Oxygen-binding Proteins Research Articles

Characterizing Steric Limitations of the Heme Pocket in the Gas-Binding Tt H-Nox Protein using Site-Specific Incorporation of Unnatural Amino Acids

Heme Nitric Oxide and/or Oxygen (H-NOX) binding proteins are bacterial O2 and/or NO gas-sensing proteins involved in signaling a variety of functions to the cell. Much work has been done to characterize the heme-binding pocket in Thermoanaerobacter tencongensis H-NOX (Tt H-NOX) using site-directed mutagenesis with the 20 naturally occurring amino acids. We aim to further characterize the heme-binding pocket of Tt H-NOX by incorporating unnatural amino acids (UAAs) into the H-NOX scaffold, shedding light on both ligand discrimination and the tuning of ligand affinity. Currently, we are working to understand the steric limitations in this pocket by incorporating halogenated phenylalanine residues and characterizing the spectroscopic, gas-binding, and structural properties of these proteins.

The Challenging World of Biofilm Physiology.

Worldwide, infectious diseases are one of the leading causes of death among children. At least 65% of all infections are caused by the biofilm mode of bacterial growth. Bacteria colonise surfaces and grow as multicellular biofilm communities surrounded by a polymeric matrix as a common survival strategy. These sessile communities endow bacteria with high tolerance to antimicrobial agents and hence cause persistent and chronic bacterial infections, such as dental caries, periodontitis, otitis media, cystic fibrosis and pneumonia. The highly complex nature and the rapid adaptability of the biofilm population impede our understanding of the process of biofilm formation, but an important role for oxygen-binding proteins herein is clear. Much research on this bacterial lifestyle is already performed, from genome/proteome analysis to in vivo antibiotic susceptibility testing, but without significant progress in biofilm treatment or eradication. This review will present the multiple challenges of biofilm research and discuss possibilities to cross these barriers in future experimental studies.

Bioinformatic characterization of Lucina pectinata hemoglobins (778.9)

Lucina pectinata is a bivalve clam that is found in sulfide rich muds environments and lives in symbiosis with chemoautotrophic bacteria. Three different hemoglobins have been described in L. pectinata and in addition to their physiological role in the clam, are believed to be responsible for transportation hydrogen sulfide (H2S) and oxygen (O2) to a chemoautotrophic bacterial symbiont. Hemoglobin I (HbI) is a sulfide‐reactive hemeprotein while Hemoglobin II (HbII) and Hemoglobin III (HbIII) are oxygen‐reactive hemeproteins. Multiple sequence alignment analysis carried with L. pectinata hemoglobins and other mollusk globin sequences showed several conserved residues within this subfamily. Motif analysis using MEME also revealed a motif shared only between HbII and HbIII sequences. A phylogenetic tree was constructed the 19 molluscan globin sequences obtain after doing the CD‐Hit clustering. The tree separated them into three main clusters, a cluster for the class of Pteriomorphia, another for Heteroconchia and other for Gastropods. Hemoglobins of L. pectinata, which are found in the heteroconchia cluster, are group with the globins of those of the Calyptogena sp, where HbI is more related to this species while HbII and HbIII seen to be more distant. Based on the phylogenetic analysis and the reconciliation with the species tree, we suggest that a first gene duplication at an early evolutionary stage resulted in the sulphide binding and oxygen binding genes. A more recent gene duplication of the oxygen binding gene occurred to give rise to two oxygen binding proteins, HbII and HbIII. This hypothesis is supported with the fact that HbI shows low sequence homology to both HbII and HbIII, while there are more similarities between HbII and HbIII. In addition, HbI appears to have been changing over time, apparently not subject to the constraint of binding oxygen and acquired a unique function for a specialized environment.

