Illuminating protein space with a programmable generative model

Three billion years of evolution has produced a tremendous diversity of protein molecules1, but the full potential of proteins is likely to be much greater. Accessing this potential has been challenging for both computation and experiments because the space of possible protein molecules is much larger than the space of those likely to have functions. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences, and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems that enables long-range reasoning with sub-quadratic scaling, layers for efficiently synthesizing three-dimensional structures of proteins from predicted inter-residue geometries and a general low-temperature sampling algorithm for diffusion models. Chroma achieves protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics and even natural-language prompts. The experimental characterization of 310 proteins shows that sampling from Chroma results in proteins that are highly expressed, fold and have favourable biophysical properties. The crystal structures of two designed proteins exhibit atomistic agreement with Chroma samples (a backbone root-mean-square deviation of around 1.0 Å). With this unified approach to protein design, we hope to accelerate the programming of protein matter to benefit human health, materials science and synthetic biology.

Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity

To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study subdomain modularity by creating 20 chimeras of an enzyme, Escherichia coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. Reversion to phenylalanine at key position 31 was found to partially restore catalytic activity, which could be explained by evolutionary coupling values. We performed molecular dynamics simulations using replica exchange with solute tempering. Chimeras with low catalytic activity exhibit nonhelical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate-binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.

Development of antibacterial compounds that constrain evolutionary pathways to resistance

Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here, we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC₅₀ 50–75 µM against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3-resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC₅₀) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which constrain evolutionary escape routes in pathogens.

Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak

The mechanisms of adaptation to inactivation of essential genes remain unknown. Here we inactivate E. coli dihydrofolate reductase (DHFR) by introducing D27G,N,F chromosomal mutations in a key catalytic residue with subsequent adaptation by an automated serial transfer protocol. The partial reversal G27- > C occurred in three evolutionary trajectories. Conversely, in one trajectory for D27G and in all trajectories for D27F,N strains adapted to grow at very low metabolic supplement (folAmix) concentrations but did not escape entirely from supplement auxotrophy. Major global shifts in metabolome and proteome occurred upon DHFR inactivation, which were partially reversed in adapted strains. Loss-of-function mutations in two genes, thyA and deoB, ensured adaptation to low folAmix by rerouting the 2-Deoxy-D-ribose-phosphate metabolism from glycolysis towards synthesis of dTMP. Multiple evolutionary pathways of adaptation converged to a suboptimal solution due to the high accessibility to loss-of-function mutations that block the path to the highest, yet least accessible, fitness peak.

Predicting how viruses and bacteria evolve remains a challenge. The ability to anticipate when and how bacteria might develop drug resistance would make treating life-threatening diseases easier and could potentially help prevent drug resistance altogether. Studying bacterial evolution under different conditions and cataloguing all possible DNA mutations that allow these bacteria to survive are crucial steps in predicting the appearance of drug resistance.

Studies have revealed that bacteria can adapt to sources of stress, such as antibiotics, in different ways – each involving mutations in distinct genes. However, not all the mutations provide the same benefits to the organism, and the factors that influence how bacteria will adapt are unclear.

Now, Rodrigues and Shakhnovich have used a new approach to push the adaptation ability of the bacterium Escherichia coli to the limit. First, they genetically engineered different E. coli strains by introducing distinct mutations to an enzyme the bacterium needs to make DNA. These mutations make the resulting strains dependent on external molecules to synthesize new DNA. Next, the cells were grown in conditions where the supply of these DNA precursors was progressively decreased, forcing them to adapt. The obvious way for bacteria to adapt to these conditions would be to ‘revert’ the mutations that Rodrigues and Shakhnovich introduced in the first place. By using this approach, Rodrigues and Shakhnovich were able to test how often the obvious evolutionary solution happens compared with presumably less-preferred alternative routes.

