Theoretical study of “deep” fragmentation of hemin ion with successive loss of methyl and vinyl groups

The electronic and geometric structures, energy stability, normal mode frequencies, and spin density distribution have been calculated by the density functional theory B3LYP method with the Gen = 6-31+G*(Fe) + 6-31G(C,H,N,O), 6-31G*, and 6-311++G** basis sets for the deep fragmentation products of the free hemin ion with successive removal of methyl and vinyl groups in the electronic states with different multiplicities. The computation results are compared with the available experimental data and previous computation results for the fragmentation products of the isolated heme molecule and hemin ion with removal of carboxymethyl groups. The trends in the behavior of these properties are analyzed as a function of multiplicity, external charge, and the number of peripheral substituents at the porphyrin core.     

Electronic structure and stability of binary and ternary aluminum‐bismuth‐nitrogen nanoclusters

The electronic structure and stability in binary and ternary aluminum‐bismuth‐nitrogen nanoclusters up to six atoms are studied using density functional theory (DFT). The lowest energy geometries were obtained by sampling the geometrical space with a Monte Carlo method and geometry optimizations, at DFT level, with M06L functional. The clusters stability is analyzed using formation and fragmentation energies. Our results show that a high concentration of nitrogen presents a tendency to form nitrogen clusters. highest occupied molecular orbital‐lowest unoccupied molecular orbital gaps show the well‐known oscillation as the number of atoms is increased. Bonding between Al, Bi, and N has mainly a π character. Bismuth and aluminum atoms tend to promote high multiplicity states in small clusters. These new binary and ternary materials provide a potential new field in optoelectronics and high energetic material compounds. © 2014 Wiley Periodicals, Inc.     

Stepwise refolding of Acid-denatured myoglobin: Evidence from electrospray mass spectrometry

Application of electrospray mass spectrometry (ES/MS) to a protein refolding study was demonstrated. Acid denaturation of equine myoglobin was reversed by adding various amounts of ammonium hydroxide to the protein that was unfolded in 10% acetic acid. The protein refolding process was followed by ES/MS, in which both the changes in the protein charge-state distribution and mass were monitored. The ES/MS results show that the pH-dependent renaturation of the acid-denatured myoglobin is stepwise, consisting of two major steps. The unfolded polypeptide chain first refolds to establish a compact nativelike structure, without the assistance of the heme prosthetic group. The newly formed binding cavity then retains the heme group by noncovalent interactions. It is also shown that inclusion of a stabilizing buffer, such as ammonium acetate, in the protein solution is greatly beneficial to the ES/MS detection of intact noncovalent globin/heme complex.     

Effects of heme on the thermal stability of mesophilic and thermophilic cytochromes c: comparison between experimental and theoretical results

We have recently proposed a measure of the thermal stability of a protein: the water-entropy gain at 25?°C upon folding normalized by the number of residues, which is calculated using a hybrid of the angle-dependent integral equation theory combined with the multipolar water model and the morphometric approach. A protein with a larger value of the measure is thermally more stable. Here we extend the study to analyses on the effects of heme on the thermal stability of four cytochromes c (PA c(551), PH c(552), HT c(552), and AA c(555)) whose denaturation temperatures are considerably different from one another despite that they share significantly high sequence homology and similar three-dimensional folds. The major conclusions are as follows. For all the four cytochromes c, the thermal stability is largely enhanced by the heme binding in terms of the water entropy. For the holo states, the measure is the largest for AA c(555). However, AA c(555) has the lowest packing efficiency of heme and the apo polypeptide with hololike structure, which is unfavorable for the water entropy. The highest stability of AA c(555) is ascribed primarily to the highest efficiency of side-chain packing of the apo polypeptide itself. We argue for all the four cytochromes c that due to covalent heme linkages, the number of accessible conformations of the denatured state is decreased by the steric hindrance of heme, and the conformational-entropy loss upon folding becomes smaller, leading to an enhancement of the thermal stability. As for the apo state modeled as the native structure whose heme is removed, AA c(555) has a much larger value of the measure than the other three. Overall, the theoretical results are quite consistent with the experimental observations (e.g., at 25?°C the α-helix content of the apo state of AA c(555) is almost equal to that of the holo state while almost all helices are collapsed in the apo states of PA c(551), PH c(552), and HT c(552)).     