Neuroglobin overexpression improves sensorimotor outcomes in a mouse model of traumatic brain injury

There is a significant need for novel treatments that will improve traumatic brain injury (TBI) outcomes. One potential neuroprotective mechanism is to increase oxygen binding proteins such as neuroglobin. Neuroglobin has a high affinity for oxygen, is an effective free radical scavenger, and is neuroprotective within the brain following hypoxia and ischemia. The purpose of this study was to determine whether neuroglobin overexpression improves sensorimotor outcomes following TBI in transgenic neuroglobin overexpressing (NGB) mice. Additional study aims were to determine if and when an endogenous neuroglobin response occurred following TBI in wild-type (WT) mice, and in what brain regions and cell types the response occurred. Controlled cortical impact (CCI) was performed in adult (5 month) C57/BL6 WT mice, and NGB mice constitutively overexpressing neuroglobin via the chicken beta actin promoter coupled with the cytomegalovirus distal enhancer. The gridwalk task was used for sensorimotor testing of both WT and NGB mice, prior to injury, and at 2, 3, and 7 days post-TBI. NGB mice displayed significant reductions in the average number of foot faults per minute walking at 2, 3, and 7 days post-TBI when compared to WT mice at each time point. Neuroglobin mRNA expression was assessed in the injured cortex of WT mice prior to injury, and at 1, 3, 7, and 14 days post-TBI using quantitative real time polymerase chain reaction (qRT-PCR). Neuroglobin mRNA was significantly increased at 7 days post-TBI. Immunostaining showed neuroglobin primarily localized to neurons and glial cells in the injured cortex and ipsilateral hippocampus of WT mice, while neuroglobin was present in all brain regions of NGB mice at 7 days post-TBI. These results showed that overexpression of neuroglobin reduced sensorimotor deficits following TBI, and that an endogenous increase in neuroglobin expression occurs during the subacute period. Increasing neuroglobin expression through novel therapeutic interventions during the acute period after TBI may improve recovery.

PDB40: The Protein Data Bank celebrates its 40th birthday

PDB40: The Protein Data Bank celebrates its 40th birthday

Genome Evolution in the Cold: Antarctic Icefish Muscle Transcriptome Reveals Selective Duplications Increasing Mitochondrial Function

Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modifications, including high mitochondrial densities in aerobic tissues. A genomic expansion accompanying the evolution of these fish was reported, but paucity of genomic information limits the understanding of notothenioid cold adaptation. We reconstructed and annotated the first skeletal muscle transcriptome of the icefish Chionodraco hamatus providing a new resource for icefish genomics (http://compgen.bio.unipd.it/chamatusbase/, last accessed December 12, 2012). We exploited deep sequencing of this energy-dependent tissue to test the hypothesis of selective duplication of genes involved in mitochondrial function. We developed a bioinformatic approach to univocally assign C. hamatus transcripts to orthology groups extracted from phylogenetic trees of five model species. Chionodraco hamatus duplicates were recorded for each orthology group allowing the identification of duplicated genes specific to the icefish lineage. Significantly more duplicates were found in the icefish when transcriptome data were compared with whole-genome data of model species. Indeed, duplicated genes were significantly enriched in proteins with mitochondrial localization, involved in mitochondrial function and biogenesis. In cold conditions and without oxygen-carrying proteins, energy production is challenging. The combination of high mitochondrial densities and the maintenance of duplicated genes involved in mitochondrial biogenesis and aerobic respiration might confer a selective advantage by improving oxygen diffusion and energy supply to aerobic tissues. Our results provide new insights into the genomic basis of icefish cold adaptation.

The globins: classic structures and new insights

The oxygen-binding proteins myoglobin and haemoglobin have a special place in the history of structural biology, and, by implication, of molecular biology and molecular medicine. When the first structures of these proteins were published, in 19581 and 19602, they were the only protein structures known. And even these structures bore very little resemblance to what we now think of as ‘protein structures’. The structures were far too crude – low resolution, as structural biologists say – to reveal the positions of any of the atoms. The beautiful and meticulous hand-drawn diagrams of the myoglobin monomer and the haemoglobin tetramer in these proteins show fat sausage-like shapes representing the eight -helices of the now well-known globin fold, with the haem group nestling in between. It took the genius of the principal scientists involved in that work, Max Perutz and John Kendrew, to imagine the potential of these rather unpromising looking structures. Perutz and Kendrew were jointly awarded the Nobel Prize for Chemistry in 1962, which was a particularly good year for structural biology; Watson, Crick and Wilkins were awarded the Physiology or Medicine Nobel for the DNA structure then too.