In rare cases, a specific mutation did restore the activity of the enzyme that enabled DNA synthesis. However, in most cases the bacteria found a different evolutionary solution whereby they all adapt to the decrease in external DNA precursors in the same way, but not by reverting the original mutation. Instead, further mutations disrupt the activity of two metabolic genes, allowing the cells to use the external DNA precursors more efficiently, and keep building DNA. These cells are therefore able to survive even when the levels of the external DNA components are very low, but they will die in the complete absence of these precursor molecules.

This evolutionary solution leads to a non-optimal effect: mutations that restore the activity of the original enzyme, which are the best solution when the two metabolic genes are intact, are no longer as effective. This finding represents a clear example of interactions between genes determining evolutionary outcomes. Rodrigues and Shakhnovich showed that, since it is more likely for a random mutation to disrupt a gene than to revert a previous mutation, adaptations that are less-than-optimal but still work might predominate simply because they happen faster.

Understanding why certain evolutionary adaptations prevail is an important step in predicting evolution and may lead to breakthroughs in many areas. For example, if scientists can identify mutations likely to make bacteria resistant to drugs, it may be possible to act proactively against the bacterial strains that carry those mutations. Eventually, if the factors that lead to specific adaptations are known, it may be possible to exploit this knowledge to create weaknesses in the bacteria’s own defences.

Evolution on the Biophysical Fitness Landscape of an RNA Virus

Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics that propagates millions of independent small viral subpopulations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction, an atypical case in evolution. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs between molecular traits of viral proteins shape viral evolution.

Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity

While reverse genetics and functional genomics have long affirmed the role of individual mutations in determining protein function, there have been fewer studies addressing how large-scale changes in protein sequences, such as in entire modular segments, influence protein function and evolution. Given how recombination can reassort protein sequences, these types of changes may play an underappreciated role in how novel protein functions evolve in nature. Such studies could aid our understanding of whether certain organismal phenotypes related to protein function-such as growth in the presence or absence of an antibiotic-are robust with respect to the identity of certain modular segments. In this study, we combine molecular genetics with biochemical and biophysical methods to gain a better understanding of protein modularity in dihydrofolate reductase (DHFR), an enzyme target of antibiotics also widely used as a model for protein evolution. We replace an integral α-helical segment of Escherichia coli DHFR with segments from a number of different organisms (many nonmicrobial) and examine how these chimeric enzymes affect organismal phenotypes (e.g., resistance to an antibiotic) as well as biophysical properties of the enzyme (e.g., thermostability). We find that organismal phenotypes and enzyme properties are highly sensitive to the identity of DHFR modules, and that this chimeric approach can create enzymes with diverse biophysical characteristics.

Differential Enzyme Flexibility Probed Using Solid-State Nanopores

Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.

Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants

In drug discovery, systematic variations of substituents on a common scaffold and bioisosteric replacements are often used to generate diversity and obtain molecules with better biological effects. However, this could saturate the small-molecule diversity pool resulting in drug resistance. On the other hand, conventional drug discovery relies on targeting known pockets on protein surfaces leading to drug resistance by mutations of critical pocket residues. Here, we present a two-pronged strategy of designing novel drugs that target unique pockets on a protein's surface to overcome the above problems. Dihydrofolate reductase, DHFR, is a critical enzyme involved in thymidine and purine nucleotide biosynthesis. Several classes of compounds that are structural analogues of the substrate dihydrofolate have been explored for their antifolate activity. Here, we describe 10 novel small-molecule inhibitors of Escherichia coli DHFR, EcDHFR, belonging to the stilbenoid, deoxybenzoin, and chalcone family of compounds discovered by a combination of pocket-based virtual ligand screening and systematic scaffold hopping. These inhibitors show a unique uncompetitive or noncompetitive inhibition mechanism, distinct from those reported for all known inhibitors of DHFR, indicative of binding to a unique pocket distinct from either substrate or cofactor-binding pockets. Furthermore, we demonstrate that rescue mutants of EcDHFR, with reduced affinity to all known classes of DHFR inhibitors, are inhibited at the same concentration as the wild-type. These compounds also exhibit antibacterial activity against E. coli harboring the drug-resistant variant of DHFR. This discovery is the first report on a novel class of inhibitors targeting a unique pocket on EcDHFR.

