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BBA - Proteins and Proteomics (v.1804, #2)

Editorial Board (pp. i).

The structural biochemistry of the superoxide dismutases by J.J.P. Perry; D.S. Shin; E.D. Getzoff; J.A. Tainer (pp. 245-262).
The discovery of superoxide dismutases (SODs), which convert superoxide radicals to molecular oxygen and hydrogen peroxide, has been termed the most important discovery of modern biology never to win a Nobel Prize. Here, we review the reasons this discovery has been underappreciated, as well as discuss the robust results supporting its premier biological importance and utility for current research. We highlight our understanding of SOD function gained through structural biology analyses, which reveal important hydrogen-bonding schemes and metal-binding motifs. These structural features create remarkable enzymes that promote catalysis at faster than diffusion-limited rates by using electrostatic guidance. These architectures additionally alter the redox potential of the active site metal center to a range suitable for the superoxide disproportionation reaction and protect against inhibition of catalysis by molecules such as phosphate. SOD structures may also control their enzymatic activity through product inhibition; manipulation of these product inhibition levels has the potential to generate therapeutic forms of SOD. Markedly, structural destabilization of the SOD architecture can lead to disease, as mutations in Cu,ZnSOD may result in familial amyotrophic lateral sclerosis, a relatively common, rapidly progressing and fatal neurodegenerative disorder. We describe our current understanding of how these Cu,ZnSOD mutations may lead to aggregation/fibril formation, as a detailed understanding of these mechanisms provides new avenues for the development of therapeutics against this so far untreatable neurodegenerative pathology.

Keywords: Abbreviations; SOD; superoxide dismutase; O; 2; ; superoxide; ROS; reactive oxygen species; ALS; amyotrophic lateral sclerosis; FALS; familial ALSSuperoxide dismutase; Reactive oxygen species; Amyotrophic lateral sclerosis; Lou Gehrig's disease; Protein crystallography


Superoxide dismutases—a review of the metal-associated mechanistic variations by Isabel A. Abreu; Diane E. Cabelli (pp. 263-274).
Superoxide dismutases are enzymes that function to catalytically convert superoxide radical to oxygen and hydrogen peroxide. These enzymes carry out catalysis at near diffusion controlled rate constants via a general mechanism that involves the sequential reduction and oxidation of the metal center, with the concomitant oxidation and reduction of superoxide radicals. That the catalytically active metal can be copper, iron, manganese or, recently, nickel is one of the fascinating features of this class of enzymes. In this review, we describe these enzymes in terms of the details of their catalytic properties, with an emphasis on the mechanistic differences between the enzymes. The focus here will be concentrated mainly on two of these enzymes, copper, zinc superoxide dismutase and manganese superoxide dismutase, and some relatively subtle variations in the mechanisms by which they function.

Keywords: Superoxide Dismutase; Manganese Superoxide Dismutase (MnSOD); CopperZinc Superoxide Dismutase (CuZnSOD); Iron Superoxide Dismutase (FeSOD); Nickel Superoxide Dismutase (NiSOD); Amyotrophic Lateral Sclerosis (ALS); Pulse Radiolysis; Stopped Flow technique


15N-NMR characterization of His residues in and around the active site of FeSOD by Anne-Frances Miller; Emine Yikilmaz; Surekha Vathyam (pp. 275-284).
We have exploited15N-NMR to observe histidine (His) side chains in and around the active site of Fe-containing superoxide dismutase (FeSOD). In the oxidized state, we observe all the non-ligand His side chains and in the reduced state we can account for all the signals in the imidazole spectral region in terms of the non-ligand His′, paramagnetically displaced signals from two backbone amides, and the side chain of glutamine 69 (Gln69). We also observe signals from the His′ that ligate FeII. These confirm that neither the Q69H nor the Q69E mutation strongly affects the FeII electronic structure, despite the 250 mV and >660 mV increases in Em they produce, respectively. In the Q69H mutant, we observe two new signals attributable to the His introduced into the active site in place of Gln69. One corresponds to a protonated N and the other is strongly paramagnetically shifted, to 500 ppm. The strong paramagnetic effects support the existence of an H-bond between His69 and the solvent molecule coordinated to FeII, as proposed based on crystallography. Based on previous information that His69 is neutral, we infer that the shifted N is not protonated. Therefore, we propose that this N represents a site of H-bond acceptance from coordinated solvent, representing a reversal of the polarity of this H-bond from that in WT (wild-type) FeSOD protein. We also present evidence that substrate analogs bind to FeIISOD outside the FeII coordination sphere, affecting Gln69 but without direct involvement of His30.