Optical Oxygen Micro- and Nanosensors for Plant Applications

Pioneered by Clark's microelectrode more than half a century ago, there has been substantial interest in developing new, miniaturized optical methods to detect molecular oxygen inside cells. While extensively used for animal tissue measurements, applications of intracellular optical oxygen biosensors are still scarce in plant science. A critical aspect is the strong autofluorescence of the green plant tissue that interferes with optical signals of commonly used oxygen probes. A recently developed dual-frequency phase modulation technique can overcome this limitation, offering new perspectives for plant research. This review gives an overview on the latest optical sensing techniques and methods based on phosphorescence quenching in diverse tissues and discusses the potential pitfalls for applications in plants. The most promising oxygen sensitive probes are reviewed plus different oxygen sensing structures ranging from micro-optodes to soluble nanoparticles. Moreover, the applicability of using heterologously expressed oxygen binding proteins and fluorescent proteins to determine changes in the cellular oxygen concentration are discussed as potential non-invasive cellular oxygen reporters.

Control of kinetics by cooperative interactions

Cooperative effects in ligand binding and dissociation kinetics are much less investigated than steady state kinetics or equilibrium binding. Nevertheless, cooperativity in ligand binding leads necessarily to characteristic properties with respect to kinetic properties of the system. In case of positive cooperativity as found in oxygen binding proteins, a typical property is an autocatalytic ligand dissociation behavior leading to a time dependent, apparent ligand dissociation rate. To follow systematically the influence of the various potentially involved parameters on this characteristic property, simulations based on the simple MWC model were performed which should be relevant for all types of models based on the concept of an allosteric unit. In cases where the initial conformational distribution is very much dominated by the R-state, the intrinsic kinetic properties of the T-state are of minor influence for the observed ligand dissociation rate. Even for fast conformational transition rates, the R-state properties together with the size of the allosteric unit and the allosteric equilibrium constant define the shape of the curve. In such a case, a simplified model of the MWC-scheme (the irreversible n-chain model) is a good approximation of the full scheme. However, if in the starting conformational distribution some liganded T-molecules are present (a few percent is enough), the average off-rates can be significantly altered. Thus, the assignment of the initial rates to R-state properties has to be done with great care. However, if the R-state strongly dominates initially it is even possible to get an estimation of the lower limit for the number of interacting subunits from kinetic data: similar to the Hill-coefficient for equilibrium conditions, a measure for "kinetic cooperativity" can be derived by comparing initial and final ligand dissociation rates.

Probing the local electronic and geometric properties of the heme iron center in a H-NOX domain

Heme-Nitric oxide and/or OXygen binding (H-NOX) proteins are a family of diatomic gas binding hemoproteins that have attracted intense research interest. Here we employ X-ray absorption near-edge structure (XANES) spectroscopy to study the nitric oxide (NO) binding site of H-NOX. This is the first time this technique has been utilized to examine the NO/H-NOX signaling pathway. XANES spectra of wildtype and a point mutant (proline 115 to alanine, P115A) of the H-NOX domain from Thermoanaerobacter tengcongensis (Tt H-NOX) were obtained and analyzed for ferrous and ferric complexes of the protein. This work provides specific structural characterization of the solution state of several Tt H-NOX ferrous complexes (− unligated, − NO, and − CO) that were previously unavailable. Our iron K-edges indicate effective charge on the iron center in the various complexes and report on the electronic environment of heme iron. We analyzed the ligand field indicator ratio (LFIR), which is extracted from XANES spectra, for each complex, providing an understanding of ligand field strength, spin state of the central iron, movement of the iron atom upon ligation, and ligand binding properties. In particular, our LFIRs indicate that the heme iron is dramatically displaced towards the distal pocket during ligand binding. Based on these results, we propose that iron displacement towards the distal heme pocket is an essential step in signal initiation in H-NOX proteins. This provides a mechanistic link between ligand binding and the changes in heme and protein conformation that have been observed for H-NOX family members during signaling.