Folding and assembly of hemoglobin monitored by electrospray mass spectrometry using an on-line dialysis system

The native structure of hemoglobin (Hb) comprises two alpha- and two beta-subunits, each of which carries a heme group. There appear to be no previous studies that report the in vitro folding and assembly of Hb from highly unfolded alpha- and beta-globin in a "one-pot" reaction. One difficulty that has to be overcome for studies of this kind is the tendency of Hb to aggregate during refolding. This work demonstrates that denaturation of Hb in 40% acetonitrile at pH 10.0 is reversible. A dialysis-mediated solvent change to a purely aqueous environment of pH 8.0 results in Hb refolding without any apparent aggregation. Fluorescence, Soret absorption, circular dichroism, and ESI mass spectra of the protein recorded before unfolding and after refolding are almost identical. By employing an externally pressurized dialysis cell that is coupled on-line to an ESI mass spectrometer, changes in heme binding behavior, protein conformation, and quaternary structure can be monitored as a function of time. The process occurs in a stepwise sequential manner, leading from monomeric alpha- and beta-globin to heterodimeric species, which then assemble into tetramers. Overall, this mechanism is consistent with previous studies employing the mixing of folded alpha- and beta-globin. However, some unexpected features are observed, e.g., a heme-deficient beta-globin dimer that represents an off-pathway intermediate. Monomeric beta-globin is capable of binding heme before forming a complex with an alpha-subunit. This observation suggests that holo-alpha-apo-beta globin does not represent an obligatory intermediate during Hb assembly, as had been proposed previously. The on-line dialysis/ESI-MS approach developed for this work represents a widely applicable tool for studying the folding and self-assembly of noncovalent biological complexes.     

Experimental and theoretical study of the structure and reactivity of Fe1-2O< or =6- clusters with CO

Synergistic studies employing experiments in the gas phase and theoretical first principles calculations have been carried out to investigate the structure, stability, and reactivity toward CO of iron oxide cluster anions, Fe(x)O(y)- (x = 1-2, y < or = 6). Collision-induced dissociation studies of iron oxide species, employing xenon collision gas, show that FeO3- and FeO2- are the stable building blocks of the larger iron oxide clusters. Theoretical calculations show that the fragmentation patterns leading to the production of O or FeO(n) fragments are governed both by the energetics of the overall process as well as the number of intermediate states and the changes in spin multiplicity. Mass-selected experiments identified oxygen atom transfer to CO as the dominant reaction pathway for most anionic iron oxide clusters. A theoretical analysis of the molecular level pathways has been carried out to highlight the role of energetics as well as the spin states of the intermediates on the oxidation reaction.     

Probing the stability and structure of metalloporphyrin complexes with basic peptides by mass spectrometry

The stability and structure of non-covalent complexes of various peptides contatining basic amino acid residues (Arg, Lys) with metalloporphyrins were studied in a quadrupole ion trap mass spectrometer. The complexes of heme and three other metalloporphyrins with a variety of basic peptides and model systems were formed via electrospray ionization (ESI) and their stability was probed by energy-variable collision-induced dissociation (CID). A linear dependence for basic peptides and model compounds/metalloporphyrin complexes was observed in the plots of stability versus degrees of freedom and was used to evaluate relative bond strength. These results were then compared with previous data obtained for complexes of metalloporphyrins with His-containing peptides and peptides containing no basic amino acids. The binding strengths of Lys-containing peptide complexes in the gas phase was found to be almost as strong as that of Arg-containing complexes. Both systems showed stronger binding than His- containing peptides studied previously. To probe the structure of Arg and Lys non-covalent complexes (charge solvation versus salt bridges), two techniques, CID and ionmolecule reactions, were used. CID experiments indicate that the gas-phase complexes are most likely formed by charge solvation of the central metal ion in the metalloporphyrin by basic side chains of Arg or Lys. Results from the ionmolecule reaction studies are consistent with the charge solvation structure as well.     