Keywords: 15; N-NMR; Fe-superoxide dismutase; Paramagnetic; Chemical shift; Redox tuning; Histidine


Reductive elimination of superoxide: Structure and mechanism of superoxide reductases by Ana Filipa Pinto; João V. Rodrigues; Miguel Teixeira (pp. 285-297).
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 ∼109 M−1 s−1. In this review, the properties of these enzymes will be thoroughly discussed.

Keywords: Superoxide; Neelaredoxin; Desulfoferrodoxin; Iron


Metal uptake by manganese superoxide dismutase by James W. Whittaker (pp. 298-307).
Manganese superoxide dismutase is an important antioxidant defense metalloenzyme that protects cells from damage by the toxic oxygen metabolite, superoxide free radical, formed as an unavoidable by-product of aerobic metabolism. Many years of research have gone into understanding how the metal cofactor interacts with small molecules in its catalytic role. In contrast, very little is presently known about how the protein acquires its metal cofactor, an important step in the maturation of the protein and one that is absolutely required for its biological function. Recent work is beginning to provide insight into the mechanisms of metal delivery to manganese superoxide dismutase in vivo and in vitro.

Keywords: Apoprotein; Metal binding; Metallation; Activation; Metalloenzyme; Metalloprotein; Metallochaperone; Free radical; Antioxidant


Understanding the influence of the protein environment on the Mn(II) centers in Superoxide Dismutases using High-Field Electron Paramagnetic Resonance by Leandro C. Tabares; Jessica Gätjens; Sun Un (pp. 308-317).
One of the most puzzling questions of manganese and iron superoxide dismutases (SODs) is what is the basis for their metal-specificity. This review summarizes our findings on the Mn(II) electronic structure of SODs and related synthetic models using high-field high-frequency electron paramagnetic resonance (HFEPR), a technique that is able to achieve a very detailed and quantitative information about the electronic structure of the Mn(II) ions. We have used HFEPR to compare eight different SODs, including iron, manganese and cambialistic proteins. This comparative approach has shown that in spite of their high structural homology each of these groups have specific spectroscopic and biochemical characteristics. This has allowed us to develop a model about how protein and metal interactions influence protein pK, inhibitor binding and the electronic structure of the manganese center. To better appreciate the thermodynamic prerequisites required for metal discriminatory SOD activity and their relationship to HFEPR spectroscopy, we review the work on synthetic model systems that functionally mimic Mn-and FeSOD. Using a single ligand framework, it was possible to obtain metal-discriminatory “activity” as well as variations in the HFEPR spectra that parallel those found in the proteins. Our results give new insights into protein-metal interactions from the perspective of the Mn(II) and new steps towards solving the puzzle of metal-specificity in SODs.

Keywords: Superoxide dismutase; Manganese; High-Field EPR; Oxidative stress


Post-translational modifications of superoxide dismutase by Fumiyuki Yamakura; Hiroaki Kawasaki (pp. 318-325).
Post-translational modifications of proteins control many biological processes through the activation, inactivation, or gain-of-function of the proteins. Recent developments in mass spectrometry have enabled detailed structural analyses of covalent modifications of proteins and also have shed light on the post-translational modification of superoxide dismutase. In this review, we introduce some covalent modifications of superoxide dismutase, nitration, phosphorylation, glutathionylaion, and glycation. Nitration has been the most extensively analyzed modification both in vitro and in vivo. Reaction of human Cu,Zn superoxide dismutase (SOD) with reactive nitrogen species resulted in nitration of a single tryptophan residue to 6-nitrotryptophan, which could be a new biomarker of a formation of reactive nitrogen species. On the other hand, tyrosine 34 of human MnSOD was exclusively nitrated to 3-nitrotyrosine and almost completely inactivated by the reaction with peroxynitrite. The nitrated MnSOD has been found in many diseases caused by ischemia/reperfusion, inflammation, and others and may have a pivotal role in the pathology of the diseases. Most of the post-translational modifications have given rise to a reduced activity of SOD. Since phosphorylation and nitration of SOD have been shown to have a possible reversible process, these modifications may be related to a redox signaling process in cells. Finally we briefly introduce a metal insertion system of SOD, focusing particularly on the iron misincorporation of nSOD, as a part of post-translational modifications.