Preface

This IUBMB special issue contains some of the contributions presented at the XVIth International Conference on Dioxygen Binding and Sensing Proteins (O2BIP), which was held at the University of Antwerp, Antwerp Belgium, 22–26 August, 2010 and organized by Sylvia Dewilde and Luc Moens. This Conference was part of a series of International Conferences on Oxygen Binding Proteins that began in September 1966, at the Statione Anton Dorhn, Naples, Italy, and was first organized by Francesco Ghiretti. Some 120 scientists from all over the world attended the 2010 Conference in Antwerp. Sessions where held on: Evolution and adaptation of oxygen binding proteins; Bacterial hemoglobins and flavohemoglobins; New structures; Oxygen sensors; Plant hemoglobins; Physiology and adaptive aspects of oxygen binding proteins; and, Comparative aspects of invertebrate and vertebrate oxygen binding proteins. We can state that the evolutionary antiquity of metaloproteins ability to bind dioxygen is going back to the origin of the cell and explains its ubiquitous occurrence. Due to the decoding of many genomes, an explosive growth of information on oxygen binding proteins has become available boosting the search for their origin and evolutionary relationships. The continuous description of new structures and functions of these old molecules confirms the necessity to study them further and in more detail. Next to these old molecules, new oxygen binding proteins have been identified and characterized. Essential in this study is the synergy of disciplines, physical and biochemical sciences, molecular and structural biology, physiology and evolutionary studies. Only by using this approach new views and paths will be opened. The conference brought the opportunity to make new personal contacts or strengthen old existing contacts and friendships and allowed collaborations, guaranteeing the rejuvenation and flourishing of the ‘Oxygen binding proteins’ community. Sylvia Dewilde and Luc MoensGuest Editors

The Redox Activity of Hemoglobins: From Physiologic Functions to Pathologic Mechanisms

Pentacoordinate respiratory hemoproteins such as hemoglobin and myoglobin have evolved to supply cells with oxygen. However, these respiratory heme proteins are also known to function as redox enzymes, reacting with compounds such as nitric oxide and peroxides. The recent discoveries of hexacoordinate hemoglobins in vertebrates and nonsymbiotic plants suggest that the redox activity of globins is inherent to the molecule. The uncontrolled formation of radical species resulting from such redox chemistry on respiratory hemoproteins can lead to oxidative damage and cellular toxicity. In this review, we examine the functions of various globins and the mechanisms by which these globins act as redox enzymes under physiologic conditions. Evidence that redox reactions also occur under disease conditions, leading to pathologic complications, also is examined, focusing on recent discoveries showing that the ferryl oxidation state of these hemoproteins is present in these disease states in vivo. In addition, we review the latest advances in the understanding of globin redox mechanisms and how they might affect cellular signaling pathways and how they might be controlled therapeutically or, in the case of hemoglobin-based blood substitutes, through rational design.

The role of a 2-on-2 haemoglobin in oxidative and nitrosative stress resistance of Antarctic Pseudoalteromonas haloplanktis TAC125

The 2-on-2 haemoglobins, previously named truncated, are monomeric, low-molecular weight oxygen-binding proteins that share the overall topology with vertebrate haemoglobins. Although several studies on 2-on-2 haemoglobins have been reported, their physiological and biochemical functions are not yet well defined, and various roles have been suggested. The genome of the psychrophilic Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125 ( PhTAC125) is endowed with three genes encoding 2-on-2 haemoglobins. To investigate the function played by one of the three trHbs, PhHbO, a PhTAC125 genomic mutant strain was constructed, in which the encoding gene was knocked-out. The mutant strain was grown under controlled conditions and several aspects of bacterium physiology were compared with those of wild-type cells when dissolved oxygen pressure in solution and growth temperature were changed. Interestingly, inactivation of the PhHbO encoding gene makes the mutant bacterial strain sensitive to high solution oxygen pressure, to H 2O 2, and to a nitrosating agent, suggesting the involvement of PhHbO in oxidative and nitrosative stress resistance.

Mitochondrial function in Antarctic notothenioid fishes that differ in the expression of oxygen-binding proteins

State III respiration rates were measured in mitochondria isolated from hearts of Antarctic notothenioid fishes that differ in the expression of hemoglobin (Hb) and myoglobin (Mb). Respiration rates were measured at temperatures between 2 and 40°C in Gobionotothen gibberifrons (+Hb/+Mb), Chaenocephalus aceratus (–Hb/–Mb) and Chionodraco rastrospinosus (–Hb/+Mb). Blood osmolarity was measured in all three species and physiological buffers prepared for isolating mitochondria and measuring respiration rates. Respiration rates were higher in mitochondria from G. gibberifrons compared to those from C. aceratus at 2°C, but were similar among all species at temperatures between 10 and 26°C. Respiration rates were significantly lower in icefishes at 35 and 40°C compared to G. gibberifrons. The respiratory control ratio of isolated mitochondria was lower in C. aceratus compared to G. gibberifrons at all temperatures below 35°C. At 35 and 40°C, mitochondria were uncoupled in all species. The Arrhenius break temperature of state III respiration was similar among all three species (30.5 ± 0.9°C) and higher than values previously reported for Antarctic notothenioids, likely due to the higher osmolarity of buffers used in this study. These results suggest that differences in mitochondrial structure, correlated with the expression of oxygen-binding proteins, minimally impact mitochondrial function.

Natural variation in a neural globin tunes oxygen sensing in wild Caenorhabditis elegans

Behaviours evolve by iterations of natural selection, but we have few insights into the molecular and neural mechanisms involved. Here we show that some Caenorhabditis elegans wild strains switch between two foraging behaviours in response to subtle changes in ambient oxygen. This finely tuned switch is conferred by a naturally variable hexacoordinated globin, GLB-5. GLB-5 acts with the atypical soluble guanylate cyclases, which are a different type of oxygen binding protein, to tune the dynamic range of oxygen-sensing neurons close to atmospheric (21%) concentrations. Calcium imaging indicates that one group of these neurons is activated when oxygen rises towards 21%, and is inhibited as oxygen drops below 21%. The soluble guanylate cyclase GCY-35 is required for high oxygen to activate the neurons; GLB-5 provides inhibitory input when oxygen decreases below 21%. Together, these oxygen binding proteins tune neuronal and behavioural responses to a narrow oxygen concentration range close to atmospheric levels. The effect of the glb-5 gene on oxygen sensing and foraging is modified by the naturally variable neuropeptide receptor npr-1 (refs 4, 5), providing insights into how polygenic variation reshapes neural circuit function.

Oxygen Pressurized X-Ray Crystallography: Probing the Dioxygen Binding Site in Cofactorless Urate Oxidase and Implications for Its Catalytic Mechanism

The localization of dioxygen sites in oxygen-binding proteins is a nontrivial experimental task and is often suggested through indirect methods such as using xenon or halide anions as oxygen probes. In this study, a straightforward method based on x-ray crystallography under high pressure of pure oxygen has been developed. An application is given on urate oxidase (UOX), a cofactorless enzyme that catalyzes the oxidation of uric acid to 5-hydroxyisourate in the presence of dioxygen. UOX crystals in complex with a competitive inhibitor of its natural substrate are submitted to an increasing pressure of 1.0, 2.5, or 4.0 MPa of gaseous oxygen. The results clearly show that dioxygen binds within the active site at a location where a water molecule is usually observed but does not bind in the already characterized specific hydrophobic pocket of xenon. Moreover, crystallizing UOX in the presence of a large excess of chloride (NaCl) shows that one chloride ion goes at the same location as the oxygen. The dioxygen hydrophilic environment (an asparagine, a histidine, and a threonine residues), its absence within the xenon binding site, and its location identical to a water molecule or a chloride ion suggest that the dioxygen site is mainly polar. The implication of the dioxygen location on the mechanism is discussed with respect to the experimentally suggested transient intermediates during the reaction cascade.

Neuroglobin and Cytoglobin Distribution in the Anterior Eye Segment

This study provides a detailed description of immunolocalization of two oxygen-binding proteins, neuroglobin (Ngb) and cytoglobin (Cygb), in the anterior segment of healthy human and canine eyes. Specific antibodies against Ngb and Cygb were used to examine their distribution patterns in anterior segment structures including the cornea, iris, trabecular meshwork, canal of Schlemm, ciliary body, and lens. Patterns of immunoreactivity (IR) were imaged with confocal scanning laser and conventional microscopy. Analysis of sectioned human and canine eyes showed Ngb and Cygb IR in the corneal epithelium and endothelium. In the iris, Ngb and Cygb IR was localized to the anterior border and the stroma, iridal sphincter, and dilator muscle. In the iridocorneal angle, Ngb and Cygb were detected in endothelial cells of the trabecular meshwork and canal of Schlemm in human. In the ciliary body, Ngb and Cygb IR was localized to the non-pigmented ciliary epithelium of the pars plana and pars plicata and in ciliary body musculature. Ngb and Cygb distribution was similar and colocalized within the same structures of healthy human and canine anterior eye segments. Based on their immunolocalization and previously reported biochemical features, we hypothesize that Ngb and Cygb may function as scavengers of reactive oxygen species. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

The Structural Analysis of Large Noncovalent Oxygen Binding Proteins by MALLS and ESI-MS: A Review on Annelid Hexagonal Bilayer Hemoglobin and Crustacean Hemocyanin

Understanding the function of macromolecular complexes is related to a precise knowledge of their structure. These large complexes are often fragile high molecular mass noncovalent multimeric proteins. Classical biochemical methods for determination of their native mass and subunit composition were used to resolve their quaternary structure, sometimes leading to different models. Recently, the development of mass spectrometry and multi-angle laser light scattering (MALLS) has enabled absolute determination of native masses and subunit masses. Electrospray ionization mass spectrometry (ESI-MS) was used in denaturing and native conditions to probe subunit composition and noncovalent assemblies masses up to 2.25 MDa. In a complementary way, MALLS provides mass and size estimation in various aqueous solvents. ESI-MS method can also give insights into post-translational modifications (glycosylation, disulfide bridges ). By combining native mass and subunit composition data, structural models can be proposed for large edifices such as annelid extracellular hexagonal bilayer hemoglobins (HBL Hb) and crustacean hemocyanins (Hc). Association/dissociation mechanisms, protein-protein interactions, structural diversity among species and environmental adaptations can also be addressed with these methods. With their absolute mass determination, the very high precision of spectrometry and the versatile nature of light scattering, ESI-MS and MALLS have provided a wealth of data helping to resolve parts of controversies for HBL-Hb models and opening access to new fields of investigation in structural diversity and molecular adaptation. In this review we will focus on annelid HBL-Hb and on crustacean Hc and on the original contributions of ESI-MS and MALLS in this field.

Diversity and distribution of hemerythrin-like proteins in prokaryotes

Hemerythrins are oxygen-binding proteins found in the body fluids and tissues of certain invertebrates. Oxygen is bound at a nonheme iron centre consisting of two oxo-bridged iron atoms bound to a characteristic set of conserved histidine: aspartate and glutamate residues with the motifs H-HxxxE-HxxxH-HxxxxD. It has recently been demonstrated biochemically that two bacterial proteins bearing the same motifs do in fact possess similar iron centres and bind oxygen in the same way. The recent profusion of prokaryotic genomic sequence data has shown that proteins bearing hemerythrin motifs are present in a wide variety of bacteria, and a few archaea. Some of these are short proteins as in eukaryotes; others appear to consist of a hemerythrin domain fused to another domain, generally a putative signal transduction domain such as a methyl-accepting chemotaxis protein, a histidine kinase, or a GGDEF protein (cyclic di-GMP synthase). If, as initial evidence suggests, these are in fact hemerythrin-like oxygen-binding proteins, then their diversity in prokaryotes far exceeds that seen in eukaryotes. Here, a survey is presented of prokaryotic protein sequences bearing hemerythrin-like motifs, for which the designation 'bacteriohemerythrins' is proposed, and their functions are speculated.

Oxypred: Prediction and Classification of Oxygen-Binding Proteins

This study describes a method for predicting and classifying oxygen-binding proteins. Firstly, support vector machine (SVM) modules were developed using amino acid composition and dipeptide composition for predicting oxygen-binding proteins, and achieved maximum accuracy of 85.5% and 87.8%, respectively. Secondly, an SVM module was developed based on amino acid composition, classifying the predicted oxygen-binding proteins into six classes with accuracy of 95.8%, 97.5%, 97.5%, 96.9%, 99.4%, and 96.0% for erythrocruorin, hemerythrin, hemocyanin, hemoglobin, leghemoglobin, and myoglobin proteins, respectively. Finally, an SVM module was developed using dipeptide composition for classifying the oxygen-binding proteins, and achieved maximum accuracy of 96.1%, 98.7%, 98.7%, 85.6%, 99.6%, and 93.3% for the above six classes, respectively. All modules were trained and tested by five-fold cross validation. Based on the above approach, a web server Oxypred was developed for predicting and classifying oxygen-binding proteins (available from http://www.imtech.res.in/raghava/oxypred/).