Heme distortions in sperm-whale carbonmonoxy myoglobin: correlations between rotational strengths and heme distortions in MD-generated structures

We have investigated the effects of heme rotational isomerism in sperm-whale carbonmonoxymyoglobin using computational techniques. Several molecular dynamics simulations have been performed for the two rotational isomers A and B, which are related by a 180 degrees rotation around the alpha-gamma axis of the heme, of sperm-whale carbonmonoxy myoglobin in water. Both neutron diffraction and NMR structures were used as starting structures. In the absence of an experimental structure, the structure of isomer B was generated by rotating the heme in the structure of isomer A. Distortions of the heme from planarity were characterized by normal coordinate structural decomposition and by the angle of twist of the pyrrole rings from the heme plane. The heme distortions of the neutron diffraction structure were conserved in the MD trajectories, but in the NMR-based trajectories, where the heme distortions are less well defined, they differ from the original heme deformations. The protein matrix induced similar distortions on the hemes in orientations A and B. Our results suggest that the binding site prefers a particular macrocycle conformation, and a 180 degrees rotation of the heme does not significantly alter the protein's preference for this conformation. The intrinsic rotational strengths of the two Soret transitions, separated according to their polarization in the heme plane, show strong correlations with the ruffling deformation and the average twist angle of the pyrrole rings. The total rotational strength, which includes contributions from the chromophores in the protein, shows a weaker correlation with heme distortions.     

Direct Electrochemistry and Catalytic Activity of Hemoglobin and Myoglobin Entrapped in PEG Film

Abstract

Direct electrochemistry and electrocatalysis of two heme proteins, hemoglobin (Hb) and myoglobin (Mb), incorporated in polyethylene glycol (PEG) films, were studied by cyclic voltammetry. The two proteins exhibited a pair of well‐defined, quasi‐reversible cyclic voltammetric peaks with the apparent formal potential at about ?0.21 V (Hb) and ?0.22 V (Mb), respectively, vs. saturated calomel electrode (SCE) in pH 5.0 acetate buffer solution, characteristic of the h eme Fe(III)/Fe(II) redox couples, indicating enhanced electron transfer between the proteins and the substrate electrode in the PEG film environment. The protein–PEG films could also exhibit excellent stability. Meanwhile, positions of Soret absorption band of the proteins in the PEG films suggested that the heme proteins kept their secondary structure similar to their native state in the medium pH range. Oxygen, trichloroacetic acid, nitric oxide, and hydrogen peroxide could all be catalytically reduced by Hb or Mb in PEG films.     

Theory favors a stepwise mechanism of porphyrin degradation by a ferric hydroperoxide model of the active species of heme oxygenase

The report uses density functional theory to address the mechanism of heme degradation by the enzyme heme oxygenase (HO) using a model ferric hydroperoxide complex. HO is known to trap heme molecules and degrade them to maintain iron homeostasis in the biosystem. The degradation is initiated by complexation of the heme, then formation of the iron-hydroperoxo species, which subsequently oxidizes the meso position of the porphyrin by hydroxylation, thereby enabling eventually the cleavage of the porphyrin ring. Kinetic isotope effect studies indicate that the mechanism is assisted by general acid catalysis, via a chain of water molecules, and that all the events occur in concert. However, previous theoretical treatments indicated that the concerted mechanism has a high barrier, much higher than an alternative mechanism that is initiated by O-O bond homolysis of iron-hydroperoxide. The present contribution studies the stepwise and concerted acid-catalyzed mechanisms using H(3)O(+)(H(2)O)(n)(), n = 0-2. The effect of the acid strength is tested using the H(4)N(+)(H(2)O)(2) cluster and a fully protonated ferric hydroperoxide. All the calculations show that a stepwise mechanism that involves proton relay and O-O homolysis, in the rate-determining step, has a much lower barrier (>10 kcal/mol) than the corresponding fully concerted mechanism. The best fit of the calculated solvent kinetic isotope effect, to the experimental data, is obtained for the H(3)O(+)(H(2)O)(2) cluster. The calculated alpha-deuterium secondary kinetic isotope effect is inverse (0.95-0.98), but much less so than the experimental value (0.7). Possible reasons for this quantitative difference are discussed. Some probes are suggested that may enable experiment to distinguish the stepwise from the concerted mechanism.     

化学平衡的多重性、稳定性和重现性

利用动力学方法讨论了非理想的化学反应体系中化学平衡态的多重性、稳定性和实验上的可重现性。分析了实验结果(化学平衡态)与初始条件以及其它动力学过程之间的依赖关系,并简略讨论了化学平衡多重性和稳定性问题在某些实际问题和工程设计中的重要性。     

Theoretical study on the relationship between spin multiplicity effects and nonlinear optical properties of the pyrrole radical (C4H4N.)

The geometrical structure and stability of neutral pi-conjugated C4H4N. with three spin states were investigated by using ab initio and density functional theory (DFT) methods. In addition, the linear and nonlinear optical properties were studied at the same level combined with the finite field approach. The calculated results show that conjugation and stability decreased with increasing spin multiplicity. These reliable UCCSD results show that the polarizability (alpha) values of C4H4N. with the quartet state are maximal, while those of C4H4N. with the doublet state are minimal. The order of betatot values is betasextet > betadoublet > betaquartet. The second hyperpolarizability (gamma) values exhibit positive values. The variation trends of gamma are consistent with alpha.     

Cytochrome P450s: creating novel ligand sets

Cytochromes P450 are a ubiquitous group of hemoproteins that perform vital cellular reactions in all lifeforms. Until recently, it was thought that P450s contained non-covalently bound heme. However, it was established that covalent linkage of the heme macrocycle occurs naturally in one major group of the P450 superfamily. The reaction involves heme linkage to a conserved amino acid and is autocatalytic, occurring as a consequence of P450 turnover. This finding presents opportunities to engineer biotechnologically important P450s to covalently link the heme, in order to stabilize cofactor binding and to enhance operational stability of these P450s. This opportunity has been taken in studies on two important bacterial P450s and has produced variants with intriguingly different properties. In this article we survey the developments in the field, the relationships with heme macrocycle ligations in other proteins and the important impact that recent studies of heme ligation have had on our general appreciation of P450 structure and mechanism.     

Fragmentation mechanisms of oligodeoxynucleotides studied by H/D exchange and electrospray ionization tandem mass spectrometry

We used solution-phase hydrogen/deuterium (H/D) exchange and multistage tandem mass spectrometry (MS/MS) experiments in an electrospray ion-trap mass spectrometer operating in the negative-ion mode to investigate the consequences of the loss of a high proton-affinity (PA) base from T-rich tetra and hexadeoxynucleotides. The T-rich oligodeoxynucleotides containing one or two other nucleobases take advantage of the mass spectral inertness of T because fragmentation of a T-rich oligomer is simple, allowing a tight focus on those processes of interest. Furthermore, determination of T-rich oligodeoxynucleotides may be a starting point in the development of a mass spectrometric scheme to understand the mutagenicity of various types of DNA damage by UV radiation. For nine oligodeoxynucleotides, the nucleobases were charged by nearly exclusive D transfer and then expelled as neutral bases. Loss of the base located at the 3' end is preferred over that from the 5' terminus when the two bases are identical. The observation of partially exchanged fragments from a completely exchanged precursor ion proves intramolecular H/D exchange between hydrogen atoms that can exchange in water and those that cannot. The multiplicity of the product-ion peaks provides information on decomposition pathways and origins of the product ions and shows that the loss of base is the first step in all fragmentation of hexanucleotides, but is a competitive process for tetranucleotide fragmentation.     

Structure and electronic properties of highly charged C60 and C58 fullerenes

We present a theoretical study of the structure and electronic properties of positively charged C60(q+) and C58(q+) fullerenes (q = 0-14). Electronic energies and optimum geometries have been obtained using density-functional theory with the B3LYP functional for exchange and correlation. We have found that closed- and semiclosed-shell C60(q+) ions (q = 0, 5, and 10) preserve the original icosahedral symmetry of neutral C60. For other charges, significant distortions have been obtained. The C58(q+) fullerenes are, in general, less symmetric, being C58(8+) the closest to the spherical shape. Most C60(q+) fullerenes follow Hund's rule for spin multiplicity, while most C58(q+) fullerenes are more stable with the lowest spin multiplicity. The calculated ionization potentials for both kinds of fullerenes increase almost linearly with charge, except in the vicinity of C60(10+) and C58(8+). We have also explored the region of the potential-energy surface of C60(q+) that leads to asymmetric fission. Minima and transition states corresponding to the last steps of the fission process have been obtained. This has led us to conclude that, for 3 < or = q < or = 8, C2(+) emission is the preferred fragmentation channel, whereas, for higher q values, emission of two charged atomic fragments is more favorable. The corresponding fission barrier vanishes for q > 14.     

Theoretical study of the structure and stability of the heme dimer (FeC34H32N4O4)2 and its ion (FeC34H32N4O4) 2+

The electronic and geometric structures and the dissociation energies of the isolated molecule of heme dimer (heme)₂ = (FeC₃₄H₃₂O₄N₄)₂ and its ion (heme) ₂ ⁺ = (FeC₃₄H₃₂O₄N₄) ₂ ⁺ in the states with different multiplicities have been calculated by the density functional theory B3LYP method with the Gen-1 = 6-31G*(Fe) + 6-31G(C,H,N,O) and Gen-2 = 6-311++G*(Fe) + 6-31G*(C,H,N,O) basis sets. The computation results are compared with the analogous calculated data on monomeric heme and hemin⁺, as well as the previously considered dimeric ferriporphyrin X molecule and ion FeC₃₄H₃₁O₄N₄) ₂ ^{0, +} . In the heme dimer cation (heme) ₂ ⁺ , which is identified in mass spectra, the rings are linked with each other by a pair of Fe carbonyl bridges Fe⋯O_b = C(OH) and a pair of hydrogen bridges OH_b⋯N. According to the calculations, the most favorable state for (heme) ₂ ⁺ is the sextet in which five unpaired electrons are approximately uniformly distributed over the metal atoms, whereas the states with higher multiplicities 8 and 10 are, respectively, 0.15 and 0.20 eV higher on the energy scale. For the neutral dimer (heme)₂, the quintet is favorable in which each of the two Fe atoms has two unpaired electrons, and the states with the higher multiplicities 7 and 9 are only 0.10–0.15 eV higher. The calculated energies of dissociation D of the dimers into monomers point to a rather high stability of the (heme) ₂ ⁺ (D ∼ 1.4 1.4eV) and to a low stability of the neutral dimer (heme)₂ (D ∼ 0.3 eV). The R(Fe⋯O_b) distances in the bridges in (heme) ₂ ⁺ are 0.2–0.4 ? shorter than in (heme)₂. The trends in the behavior of the energetic and structural characteristics of the dimers (R(Fe-N), displacements of Fe atoms from the porphyrin ring plane, character of ring distortions, etc.) associated with the involvement of the and AOs of Fe atoms in bonding, as well as the spin density distribution over the Fe atoms and the rings, are analyzed as a function of the multiplicity and charge of the system. Differences in the character of interaction of the heme and ferriporphyrin dimers with molecular oxygen are discussed. Original Russian Text ? O.P. Charkin, N.M. Klimenko, D.O. Charkin, S.H. Lin, 2007, published in Zhurnal Neorganicheskoi Khimii, 2007, Vol. 52, No. 7, pp. 1166–1174.     

Activity and Stability of Chloroperoxidase in the Presence of Small Quantities of Polysaccharides: A Catalytically Favorable Conformation Was Induced

Chloroperoxidase (CPO) is thought to be the most versatile heme-containing enzyme with enormous applications in organic synthesis, biotransformation, pharmaceutical production, and detoxification of environmental pollutants. Any improvement in the stability of this enzyme will greatly enhance its application in the mentioned areas. In the present study, the effects of three polysaccharides (soluble starch, β-cyclodextrin, and dextrin) on the stability of CPO at elevated temperatures (20, 30, 35, 40, and 50 °C) or in aqueous-organic solvents media (methanol, dioxane, DMSO, and DMF) were investigated. An improved catalytic performance of CPO was observed in the presence of a small amount of the three polysaccharides, where dextrin provided the most effective promotion. The changes of enzyme structure and microenvironment around heme in the presence of additives were studied by fluorescence, circular dichroism, and UV-vis spectra analyses, as well as kinetic parameters measurement. A catalytically favorable structure of CPO was induced, including the strengthening of the α-helix structure and more exposure of heme for easy access of the substrate, resulting in an increase of catalytic turnover frequency (k (cat)) and the improvement of affinity and selectivity of CPO to substrate. The results revealed that the introduction of trace soluble starch, β-cyclodextrin, and dextrin (<10 μmol/L) in reaction media was an effective strategy for the enhancement of the thermodynamic and the operational stability of the enzyme, which are promising in view of the industrial applications of this versatile biological catalyst.     

二氯二乙烯——μú——二氯二铂络合物的质谱测定

本文报导了二氯二乙烯—μμ′—二氯二铂络合物的质谱,并基于各种同位素组合的质量及其相对丰度的计算,对其质谱做了归属。该络合物在电子轰击下的碎裂行为,我们提出两个主要的碎裂历程:端基配位基C_2H_4和C1的竞争失去,形成一系列含有稳定的四元环结构单元(Pt_2C1_2)的碎片离子,以及端基配位基和桥联氯的逐步断裂,形成另一系列含有Pt—Pt键的碎片离子。     

Interaction between the Heme and a G-Quartet in a Heme-DNA Complex

The structure of a complex between heme(Fe(3+)) and a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), has been characterized by (1)H NMR. The study demonstrated that the heme(Fe(3+)) is sandwiched between the 3'-terminal G-quartets of the G-quadruplex DNA. Hence, the net +1 charge of the heme(Fe(3+)) in the complex is surrounded by the eight carbonyl oxygen atoms of the G-quartets. Interaction between the heme Fe(3+) and G-quartets in the complex was clearly manifested in the solvent (1)H/(2)H isotope effect on the NMR parameters of paramagnetically shifted heme methyl proton signals, and interaction of the heme Fe(3+) with the eight carbonyl oxygen atoms of the two G-quartets was shown to provide a strong and axially symmetric ligand field surrounding the heme Fe(3+), yielding a heme(Fe(3+)) low-spin species with a highly symmetric heme electronic structure. This finding provides new insights as to the design of the molecular architecture and functional properties of various heme-DNA complexes.     

Tandem mass spectrometry of coprogen and deferoxamine hydroxamic siderophores

Mechanisms of fragmentation of hydroxamic siderophores are proposed comparing deuterated and nondeuterated samples. Standard siderophores (e.g. deferoxamine and coprogen) were directly injected into both ion trap and linear quadrupole mass spectrometers with electrospray ionization (ESI). Four and two fragmentation steps were carried out for deferoxamine and coprogen (analyzed by positive and negative ESI, respectively). Deferoxamine cleavages occurred in both peptide and hydroxamic bonds while the coprogen fragmentation pattern is more elaborate, since it contains Fe(III) in its structure.