Keywords: Abbreviations; ADR; adriamycin; I/R; Ischemia/reperfusion; iNOS; inducible nitric oxide synthase; eNOS; endotherial nitric oxide synthase; nNOS; neuronal nitric oxide synthase; PAGE; polyacrylamide gel electrophoresis; RNS; reactive nitrogen species; SOD; superoxide dismutasePost-tanslational modification; Superoxide dismutase; Nitration; Phosphorylation; Glutathionylation; Metal misincorporation


Sequestration of carbon dioxide by the hydrophobic pocket of the carbonic anhydrases by John F. Domsic; Robert McKenna (pp. 326-331).
The interaction between carbon dioxide (CO2) and the α-class carbonic anhydrase, human CA 2 (HCA2) exists for only a short period due to the rapid catalytic turnover by this enzyme. The fleeting nature of this interaction has led to difficulties in its direct analysis, with previous studies placing the CO2 in the hydrophobic pocket of HCA2's active site. A more precise location was determined via the crystal structure of CO2 trapped in both wild-type (holo) and zinc-free (apo) HCA2. This provided a detailed description of the means by which CO2 is held and orientated for optimal catalysis. This information can be extended to the β and γ class enzymes to help elucidate the binding mode of CO2 in these enzymes.

Keywords: Carbonic anhydrase; Carbon dioxide; Sequestration of carbon dioxide


Proton transport in carbonic anhydrase: Insights from molecular simulation by C. Mark Maupin; Gregory A. Voth (pp. 332-341).
This article reviews the insights gained from molecular simulations of human carbonic anhydrase II (HCA II) utilizing non-reactive and reactive force fields. The simulations with a reactive force field explore protein transfer and transport via Grotthuss shuttling, while the non-reactive simulations probe the larger conformational dynamics that underpin the various contributions to the rate-limiting proton transfer event. Specific attention is given to the orientational stability of the His64 group and the characteristics of the active site water cluster, in an effort to determine both of their impact on the maximal catalytic rate. The explicit proton transfer and transport events are described by the multistate empirical valence bond (MS-EVB) method, as are alternative pathways for the excess proton charge defect to enter/leave the active site. The simulation results are interpreted in light of experimental results on the wild-type enzyme and various site-specific mutations of HCA II in order to better elucidate the key factors that contribute to its exceptional efficiency.

Keywords: Carbonic Anhydrase; Proton Transfer; Molecular Dynamics; Multi-State Empirical Valence Bond; Proton Transport; Simulation


Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations by Demian Riccardi; Shuo Yang; Qiang Cui (pp. 342-351).
Recent QM/MM analyses of proton transfer function of human carbonic anhydrase II (CAII) are briefly reviewed. The topics include a preliminary analysis of nuclear quadrupole coupling constant calculations for the zinc ion and more detailed analyses of microscopic pKa of the zinc-bound water and free energy profile for the proton transfer. From a methodological perspective, our results emphasize that performing sufficient sampling is essential to the calculation of all these quantities, which reflects the well solvated nature of CAII active site. From a mechanistic perspective, our analyses highlight the importance of electrostatics in shaping the energetics and kinetics of proton transfer in CAII for its function. We argue that once the pKa for the zinc-bound water is modulated to be in the proper range (~7.0), proton transfer through a relatively well solvated cavity towards/from the protein surface (His64) does not require any major acceleration. Therefore, although structural details like the length of the water wire between the donor and acceptor groups still may make a non-negligible contribution, our computational results and the framework of analysis suggest that the significance of such “fine-tuning” is likely secondary to the modulation of pKa of the zinc-bound water. We encourage further experimental analysis with mutation of (charged) residues not in the immediate neighborhood of the zinc ion to quantitatively test this electrostatics based framework; in particular, Φ analysis based on these mutations may shed further light into the relative importance of the classical Grotthus mechanism and the “proton hole” pathway that we have proposed recently for CAII.

Keywords: Carbonic anhydrase; Proton transfer; pK; a; QM/MM; Electric field gradient; Grotthus; Proton hole


Role of protein motions on proton transfer pathways in human carbonic anhydrase II by Arijit Roy; Srabani Taraphder (pp. 352-361).
We report here a theoretical study on the formation of long-range proton transfer pathways in proteins due to side chain conformational fluctuations of amino acid residues and reorganization of interior hydration positions. The proton transfer pathways in such systems may be modeled as fluctuating hydrogen-bonded networks with both short- and long-lived connections between the networked nodes, the latter being formed by polar protein atoms and water molecules. It is known that these fluctuations may extend over several decades of time ranging from a few femtoseconds to a few milliseconds. We have shown in this article how the use of a variety of theoretical methods may be utilized to detect a generic set of pathways and assess the feasibility of forming one or more transient connections. We demonstrate the application of these methods to the enzyme human carbonic anhydrase II and its mutants. Our results reveal several alternative pathways in addition to the one mediated by His-64. We also probe at length the mechanism of key conformational fluctuations contributing to the formation of the detected pathways.

Keywords: Proton transfer; Pathway; Conformational dynamics; Carbonic anhydrase


Structure and catalytic mechanism of the β-carbonic anhydrases by Roger S. Rowlett (pp. 362-373).
The β-carbonic anhydrases (β-CAs) are a diverse but structurally related group of zinc-metalloenzymes found in eubacteria, plant chloroplasts, red and green algae, and in the Archaea. The enzyme catalyzes the rapid interconversion of CO2 and H2O to HCO3 and H+, and is believed to be associated with metabolic enzymes that consume or produce CO2 or HCO3. For many organisms, β-CA is essential for growth at atmospheric concentrations of CO2. Of the five evolutionarily distinct classes of carbonic anhydrase, β-CA is the only one known to exhibit allosterism. Here we review the structure and catalytic mechanism of β-CA, including the structural basis for allosteric regulation.

Keywords: Abbreviations; CA; carbonic anhydrase; EXAFS; extended X-ray absorption fine structure; Rubisco; ribulose-1,5-bisphoshate carboxylase; HICA; Haemophilus influenzae; β-CA; ECCA; Escherichia coli; β-CA; MTCA; Methanobacterium thermoautotrophicum; β-CA; PPCA; Porphyridium purpureum; β-CA; PSCA; Pisium sativum; β-CA; HTCA; Halothiobacillus neapoliatanus; β-CA; Rv3588; Mycobacterium tuberculosis; Rv3588 β-CA; Rv1284; Mycobacterium tuberculosis; Rv1284 β-CA; HCAII; human α-CA II; ATCA; Arabidopsis thaliana; β-CA; SOCA; Spinacea oleracea; β-CA; HEPES; 4-(2-hydroxyethyl)piperazineethanesulfonic acid; MOPS; 2-(; N; -morpholino)ethanesulfonic acidβ-Carbonic anhydrase; Carbon dioxide; Bicarbonate; Catalytic mechanism; Kinetics; Allostery


The γ class of carbonic anhydrases by James G. Ferry (pp. 374-381).
Homologs of the γ class of carbonic anhydrases, one of five independently evolved classes, are found in the genomic sequences of diverse species from all three domains of life. The archetype (Cam) from the Archaea domain is a homotrimer of which the crystal structure reveals monomers with a distinctive left-handed parallel β-helix fold. Histidines from adjacent monomers ligate the three active site metals surrounded by residues in a hydrogen bond network essential for activity. Cam is most active with iron, the physiologically relevant metal. Although the active site residues bear little resemblance to the other classes, kinetic analyses indicate a two-step mechanism analogous to all carbonic anhydrases investigated. Phylogenetic analyses of Cam homologs derived from the databases show that Cam is representative of a minor subclass with the great majority belonging to a subclass (CamH) with significant differences in active site residues and apparent mechanism from Cam. A physiological function for any of the Cam and CamH homologs is unknown, although roles in transport of carbon dioxide and bicarbonate across membranes has been proposed.

Keywords: Carbonic anhydrase; