Nature of the FeO2 bonding in myoglobin: An overview from physical to clinical biochemistry

Summary The iron(II)-dioxygen bond in myoglobin and hemoglobin is a subject of wide interest. Studieas range from examinations of physical-chemical properties dependent on electronic structure, to investigations of stability as a function of oxygen supply. Stability properties are of particular importance in vivo, since the oxygenated form is known to be oxidized easily to the ferric form, which cannot be oxygenated and is therefore physiologically inactive.Kinetic and thermodynamic studies of the stability of native oxymyoglobin have revealed a new feature in FeO₂ bonding. In vivo. the iron center is always subject to a nucleophilic attack of the water molecule or hydroxyl ion, which can enter the heme pocket from the surrounding solvent, and thereby irreversibly displace the bound dioxygen from MbO₂ in the form of O ₂ ^– so that the iron is converted to the ferric form. A free energy diagram for the potential reactions of FeO₂ visualizes myoglobin as a molecular structure that can provide in solution the delicate balance of kinetic and thermodynamic factors necessary to stabilize reversible oxygenation, as opposed to irreversible autoxidation to metmyoglobin.     

A tale of tails: deciphering the contribution of terminal tails to the biochemical properties of two Dps proteins from Streptomyces coelicolor

Dps proteins are members of an extensive family of proteins that oxidise and deposit iron in the form of ferric oxide, and are also able to bind DNA. Ferroxidation centres are formed at the interface of anti-parallel dimers, which further assemble into dodecameric nanocages with a hollow core where ferric oxide is deposited. Streptomyces coelicolor encodes three Dps-like proteins (DpsA, B and C). Despite sharing the conserved four-helix bundle organisation observed in members of the Dps family, they display significant differences in the length of terminal extensions, or tails. DpsA possess both N- and C-terminal tails of different lengths, and their removal affects quaternary structure assembly to varying degrees. DpsC quaternary structure, on the other hand, is heavily dependent on its N-terminal tail as its removal abolishes correct protein folding. Analysis of the crystal structure of dodecamers from both proteins revealed remarkable differences in the position of tails and interface surface area; and provides insight to explain the differences in biochemical behaviour observed while comparing DpsA and DpsC.     

The ear-shell (Sulculus diversicolor aquatilis) myoglobin is composed of an unusual 39 kDA polypeptide chain

An unusual myoglobin was isolated from the buccal mass of the ear-shell Sulculus diversicolor aquatilis. The myoglobin consists of a 39 kDa polypeptide chain which is about double the size of the usual myoglobin subunit, contains one heme per molecule, and has an unusual spectral property ion the oxy-form. On the basis of these properties and partial amino acid sequencing, we propose that Sulculus myoglobin has a didomain structure, and that one of the two domains does not function as an oxygen-binding domain. So far, a myoglobin of this type has not been described in molluscs.     

The ear-shell (Sulculus diversicolor aquatilis) myoglobin is composed of an unusual 39 kDA polypeptide chain

Summary An unusual myoglobin was isolated from the buccal mass of the ear-shellSulculus diversicolor aquatilis. The myoglobin consists of a 39 kDa polypeptide chain which is about double the size of the usual myoglobin subunit, contains one heme per molecule, and has an unusual spectral property in the oxy-form. On the basis of these properties and partial amino acid sequencing, we propose thatSulculus myoglobin has a didomain structure, and that one of the two domains does not function as an oxygen-binding domain. So far, a myoglobin of this type has not been described in mollusos.     

Iron (III) tris(monohydrogen phosphito) chloride—a novel complex

Summary This paper describes the spectral and magnetic properties of a novel complex, iron(III) tris(monohydrogen phosphito) chloride, obtained unexpectedly by the reaction of ferric chloride, L-valine, and phosphorous acid.     

The dimeric and co-operative myoglobin ofNassa mutabilis. A peculiar case

The myoglobin present in the radular muscle of the Prosobranchia sea snailNassa mutabilis is a peculiar case among myoglobins. It is a dimer showing co-operative oxygen binding equilibrium curves with pO_{2 1/2}=4.7 mmHg, invariant with pH, and n=1.6. Although the globin is composed of 147 amino acid residues, corresponding to a molecular mass of 15760 D, gel filtration chromatography of the native myoglobin indicate Mr=26000±2000 D. Similarly, acrylamide electrophoretic analyses in SDS and velocity sedimentation indicate a molecular mass of about 13000 D for the denatured globin. The molecule is highly unstable and forms slowly a chromogen when aged or immediately upon oxidation to the ferric state. The visible region of the absorption spectrum of the O₂ or CO liganded myoglobin derivatives indicate an altered heme environment. Circular dichroism analyses confirm this indication showing negative Cotton effects in all regions of the heme absorption spectra of the MbO₂ and MbCO derivatives. Interestingly, the CD spectrum of the oxidised met-form shows a positive band almost symmetrical with respect to that of the MbO₂ derivative. This is similar to what reported for the monomeric hemoglobin ofGlycera dibranchiata for which a reversed heme orientation was proposed. Detailed resonance Raman spectroscopic studies have permitted a more direct investigation of the interactions between the heme and the protein. The proximal Fe-Im bond shows a stretching mode frequency down shifted by 5 cm^–1 with respect to the corresponding band of horse heart myoglobin, in good correlation with the much higher instability ofNassa m. myoglobin and its much lower oxygen affinity. The unusual bond instability finds additional support in a kinetic study in which the myoblogin is mixed with CO in buffered solutions at different pH values. This approach gives evidence that the Fe-Im bond is broken upon lowering the pH, with a pK of 4.0±0.2, the highest among those of deoxy hemoproteins. The rupture of the proximal bond appears to occur with a proton-linked transition showing n=1.8±0.1, again indicating cooperativity between the two subunits. The vinyl and propionate heme substituents show resonance Raman spectroscopic bands indicating different modes of interaction with their environment with respect to other myoglobins. Most interestingly, the vinyl stretching mode frequency, typically a single band, appears split in two bands inNassa m. myoglobin. This splitting is evident in all the investigated derivatives of the myoglobin, indicating that vinyl 2 and 4 are not equivalent in this molecule. A similar splitting has been found so far only inChironomus t.t. hemoglobin.     

Structural and functional properties of porin channels in E. coli outer membranes.

Porin is a channel-forming, voltage-dependent protein of E. coli outer membranes. It exhibits relatively unspecific molecular sieve properties (exclusion size 600 Da). The trimer (110 kDa) consists of three identical polypeptides. Its secondary structure is mostly beta-structure, part of which can be visualized by electron microscopy to form a single beta-pleated sheet near the protein-lipid interface of the trimer. This folding pattern is significantly different from those of the reaction centers and of bacteriorhodopsin. Moreover, it contains many polar and ionizable side chains. It is argued that local as well as global electroneutrality, and complete saturation of the entire hydrogen bonding potential not only allow the protein to reside in the hydrophobic membrane core, but also confer upon it its unusual stability.     

Life without myoglobin

Hemoproteins are widely distributed among prokaryotes, unicellular eukaryotes, plants and animals [1]. Myoglobin, a cytoplasmic hemoprotein that is restricted to cardiomyocytes and oxidative skeletal myofibers in vertebrates, has been proposed to facilitate oxygen transport to the mitochondria [1-3]. This cytoplasmic hemoprotein was the first protein to be subjected to definitive structural analysis and has been a subject of long-standing and ongoing interest to biologists [1-3]. Recently, we utilized gene disruption technology to generate mice that are viable and fertile despite a complete absence of myoglobin [4]. This unexpected result led us to reexamine existing paradigms regarding the function of myoglobin in striated muscle.     

Targeted polymeric micelles for delivery of poorly soluble drugs

Polymeric micelles (micelles formed by amphiphilic block copolymers) demonstrate a series of attractive properties as drug carriers, such as high stability both in vitro and in vivo and good biocompatibility, and can be successfully used for the solubilization of various poorly soluble pharmaceuticals. These micelles can also be used as targeted drug delivery systems. The targeting can be achieved via the enhanced permeability and retention effect (into the areas with the compromised vasculature), by making micelles of stimuli-responsive amphiphilic block copolymers, or by attaching specific targeting ligand molecules to the micelle surface. Immunomicelles prepared by coupling monoclonal antibody molecules to p-nitrophenylcarbonyl groups on the water-exposed termini of the micelle corona-forming blocks demonstrate high binding specificity and targetability. Immunomicelles prepared with cancer-specific monoclonal antibody 2C5 specifically bind to different cancer cells in vitro and demonstrate increased therapeutic activity in vivo. This new family of pharmaceutical carriers can be used for the solubilization and targeted delivery of poorly soluble drugs to various pathological sites in the body.     

Synthetic oligonucleotides as RNA mimetics: 2'-modified Rnas and N3'-->P5' phosphoramidates

Significant interest in synthetic DNA and RNA oligonucleotides and their analogues has marked the past two decades of research in chemistry and biochemistry. This attention was largely determined by the great potential of these compounds for various therapeutic applications such as antisense, antigene and ribozyme-based agents. Modified oligonucleotides have also become powerful molecular biological and biochemical research tools that allow fast and efficient regulation of gene expression and gene functions in vitro and in vivo. These applications in turn are based on the ability of the oligonucleotides to form highly sequence-specific complexes with nucleic acid targets of interest. This review summarizes recent advances in the design, synthesis, biochemical and structural properties of various RNA analogues. These comprise 3'-modified oligonucleotide N3'-->P5' phosphoramidates, analogues with modifications at the 2'-position of nucleoside sugar rings, or combinations of the two. Among the properties of the RNA minetics reviewed here are the thermal stability of their duplexes and triplexes, hydrolytic resistance to cellular nucleases and biological activity in in vitro and in vivo systems. In addition, key structural aspects of the complexes formed by the RNA analogues, including interaction with water molecules and ions, are analyzed and presented.     

无机功能晶体材料的结晶过程研究

功能晶体材料作为光、声、电等转换的重要介质,已经被广泛应用于能源、信息、航空航天等高新技术领域,是目前国际材料科学与工程学科发展的热点和前沿课题.结晶过程是制备功能材料的核心环节,结晶习性直接影响材料的光、电、磁、催化等功能特性.在无机材料的结晶过程中,晶体组成在微观上经历了从自由态离子到结晶态固体的相变过程.可以借助晶体组成离子的电负性及基团微观对称性的变化,研究结晶过程中聚集体的形成和结构演变规律.利用分子振动光谱能够从分子尺度上揭示非线性光学晶体材料在水溶液结晶过程中结晶学结构的形成过程,克服了传统原位观测手段中缺乏对非长程有序结构的确定.利用结晶生长的化学键合理论从热力学和动力学两个方面指导大块晶体的生长实践,合理调控晶体的生长表/界面热力学和动力学.将结晶生长的化学键合理论应用到大尺寸晶体提拉生长参数的设计和优化,成功搭建了大尺寸晶体智能生长系统,并成功生长了φ2″蓝宝石晶体、φ3″YAG晶体和φ4″铌酸锂晶体.     

Lipid peroxidation caused by chinoform-ferric chelate in cultured neural retinal cells

Incorporation of chinoform-ferric chelate was demonstrable in cultured neural retinal cells of chick embryos after 1 h of incubation, and the lipid peroxide level in the cells was increased strikingly 1 h thereafter. On the other hand, free ferric ions were scarcely incorporated into the cells, and a significant increase in the lipid peroxide level in the cells was not observed. These data indicate that chinoform is carrier of iron for its passage through cell membranes and that the incorporated iron induces lipid peroxidation which in turn leads to neural cell degeneration.     

Protein folding: concepts and perspectives

In this review, the main concepts of protein folding, as deduced from both theoretical and experimental in vitro studies, are presented. The thermodynamic aspects from Anfinsen's postulate, Levinthal's paradox to the concept of folding funnel as proposed by Wolynes and coworkers are described. Concerning the folding pathway(s), particular attention is brought to bear on the early steps that initiate the process in the light of the results of the fast and even ultrafast techniques presently being used. The role of structural domains as folding units is discussed. Last, from the recent studies, it can be concluded that the main rules deduced from the in vitro folding studies are valid for the folding of a nascent polypeptide chain in vivo.     

Lipoperoxide formation in the retina in ocular siderosis

Summary Insertion of iron nail into the vitreous cavity provoked the formation of lipoperoxide in the retina. In accord with the increase in lipoperoxide in the retina, ERG began to decrease. In vitro experiment using isolated retina, lipoperoxide was found to be increased in the presence of ferric or ferrous ions, while it was inhibited by adding antioxidants or ethylenediamine tetraacetate. From these results, direct cause of retinal degeneration in siderosis could be ascribed to the formation of lipoperoxide by iron-ions liberated from the piece of iron, resulting into the degeneration of the visual cell layers of the retina.     

Curcumin: From ancient medicine to current clinical trials

Curcumin is the active ingredient in the traditional herbal remedy and dietary spice turmeric (Curcuma longa). Curcumin has a surprisingly wide range of beneficial properties, including anti-inflammatory, antioxidant, chemopreventive and chemotherapeutic activity. The pleiotropic activities of curcumin derive from its complex chemistry as well as its ability to influence multiple signaling pathways, including survival pathways such as those regulated by NF-kappaB, Akt, and growth factors; cytoprotective pathways dependent on Nrf2; and metastatic and angiogenic pathways. Curcumin is a free radical scavenger and hydrogen donor, and exhibits both pro- and antioxidant activity. It also binds metals, particularly iron and copper, and can function as an iron chelator. Curcumin is remarkably non-toxic and exhibits limited bioavailability. Curcumin exhibits great promise as a therapeutic agent, and is currently in human clinical trials for a variety of conditions, including multiple myeloma, pancreatic cancer, myelodysplastic syndromes, colon cancer, psoriasis and Alzheimer's disease.     

Lipid peroxidation caused by chinoform-ferric chelate in cultured neural retinal cells

Summary Incorporation of chinoform-ferric chelate was demonstrable in cultured neural retinal cells of chick embryos after 1 h of incubation, and the lipid peroxide level in the cells was increased strikingly 1 h thereafter. On the other hand, free ferric ions were scarcely incorporated into the cells, and a significant increase in the lipid peroxide level in the cells was not observed. These data indicate that chinoform is carrier of iron for its passage through cell membranes and that the incorporated iron induces lipid peroxidation which in turn leads to neural cell degeneration.This work was supported in part by a grant from the Ministry of Health and Welfare of Japan     

AS-48 bacteriocin: close to perfection

Bacteriocin AS-48 is an intriguing molecule because of its unique structural characteristics, genetic regulation, broad activity spectrum, and potential biotechnological applications. It was the first reported circular bacteriocin and has been undoubtedly the best characterized for the last 25 years. Thus, AS-48 is the prototype of circular bacteriocins (class IV), for which the structure and genetic regulation have been elucidated. This review discusses the state-of-the-art in genetic engineering with regard to this circular protein, with the use of site-directed mutagenesis and circular permutation. Mutagenesis studies have been used to unravel the role of (a) different residues in the biological activity, underlining the relevance of several residues involved in membrane interaction and the low correlation between stability and activity and (b) three amino acids involved in maturation, providing information on the specificity of the leader peptidase and the circularization process itself. To investigate the role of circularity in the stability and biological properties of the enterocin AS-48, two different ways of linearization have been attempted: in vitro by limited proteolysis experiments and in vivo by circular permutation in the structural gene as-48A. The results summarized here show the significance of circularization on the secondary structure, potency and, especially, the stability of AS-48 and point as well to a putative role of the leader peptide as a protecting moiety in the pre-proprotein. Taken all together, the data available on circular bacteriocins support the idea that AS-48 has been engineered by nature to make a remarkably active and stable protein with a broad spectrum of activity.     

Products of the isoprostane pathway: unique bioactive compounds and markers of lipid peroxidation

We previously reported the discovery of prostaglandin F2-like compounds (F2-isoprostanes) formed by nonenzymatic free-radical-induced peroxidation of arachidonic acid. Quantification of F2-isoprostanes has proven to be a major advance in assessing oxidative stress status in vivo. Central in the pathway of formation of isoprostanes are prostaglandin H2-like endoperoxides, which also undergo rearrangement in vivo to form E-ring, D-ring, and thromboxane-ring compounds. E2- and D2-isoprostanes also undergo dehydration in vivo to form reactive cyclopentenone A2- and J2-isoprostanes, which are susceptible to Michael addition reactions with thiols. Recently, we described the formation of highly reactive gamma-ketoaldehydes (now termed isoketals) as products of isoprostane endoperoxide rearrangement which readily adduct to lysine residues on proteins and induce cross-links at rates that far exceed other aldehyde products of lipid peroxidation. Isoprostane-like compounds (neuroprostanes) and isoketal-like compounds (neuroketals) are formed from oxidation of docosahexaenoic acid, which is enriched in the brain, and measurement of neuroprostanes may provide a unique marker of oxidative neuronal injury.     

Amelogenin gene splice products: potential signaling molecules

The amelogenins, the major proteins of the developing tooth enamel matrix, are highly conserved throughout most species studied. The gene structure is similar, with a set of seven exons and intervening introns, and remarkable conservation of particular exon sizes over divergent species. Studies of exon skipping and consequent alternative gene splicing suggest that, in vertebrates, exon definition is crucial. In this mechanism, exon size is important. If too small, an exon can be readily skipped, if too large, internal cryptic splice sites may be utilized. Other factors, such as intron length and specific nucleotide sequences at the splice boundaries also modulate splicing efficiency, but amelogenin gene splicing conforms well to the generalized exon length model. Exons 1, 2 and 7 are not subject to splicing that affects the secreted protein product, but exons 3, 4 and 5 are at the lower boundary of exon size, rendering them, 4 and 5 especially, subject to skipping. On the other hand, exon 6 is very long and has cryptic splicing sites that can be used. In the mouse, nine distinct splice product proteins have been detected. The question now is the functions of these products. The larger forms, those that contain the intact proline-rich, hydrophobic exon 6 domains, are important for enamel mineralization. Recent work suggests that the small proteins resulting from deletion of a major part of amelogenin gene exon 6 via utilization of a cryptic site may have signal transduction functions during tooth development. Furthermore, new work also suggests that odontoblasts transiently express the small amelogenins during the period that epithelial-mesenchymal signaling between preodontoblasts and preameloblasts determines the course of tooth development. The same peptides have been demonstrated to act on non-odontogenic cells and effect their phenotypic expression patterns in vitro, and to induce bone formation in implants in vivo. Received 20 March 2002; received after revision 2 July 2002; accepted 3 July 2002     

Local Fluctuations and Local Observers in Equilibrium Statistical Mechanics

The distribution function associated with a classical gas at equilibrium is considered. We prove that apart from a factorisable multiplier, the distribution function is fully determined by the correlations among local momenta fluctuations. Using this result we discuss the conditions which enable idealised local observers, who are immersed in the gas and form a part of it, to determine the distribution ‘from within’. This analysis sheds light on two views on thermodynamic equilibrium, the ‘ergodic’ and the ‘thermodynamic limit’ schools, and the relations between them. It also provides an outline for a new definition of equilibrium that is weaker than full ergodicity. Finally, we briefly discuss the possibility that the distribution can be determined by external observers.