Free Superoxide is an Intermediate in the Production of H2O2 by Copper(I)-Aβ Peptide and O2

Oxidative stress is considered as an important factor and an early event in the etiology of Alzheimer's disease (AD). Cu bound to the peptide amyloid-β (Aβ) is found in AD brains, and Cu-Aβ could contribute to this oxidative stress, as it is able to produce in vitro H2O2 and HO˙ in the presence of oxygen and biological reducing agents such as ascorbate. The mechanism of Cu-Aβ-catalyzed H2O2 production is however not known, although it was proposed that H2O2 is directly formed from O2 via a 2-electron process. Here, we implement an electrochemical setup and use the specificity of superoxide dismutase-1 (SOD1) to show, for the first time, that H2O2 production by Cu-Aβ in the presence of ascorbate occurs mainly via a free O2˙(-) intermediate. This finding radically changes the view on the catalytic mechanism of H2O2 production by Cu-Aβ, and opens the possibility that Cu-Aβ-catalyzed O2˙(-) contributes to oxidative stress in AD, and hence may be of interest.

On the hunt for truly biocompatible ionic liquids for lipase-catalyzed reactions

One of the challenges in the field of biocatalysis is the search for efficient reaction media avoiding enzyme deactivation.

Mechanism of superoxide and hydrogen peroxide generation by human electron-transfer flavoprotein and pathological variants

Reactive oxygen species production by mitochondrial enzymes plays a fundamental role both in cellular signaling and in the progression of dysfunctional states. However, sources of reactive oxygen species and the mechanisms by which enzymes produce these reactive species still remain elusive. We characterized the generation of reactive oxygen species by purified human electron-transfer flavoprotein (ETF), a mitochondrial enzyme that has a central role in the metabolism of lipids, amino acids, and choline. The results showed that ETF produces significant amounts of both superoxide and hydrogen peroxide in the presence of its partner enzyme medium-chain acyl-CoA dehydrogenase (MCAD). ETF-mediated production of reactive oxygen species is partially inhibited at high MCAD/ETF ratios, whereas it is enhanced at high ionic strength. Determination of the reduction potentials of ETF showed that thermodynamic properties of the FAD cofactor are changed upon formation of a complex between ETF and MCAD, supporting the notion that protein:protein interactions modulate the reactivity of the protein with dioxygen. Two pathogenic ETF variants were also studied to determine which factors modulate the reactivity toward molecular oxygen and promote reactive oxygen species production. The results obtained show that destabilized conformations and defective protein:protein interactions increase the ability of ETF to generate reactive oxygen species. A possible role for these processes in mitochondrial dysfunction in metabolic disorders of fatty acid β-oxidation is discussed.

Mutations at the flavin binding site of ETF:QO yield a MADD-like severe phenotype in Drosophila

Following a screening on EMS-induced Drosophila mutants defective for formation and morphogenesis of epithelial cells, we have identified three lethal mutants defective for the production of embryonic cuticle. The mutants are allelic to the CG12140 gene, the fly homologue of electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO). In humans, inherited defects in this inner membrane protein account for multiple acyl-CoA dehydrogenase deficiency (MADD), a metabolic disease of β-oxidation, with a broad range of clinical phenotypes, varying from embryonic lethal to mild forms. The three mutant alleles carried distinct missense mutations in ETF:QO (G65E, A68V and S104F) and maternal mutant embryos for ETF:QO showed lethal morphogenetic defects and a significant induction of apoptosis following germ-band elongation. This phenotype is accompanied by an embryonic accumulation of short- and medium-chain acylcarnitines (C4, C8 and C12) as well as long-chain acylcarnitines (C14 and C16:1), whose elevation is also found in severe MADD forms in humans under intense metabolic decompensation. In agreement the ETF:QO activity in the mutant embryos is markedly decreased in relation to wild type activity. Amino acid sequence analysis and structural mapping into a molecular model of ETF:QO show that all mutations map at FAD interacting residues, two of which at the nucleotide-binding Rossmann fold. This structural domain is composed by a β-strand connected by a short loop to an α-helix, and its perturbation results in impaired cofactor association via structural destabilisation and consequently enzymatic inactivation. This work thus pinpoints the molecular origins of a severe MADD-like phenotype in the fruit fly and establishes the proof of concept concerning the suitability of this organism as a potential model organism for MADD.

Cofactors and metabolites as potential stabilizers of mitochondrial acyl-CoA dehydrogenases

Protein misfolding is a hallmark of a number of metabolic diseases, in which fatty acid oxidation defects are included. The latter result from genetic deficiencies in transport proteins and enzymes of the mitochondrial β-oxidation, and milder disease conditions frequently result from conformational destabilization and decreased enzymatic function of the affected proteins. Small molecules which have the ability to raise the functional levels of the affected protein above a certain disease threshold are thus valuable tools for effective drug design. In this work we have investigated the effect of mitochondrial cofactors and metabolites as potential stabilizers in two β-oxidation acyl-CoA dehydrogenases: short chain acyl-CoA dehydrogenase and the medium chain acyl-CoA dehydrogenase as well as glutaryl-CoA dehydrogenase, which is involved in lysine and tryptophan metabolism. We found that near physiological concentrations (low micromolar) of FAD resulted in a spectacular enhancement of the thermal stabilities of these enzymes and prevented enzymatic activity loss during a 1h incubation at 40°C. A clear effect of the respective substrate, which was additive to that of the FAD effect, was also observed for short- and medium-chain acyl-CoA dehydrogenase but not for glutaryl-CoA dehydrogenase. In conclusion, riboflavin may be beneficial during feverish crises in patients with short- and medium-chain acyl-CoA dehydrogenase as well as in glutaryl-CoA dehydrogenase deficiencies, and treatment with substrate analogs to butyryl- and octanoyl-CoAs could theoretically enhance enzyme activity for some enzyme proteins with inherited folding difficulties.

Enhanced superoxide and hydrogen peroxide detection in biological assays

Superoxide reductase (SOR) is an enzyme that converts superoxide into hydrogen peroxide at a twofold higher yield than canonical superoxide dismutases (SOD). Superoxide radical detection was investigated using the Amplex red (AR)/peroxidase system to measure the difference in hydrogen peroxide production yield in the presence of SOR or SOD. We found that reduced SOR reacts with the AR oxidation intermediate, a one-electron reduced AR(*) radical, by reducing this intermediate back to the initial AR leuco compound. Ascorbate also quenched this radical in a concentration-dependent manner and could be used to compete efficiently with SOR; at concentrations of ascorbate higher than 5 microM, SOR no longer interfered with the detection of H(2)O(2). By using xanthine/xanthine oxidase as a superoxide-generating system, it was possible to successfully quantify superoxide and hydrogen peroxide in vitro using the AR/peroxidase/SOR system, either by visible absorption or by fluorescence emission, with a considerable low detection limit of 10nM/min. The use of enzymes with diffusion-limited reactivity toward superoxide substantially increases specificity and detection threshold for superoxide and turns this approach into a powerful system to detect ROS in biological systems.

Purification, crystallization and X-ray crystallographic analysis of Archaeoglobus fulgidus neelaredoxin

Neelaredoxins are a type of superoxide reductase (SOR), which are blue 14 kDa metalloproteins with a catalytic nonhaem iron centre coordinated by four histidines and one cysteine in the ferrous form. Anaerobic organisms such as Archaeoglobus fulgidus, a hyperthermophilic sulfate-reducing archaeon, have developed defence mechanisms against toxic oxygen species in which superoxide reductases play a key role. SOR is responsible for scavenging toxic superoxide anion radicals (O(2)(*-)), catalysing the one-electron reduction of superoxide to hydrogen peroxide. Crystals of recombinant A. fulgidus neelaredoxin in the oxidized form (13.7 kDa, 125 residues) were obtained using polyethylene glycol and ammonium sulfate. These crystals diffracted to 1.9 A resolution and belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 75.72, c = 185.44 A. Cell-content analysis indicated the presence of a tetramer in the asymmetric unit, with a Matthews coefficient (V(M)) of 2.36 A(3) Da(-1) and an estimated solvent content of 48%. The three-dimensional structure was determined by the MAD method and is currently under refinement.

Reductive elimination of superoxide: Structure and mechanism of superoxide reductases

Superoxide anion is among the deleterious reactive oxygen species, towards which all organisms have specialized detoxifying enzymes. For quite a long time, superoxide elimination was thought to occur through its dismutation, catalyzed by Fe, Cu, and Mn or, as more recently discovered, by Ni-containing enzymes. However, during the last decade, a novel type of enzyme was established that eliminates superoxide through its reduction: the superoxide reductases, which are spread among anaerobic and facultative microorganisms, from the three life kingdoms. These enzymes share the same unique catalytic site, an iron ion bound to four histidines and a cysteine that, in its reduced form, reacts with superoxide anion with a diffusion-limited second order rate constant of approximately 10(9) M(-1) s(-1). In this review, the properties of these enzymes will be thoroughly discussed.

Role of flavinylation in a mild variant of multiple acyl-CoA dehydrogenation deficiency: a molecular rationale for the effects of riboflavin supplementation

Mutations in the genes encoding the alpha-subunit and beta-subunit of the mitochondrial electron transfer flavoprotein (ETF) and the electron transfer flavoprotein:ubiquinone oxidoreductase (ETF:QO) cause multiple acyl-CoA dehydrogenation deficiency (MADD), a disorder of fatty acid and amino acid metabolism. Point mutations in ETF, which may compromise folding, and/or activity, are associated with both mild and severe forms of MADD. Here we report the investigation on the conformational and stability properties of the disease-causing variant ETFbeta-D128N, and our findings on the effect of flavinylation in modulating protein conformational stability and activity. A combination of biochemical and biophysical methods including circular dichroism, visible absorption, flavin, and tryptophan fluorescence emission allowed the analysis of structural changes and of the FAD moiety. The ETFbeta-D128N variant retains the overall fold of the wild type, but under stress conditions its flavin becomes less tightly bound. Flavinylation is shown to improve the conformational stability and biological activity of a destabilized D128N variant protein. Moreover, the presence of flavin prevented proteolytic digestion by avoiding protein destabilization. A patient homozygous for the ETFbeta-D128N mutation developed severe disease symptoms in association with a viral infection and fever. In agreement, our results suggest that heat inactivation of the mutant may be more relevant at temperatures above 37 degrees C. To mimic a situation of fever in vitro, the flavinylation status was tested at 39 degrees C. FAD exerts the effect of a pharmacological chaperone, improving ETF conformation, and yielding a more stable and active enzyme. Our results provide a structural and functional framework that could help to elucidate the role that an increased cellular FAD content obtained from riboflavin supplementation may play in the molecular pathogenesis of not only MADD, but genetic disorders of flavoproteins in general.

Kinetics of electron transfer from NADH to the Escherichia coli nitric oxide reductase flavorubredoxin

Escherichia coli flavorubredoxin (FlRd) belongs to the family of flavodiiron proteins (FDPs), microbial enzymes that are expressed to scavenge nitric oxide (NO) under anaerobic conditions. To degrade NO, FlRd has to be reduced by NADH via the FAD-binding protein flavorubredoxin reductase, thus the kinetics of electron transfer along this pathway was investigated by stopped-flow absorption spectroscopy. We found that NADH, but not NADPH, quickly reduces the FlRd-reductase (k = 5.5 +/- 2.2 x 10(6) M(-1).s(-1) at 5 degrees C), with a limiting rate of 255 +/- 17 s(-1). The reductase in turn quickly reduces the rubredoxin (Rd) center of FlRd, as assessed at 5 degrees C working with the native FlRd enzyme (k = 2.4 +/- 0.1 x 10(6) m(-1).s(-1)) and with its isolated Rd-domain (k approximately 1 x 10(7) M(-1).s(-1)); in both cases the reaction was found to be dependent on pH and ionic strength. In FlRd the fast reduction of the Rd center occurs synchronously with the formation of flavin mononucleotide semiquinone. Our data provide evidence that (a) FlRd-reductase rapidly shuttles electrons between NADH and FlRd, a prerequisite for NO reduction in this detoxification pathway, and (b) the electron accepting site in FlRd, the Rd center, is in very fast redox equilibrium with the flavin mononucleotide.

Superoxide reduction by Archaeoglobus fulgidus desulfoferrodoxin: comparison with neelaredoxin

Superoxide reductases (SORs) are non-heme iron-containing enzymes that remove superoxide by reducing it to hydrogen peroxide. The active center of SORs consists of a ferrous ion coordinated by four histidines and one cysteine in a square-pyramidal geometry. In the 2Fe-SOR, a distinct family of SORs, there is an additional desulforedoxin-like site that does not appear to be involved in SOR activity. Our previous studies on recombinant Archaeoglobus fulgidus neelaredoxin (1Fe-SOR) have shown that the reaction with superoxide involves the formation of a transient ferric form that, upon protonation, decays to yield an Fe(3+)-OH species, followed by binding of glutamate to the ferric ion via replacement of hydroxide (Rodrigues et al. in Biochemistry 45:9266-9278, 2006). Here, we report the characterization of recombinant desulfoferrodoxin from the same organism, which is a member of the 2Fe-SOR family, and show that the steps involved in the superoxide reduction are similar in both families of SOR. The electron donation to the SOR from its redox partner, rubredoxin, is also presented here.

Superoxide reduction mechanism of Archaeoglobus fulgidus one-iron superoxide reductase

Superoxide reductases (SORs), iron-centered enzymes responsible for reducing superoxide (O2(-)) to hydrogen peroxide, are found in many anaerobic and microaerophilic prokaryotes. The rapid reaction with an exogenous electron donor renders the reductase activity catalytic. Here, we demonstrate using pulse radiolysis that the initial reaction between O2(-) and Archaeoglobus fulgidus neelaredoxin, a one-iron SOR, leads to a short-lived transient that immediately disappears to yield a solvent-bound ferric species in acid-base equilibrium. Through comparison of wild-type neelaredoxin with mutants lacking the ferric ion coordinating glutamate, we demonstrate that the remaining step is related to the final coordination of this ligand to the oxidized metal center and kinetically characterize it for the first time, by pulse radiolysis and stopped-flow kinetics. The way exogenous phosphate perturbs the kinetics of superoxide reduction by neelaredoxin and mutant proteins was also investigated.

Rubredoxin acts as an electron donor for neelaredoxin in Archaeoglobus fulgidus

Archaeoglobus fulgidus neelaredoxin (Nlr) is an electron donor:superoxide oxidoreductase. The reaction of superoxide with reduced Nlr is almost diffusion-limited, but the overall efficiency for detoxifying superoxide in vivo depends on the rate of reduction of Nlr by electron donors. Here, we report the purification and characterization of the two type I rubredoxins from A. fulgidus (AF0880 and AF1349) and show that they act as efficient electron donors for neelaredoxin, in vitro, with a second-order rate constant of 10(7)M(-1)s(-1) at 10 degrees C and pH 7.2.

[Management of tricuspid atresia in neonates. Report of three cases and review of literature]

The present article describes the management of three neonates with tricuspid atresia and duct dependent pulmonary circulation referred to the Instituto de Coração de Pernambuco in November 1992. A brief literature review of the condition is added. Full diagnosis was established with echocardiography at the neonatal ICU; all of them were intubated, mechanically ventilated and started on PGE1 and Dopamine infusions. Within 10h to 24h of hospitalization, all were submitted to surgery. One patient died on the third postoperative day the other two were discharged in good clinical condition. Despite the small our experience shows that clinical and surgical management of tricuspid atresia with duct dependent pulmonary circulation can reach satisfactory results in our region providing that early diagnosis of cyanotic heart disease is established by the pediatrician with timely transferal of the neonate to a reference center in paediatric cardiology.

[The heart transplant. The initial experience of the Instituto do Coração de Pernambuco]

PURPOSE

To describe the initial experience of a heart transplant program in Recife, Pernambuco.

METHODS

Six patients in the final stage of heart failure were submitted to heart transplant. There were 4 male and 2 female patients, ranging in age from 15 to 61 years (mean, 43.8). Four had coronary heart disease and two dilated cardiomyopathy. The conventional operative technique of orthotopic heart transplant was used. All patients received a triple drug immunosuppressive therapy.

RESULTS

There was one death due to acute rejection on the 28th postoperative day. The 5 survivors are in functional class I in a mean follow-up period of 113 days.

CONCLUSION

The initial experience of a heart transplant program in Recife, Pernambuco, suggests that good long term results could be expected.

[Tricuspid valve endocarditis in children]

Four children, three males, with ages 5, 1, 16 and 6 years, presented with isolated tricuspid valve endocarditis. Two of them were submitted to surgical treatment. Sepsis, cardiac murmur and heart failure were present in all of them. Three presented pulmonary embolism. Echocardiography demonstrated vegetation in the tricuspid valve in all cases. Two patients, one of them submitted to surgery, died. Tricuspid valve endocarditis in children with sepsis, heart failure and pulmonary embolism is a severe condition and early surgical treatment may diminished the high mortality.

[Influence of age on the morbidity and mortality in coronary artery surgery]

To study the effects of age on the results of coronary artery bypass grafting (CABG), 250 patients operated on from 1986 to 1989 were divided into two groups: 1) less than 65 years of age and 2) older than 65. Pre, intra and postoperative data collected in all patients included: sex, type and class of angina, associated diseases, previous myocardial infarction, previous CABG, left ventricular aneurysm, bypass time, aortic cross-clamp time, number of grafts per patient, need for prolonged inotropic support, postoperative complications, and mortality. A large number of elderly patients had unstable angina (20.3% vs 6.2%), post-infarction angina (10.1% vs 7.8%), angina at rest (10.1% vs 3.6%), peripheral vascular disease (8.4% vs 2.6%), required prolonged inotropic support (18.6% vs 3.1%), had major neurological complications (8.4% vs 0.1%) and perioperative myocardial infarction (5.0% vs 0.5%). Overall mortality was 3.6% but mortality rates were significantly higher in elderly patients (11.8% vs 1.0%). These data suggest that elderly patients have an increased risk of cardiac and neurologic morbidity and mortality. It appear that the increased morbidity and mortality is related to an increased susceptibility of the elderly to serious postoperative complications.

Spontaneous development of paraplegia after repair of coarctation of the aorta

This report describes the case of a 19-month-old boy in whom paraplegia developed spontaneously 2 days after a technically uncomplicated coarctation of the aorta repair.

Technical aspects in surgery for endomyocardial fibrosis: experience with 37 patients

The surgical technique of endocardiectomy and valve replacement for patients with uni- or biventricular endomyocardial fibrosis is described. Technical details of the operation are outlined, based upon experience with 37 surgical cases.

Successful excision of an intramural fibroma of the left ventricle

A 2-year-old boy who presented with unrelated recurrent respiratory infections was found to have an enlarged cardiac silhouette on his chest roentgenogram. Clinical evaluation, echocardiography and cardiac cineangiograms failed to provide an accurate diagnosis. A left ventricular tumor was identified by exploratory thoracotomy and successful excision of an intramural fibroma of the left ventricle subsequently accomplished.