole binding sites forms spokes between the two rings, resulting in a highly cooperative supramolecular self-assembly process. Excitation is transferred from the inner 6-ring to the outer 12-ring of this Russian doll complex within 40 ps. These complexes lead to a form of template-directed synthesis in which one nanoring promotes formation of a larger concentric homologous ring; here, the effective template is an eight-component noncovalent assembly. Russian doll templating provides a new approach to amplifying the size of a covalent nanostructure.

Enhanced heme accessibility in horse heart mini-myoglobin: Insights from molecular modelling and reactivity studies

Mini-myoglobin (mini-HHMb) is a fragment of horse-heart myoglobin (HHMb) considered to be the prototype of the product encoded by the central exon of the HHMb gene. For this reason, mini-HHMb has been studied extensively showing that carbonylation and oxygenation properties of the ferrous form are similar to those of the full-length protein, while kinetics and thermodynamics of azide binding to the ferric form are significantly different from those of HHMb. To analyze the structure–function relationships in mini-HHMb and the role of conformational fluctuations in ligand accessibility, the molecular model of mini-HHMb has been built and refined by molecular dynamics simulations, and analyzed in parallel with that of full length HHMb. Moreover, imidazole binding parameters of ferric mini-HHMb and HHMb have been determined. Furthermore, structural data of ferric mini-HHMb and HHMb have been correlated with the imidazole and previously determined azide binding properties. Present results indicate that, despite the extensive trimming, the heme-α-helices E-F substructure is essentially unaltered in mini-HHMb with respect to HHMb. However, the heme-Fe atom displays an enhanced accessibility in mini-HHMb, which may affect both ligand association and dissociation kinetics.

Binding of Imidazole Stabilizes Low‐spin State of Heme Iron in Dual‐Substrate‐Specific Rice Allene Oxide Synthase‐1

Kinetic studies have indicated that imidazole is a competitive inhibitor of rice allene oxide synthase‐1 with K i of 34.9, 14.3, 40.3, and 23.3 mM for 13(S)‐HPODE, 13(S)‐HPOTE, 9(S)‐HPODE, and 9(S)‐HPOTE as substrates, respectively. Imidazole‐free rice allene oxide synthase‐1 has a Soret absorbance maximum at 393 nm and occupied high‐spin (g = 6.0) and low‐spin (g = 2.39, 2.24, 1.93) states in the ratio 1:10, as detected by EPR spectroscopy, while in the presence of imidazole the occupancy of the low‐spin state increased to 100%. The results support the hypothesis that imidazole competes with the substrate of allene oxide synthase‐1 for binding to the sixth position of heme iron(III) and that binding of imidazole stabilizes the low‐spin state. The role of detergent binding and implications for the mechanism by which allene oxide synthase‐1 cleaves the RO‐OH bond are discussed.

Binding of imidazole, 1-methylimidazole and 4-nitroimidazole to yeast cytochrome c peroxidase (CcP) and the distal histidine mutant, CcP(H52L)

Imidazole, 1-methylimidazole and 4-nitroimidazole bind to yeast cytochrome c peroxidase (yCcP) with apparent equilibrium dissociation constants (KDapp) of 3.3±0.4, 0.85±0.11, and ~0.2M, respectively, at pH7. This is the weakest imidazole binding to a heme protein reported to date and it is about 120 times weaker than imidazole binding to metmyoglobin. Spectroscopic changes associated with imidazole and 1-methylimidazole binding to yCcP suggest partial ionization of bound imidazole to imidazolate. The pKa for ionization of bound imidazole is estimated to be 7.4±0.2, about 7 units lower than that of free imidazole and about 3 units lower than imidazole bound to metmyoglobin. Equilibrium binding of imidazole to CcP(H52L) is biphasic with low- and high-affinity phases having KDapp values of 9.5±4.5 and 0.13±0.04M, respectively. CcP(H52L) binding of 1-methylimidazole is monophasic with an affinity similar to those of yCcP and rCcP. Binding of 1-methylimidazole to rCcP is associated with two kinetic phases, the initial binding complete within 10s, followed by a process that is consistent with 1-methylimidazole binding to a cavity created by movement of Trp-191 from the interior of the protein to the surface. Both the equilibrium binding and kinetics of 1-methylimidazole binding to yCcP are pH dependent. yCcP has a four-fold increase in 1-methylimidazole binding affinity on decreasing the pH from 7.5 to 4.0, an observation that is unique among the many studies on binding of imidazole and imidazole derivatives to heme proteins.

Apolar distal pocket mutants of yeast cytochrome c peroxidase: Binding of imidazole, 1-methylimidazole and 4-nitroimidazole to the triAla, triVal, and triLeu variants

Imidazole binding to three apolar distal heme pocket mutants of yeast cytochrome c peroxidase (CcP) has been investigated between pH4 and 8. The three CcP variants have Arg-48, Trp-51, and His-52 mutated to either all alanine, CcP(triAla), all valine, CcP(triVal), or all leucine residues, CcP(triLeu). The imidazole binding curves for all three mutants are biphasic indicating that each of the mutants exists in at least two conformational states with different affinities for imidazole. At pH7, the high-affinity conformations of the three CcP mutants bind imidazole between 3.8 and 4.7 orders of magnitude stronger than that of wild-type CcP while the low-affinity conformations have binding affinities about 2.5 orders of magnitude larger than wild-type CcP. Imidazole binding to the three CcP mutants is pH dependent with the strongest binding observed at high pH. Apparent pKa values for the transition in binding vary between 5.6 and 7.5 for the high-affinity conformations and between 6.2 and 6.8 for the low-affinity conformations of the CcP triple mutants. The kinetics of imidazole binding are also biphasic. The fast phase of imidazole binding to CcP(triAla) and CcP(triLeu) is linearly dependent on the imidazole concentration while the slow phase is independent of imidazole concentration. Both phases of imidazole binding to CcP(triVal) have a hyperbolic dependence on the imidazole concentration. The apparent association rate constants vary between 30 and 170M−1s−1 while the apparent dissociation rate constants vary between 0.05 and 0.43s−1. The CcP triple mutants have higher binding affinities for 1-methylimidazole and 4-nitroimidazole than does wild-type CcP.

The nature of interfacial binding of imidazole and carbene ligands with M20nanoclusters (M = Au, Ag and Cu) – a theoretical study

To inspire more exciting developments in the design and advances of self-assembled monolayers (SAMs), the fundamental understanding of the nature of interaction between metal nanoparticles and certain functional groups is very crucial.

Tuning the adsorption interactions of imidazole derivatives with specific metal cations.

In this work, we report a computational study of the interactions between metal cations and imidazole derivatives in the gas phase. We first performed a systematic assessment of various density functionals and basis sets for predicting the binding energies between metal cations and the imidazoles. We find that the M11L functional in combination with the 6-311++G(d,p) basis set provides the best compromise between accuracy and computational cost with our metal···imidazole complexes. We then evaluated the binding of a series of metal cations, including Li(+), Na(+), K(+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Ba(2+), Hg(2+), and Pb(2+), with several substituted imidazole derivatives. We find that electron-donating groups increase the metal-binding energy, whereas electron-withdrawing groups decrease the metal-binding energy. Furthermore, the binding energy trends can be rationalized by the hardness of the metal cations and imidazole derivatives, providing a quick way to estimate the metal···imidazole binding strength. This insight can enable efficient screening protocols for identifying effective imidazole-based solvents and membranes for metal adsorption and provide a framework for understanding metal···imidazole interactions in biological systems.

Pump-Probe X-ray Solution Scattering Reveals Accelerated Folding of Cytochrome c Upon Suppression of Misligation.

Pump-Probe X-ray Solution Scattering Reveals Accelerated Folding of Cytochrome c Upon Suppression of Misligation.

Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles.

Human carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration and dehydration of CO2 and HCO3 (-), respectively. The reaction follows a ping-pong mechanism, in which the rate-limiting step is the transfer of a proton from the zinc-bound solvent (OH(-)/H2O) in/out of the active site via His64, which is widely believed to be the proton-shuttling residue. The decreased catalytic activity (∼20-fold lower with respect to the wild type) of a variant of CA II in which His64 is replaced with Ala (H64A CA II) can be enhanced by exogenous proton donors/acceptors, usually derivatives of imidazoles and pyridines, to almost the wild-type level. X-ray crystal structures of H64A CA II in complex with four imidazole derivatives (imidazole, 1--methylimidazole, 2--methylimidazole and 4-methylimidazole) have been determined and reveal multiple binding sites. Two of these imidazole binding sites have been identified that mimic the positions of the 'in' and 'out' rotamers of His64 in wild-type CA II, while another directly inhibits catalysis by displacing the zinc-bound solvent. The data presented here not only corroborate the importance of the imidazole side chain of His64 in proton transfer during CA catalysis, but also provide a complete structural understanding of the mechanism by which imidazoles enhance (and inhibit when used at higher concentrations) the activity of H64A CA II.

Preparation of an aminopropyl imidazole-modified silica gel as a sorbent for solid-phase extraction of carboxylic acid compounds and polycyclic aromatic hydrocarbons

In this paper, a kind of aminopropyl imidazole-modified silica sorbent was synthesized and used as a solid-phase extraction (SPE) sorbent for the determination of carboxylic acid compounds and polycyclic aromatic hydrocarbons (PAHs). The resultant aminopropyl imidazole-modified silica sorbent was characterized by Fourier transform infrared spectroscopy (FT-IR) and elemental analysis (EA) to ensure the successful binding of aminopropyl imidazole on the surface of silica gel. Then the aminopropyl imidazole-modified silica sorbent served as a SPE sorbent for the enrichment of carboxylic acid compounds and PAHs. The new sorbent exhibited high extraction efficiency towards the tested compounds and the results show that such a sorbent can offer multiple intermolecular interactions: electrostatic, π-π, and hydrophobic interactions. Several parameters affecting the extraction recovery, such as the pH of sample solution, the pH of eluent, the solubility of eluent, the volume of eluent, and sample loading, were also investigated. Under the optimized conditions, the proposed method was applied to the analysis of four carboxylic acid compounds and four PAHs in environmental water samples. Good linearities were obtained for all the tested compounds with R(2) larger than 0.9903. The limits of detection were found to be in the range of 0.0065-0.5 μg L(-1). The recovery values of spiked river water samples were from 63.2% to 112.3% with relative standard deviations (RSDs) less than 10.1% (n = 4).

Electrochemical measurement of intraprotein and interprotein electron transfer

Intramolecular and intermolecular direct (unmediated) electron transfer was studied by means of electrochemical techniques in flavohemoprotein cytochrome P450 BM3 (CYP102A1 from Bacillius megaterium) and between cytochrome b5 and cytochrome c. Flavohemoprotein cytochrome P450 BM3 was immobilized on a screen printed graphite electrode, modified with a biocompatible nanocomposite material based on the didodecyldimethylammonium bromide DDAB and gold nanoparticles. Analytical characterictics of DDAB/Au/P450 BM3 electrodes were studied with cyclic voltammetry and square wave voltammetry. It was shown that intramolecular electron transfer was realized between diflavin (FAD/FMN) and heme domain of CYP102A1. An electron transport chain of flavohemoprotein P450 BM3 immobilized at nanostructued electrode is realized as: electrode --> FAD --> FMN --> heme. Electron transfer occurs inside the protein, and it is an evidence of functional interaction between diflavin and heme domains. The effect of a substrate (lauric acid) or inhibitors (metyrapone or imidazole) binding on the electrochemical parameters of flavohemoprotein P450 BM3 was also studied. Interprotein electron transfer was analyzed between cytochrome b5 and cytochrome c. Electrochemical analysis revealed that electron transfer takes place in protein-protein complexes with participants possessing different redox potentials.

Crystal structure of two anti-porphyrin antibodies with peroxidase activity.

We report the crystal structures at 2.05 and 2.45 Å resolution of two antibodies, 13G10 and 14H7, directed against an iron(III)-αααβ-carboxyphenylporphyrin, which display some peroxidase activity. Although these two antibodies differ by only one amino acid in their variable λ-light chain and display 86% sequence identity in their variable heavy chain, their complementary determining regions (CDR) CDRH1 and CDRH3 adopt very different conformations. The presence of Met or Leu residues at positions preceding residue H101 in CDRH3 in 13G10 and 14H7, respectively, yields to shallow combining sites pockets with different shapes that are mainly hydrophobic. The hapten and other carboxyphenyl-derivatized iron(III)-porphyrins have been modeled in the active sites of both antibodies using protein ligand docking with the program GOLD. The hapten is maintained in the antibody pockets of 13G10 and 14H7 by a strong network of hydrogen bonds with two or three carboxylates of the carboxyphenyl substituents of the porphyrin, respectively, as well as numerous stacking and van der Waals interactions with the very hydrophobic CDRH3. However, no amino acid residue was found to chelate the iron. Modeling also allows us to rationalize the recognition of alternative porphyrinic cofactors by the 13G10 and 14H7 antibodies and the effect of imidazole binding on the peroxidase activity of the 13G10/porphyrin complexes.

Erratum to: Axial Imidazole Binding Strengths in Porphyrinoid Cobalt(III) Complexes as Studied by Tandem Mass Spectrometry

The Co(II) complexes of twelve meso-tetraaryl-porphyrins, -chlorins, and chlorin analogues containing non-pyrrolic heterocycles were synthesized and converted in situ to the corresponding Co(III) complexes coordinated to one or two imidazoles. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) in conjunction with the energy-variable collision-induced dissociation (CID) technique was used to compare the relative gas-phase binding strength of the axially coordinated imidazoles to the octahedral and square planar Co(III) porphyrinoid complex ions. The observed binding energies of these ligands were rationalized in terms of the effects of porphyrinoid core structure and meso-substitution on the electron density on the central Co(III) centers. Some of these trends were supported by DFT-based computational studies. The study highlights to which extend porphyrins vary from chlorins and chlorin analogues in their coordination abilities and to which extraordinary degree meso-thienyl-substituents influence the electronic structure of porphyrins. The study also defines further the scope and limits CID experiments can be used to interrogate the electronic structures of metalloporphyrin complexes.

Unusual Spectroscopic and Ligand Binding Properties of the Cytochrome P450-Flavodoxin Fusion Enzyme XplA

The Rhodococcus rhodochrous strain 11Y XplA enzyme is an unusual cytochrome P450-flavodoxin fusion enzyme that catalyzes reductive denitration of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazene (RDX). We show by light scattering that XplA is a monomeric enzyme. XplA has high affinity for imidazole (K(d) = 1.6 μM), explaining previous reports of a red-shifted XplA Soret band in pure enzyme. The true Soret maximum of XplA is at 417 nm. Similarly, unusually weak XplA flavodoxin FMN binding (K(d) = 1.09 μM) necessitates its purification in the presence of the cofactor to produce hallmark flavin contributions absent in previously reported spectra. Structural and ligand-binding data reveal a constricted active site able to accommodate RDX and small inhibitory ligands (e.g. 4-phenylimidazole and morpholine) while discriminating against larger azole drugs. The crystal structure also identifies a high affinity imidazole binding site, consistent with its low K(d), and shows active site penetration by PEG, perhaps indicative of an evolutionary lipid-metabolizing function for XplA. EPR studies indicate heterogeneity in binding mode for RDX and other ligands. The substrate analog trinitrobenzene does not induce a substrate-like type I optical shift but creates a unique low spin EPR spectrum due to influence on structure around the distal water heme ligand. The substrate-free heme iron potential (-268 mV versus NHE) is positive for a low spin P450, and the elevated potential of the FMN semiquinone/hydroquinone couple (-172 mV) is also an adaptation that may reflect (along with the absence of a key Thr/Ser residue conserved in oxygen-activating P450s) the evolution of XplA as a specialized RDX reductase catalyst.

Axial Imidazole Binding Strengths in Porphyrinoid Cobalt(III) Complexes as Studied by Tandem Mass Spectrometry

The Co(II) complexes of twelve meso-tetraaryl-porphyrins, -chlorins, and chlorin analogues containing non-pyrrolic heterocycles were synthesized and converted in situ to the corresponding Co(III) complexes coordinated to one or two imidazoles. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) in conjunction with the energy-variable collision-induced dissociation (CID) technique was used to compare the relative gas-phase binding strength of the axially coordinated imidazoles to the octahedral and square planar Co(III) porphyrinoid complex ions. The observed binding energies of these ligands were rationalized in terms of the effects of porphyrinoid core structure and meso-substitution on the electron density on the central Co(III) centers. Some of these trends were supported by DFT-based computational studies. The study highlights to which extend porphyrins vary from chlorins and chlorin analogues in their coordination abilities and to which extraordinary degree meso-thienyl-substituents influence the electronic structure of porphyrins. The study also defines further the scope and limits CID experiments can be used to interrogate the electronic structures of metalloporphyrin complexes.

Dynamic Assembly of Porphyrin Wires Trapped on a Highly Oriented Pyrolitic Graphite Surface

Carefully designed porphyrin building blocks assemble through selective imidazole binding in various solvents to form linear multiporphyrin objects. From a dynamic mixture of monomers, dimers, and oligomers, linear objects were observed on a highly oriented pyrolitic graphite (HOPG) surface. On the surface, the objects' morphology clearly depended on the solvent used for deposition and was modified upon heating.

Understanding How the Distal Environment Directs Reactivity in Chlorite Dismutase: Spectroscopy and Reactivity of Arg183 Mutants

The chlorite dismutase from Dechloromonas aromatica (DaCld) catalyzes the highly efficient decomposition of chlorite to O(2) and chloride. Spectroscopic, equilibrium thermodynamic, and kinetic measurements have indicated that Cld has two pH sensitive moieties; one is the heme, and Arg183 in the distal heme pocket has been hypothesized to be the second. This active site residue has been examined by site-directed mutagenesis to understand the roles of positive charge and hydrogen bonding in O-O bond formation. Three Cld mutants, Arg183 to Lys (R183K), Arg183 to Gln (R183Q), and Arg183 to Ala (R183A), were investigated to determine their respective contributions to the decomposition of chlorite ion, the spin state and coordination states of their ferric and ferrous forms, their cyanide and imidazole binding affinities, and their reduction potentials. UV-visible and resonance Raman spectroscopies showed that DaCld(R183A) contains five-coordinate high-spin (5cHS) heme, the DaCld(R183Q) heme is a mixture of five-coordinate and six-coordinate high spin (5c/6cHS) heme, and DaCld(R183K) contains six-coordinate low-spin (6cLS) heme. In contrast to wild-type (WT) Cld, which exhibits pK(a) values of 6.5 and 8.7, all three ferric mutants exhibited pH-independent spectroscopic signatures and kinetic behaviors. Steady state kinetic parameters of the chlorite decomposition reaction catalyzed by the mutants suggest that in WT DaCld the pK(a) of 6.5 corresponds to a change in the availability of positive charge from the guanidinium group of Arg183 to the heme site. This could be due to either direct acid-base chemistry at the Arg183 side chain or a flexible Arg183 side chain that can access various orientations. Current evidence is most consistent with a conformational adjustment of Arg183. A properly oriented Arg183 is critical for the stabilization of anions in the distal pocket and for efficient catalysis.

Identification of two imidazole binding sites in VAP-1

Identification of two imidazole binding sites in VAP-1

Structures and Stabilities of Fe2+/3+ Complexes Relevant to Alzheimer’s Disease: An ab Initio Study

Iron is one of the most abundant metals found in senile plaques of post mortem patients with Alzheimer's disease. However, the interaction mode between iron ions and β-amyloid peptide as well as their precise affinity is unknown. In this study we apply ab initio computational methodology to calculate binding energies of Fe(2+/3+) with the His13-His14 sequence of Aβ, as well as other important ligands such as His6 and Tyr10. Calculations were carried out at the "MP2/6-311+G(2df,2p)"//B3LYP/6-31+G(d) level of theory and solvent effects included by the IEFPCM procedure. Several reaction paths for the binding of imidazole, phenol, and the His13-His14 fragment (modeled by N-(2-(1H-imidazol-4-yl)ethyl)-3-(1H-imidazol-4-yl)propanamide) were sequentially explored. The results show that the most stable complexes containing His13-His14 and phenolate of Tyr10 are the pentacoordinated [Fe(2+)(O-HisHis)(PhO(-))(H(2)O)](+) and [Fe(3+)(N-HisHis)(PhO(-))(H(2)O)](+) compounds and that simultaneous coordination of tyrosine and His13-His14 to Fe(2+/3+) is thermodynamically favorable in water at physiological pH. Computed Raman spectra confirm the conclusion obtained by Miura et al. ( Biochemistry 2000 , 39 , 7024 ) that tyrosine is coordinated to Fe(3+) but do not exclude coordination of imidazoles. Finally, calculations of standard reduction potentials indicate that phenol coordination reduces the redox activity of the iron/Aβ complexes.

Identification of Two Imidazole Binding Sites and Key Residues for Substrate Specificity in Human Primary Amine Oxidase AOC3

Human membrane primary amine oxidase (hAOC3; also known as vascular adhesion protein-1, VAP-1) is expressed upon inflammation in most tissues, where its enzymatic activity plays a crucial role in leukocyte trafficking. We have determined two new structures of a soluble, proteolytically cleaved form of hAOC3 (sAOC3), which was extracted from human plasma. In the 2.6 Å sAOC3 structure, an imidazole molecule is hydrogen bonded to the topaquinone (TPQ) cofactor, which is in an inactive on-copper conformation, while in the 2.95 Å structure, an imidazole molecule is covalently bound to the active off-copper conformation of TPQ. A second imidazole bound by Tyr394 and Thr212 was identified in the substrate channel. We furthermore demonstrated that imidazole has an inhibitory role at high concentrations used in crystallization. A triple mutant (Met211Val/Tyr394Asn/Leu469Gly) of hAOC3 was previously reported to change substrate preferences toward those of hAOC2, another human copper-containing monoamine oxidase. We now mutated these three residues and Thr212 individually to study their distinct role in the substrate specificity of hAOC3. Using enzyme activity assays, the effect of the four single mutations was tested with four different substrates (methylamine, benzylamine, 2-phenylethylamine, and p-tyramine), and their binding modes were predicted by docking studies. As a result, Met211 and Leu469 were shown to be key residues for substrate specificity. The native structures of sAOC3 and the mutational data presented in this study will aid the design of hAOC3 specific inhibitors.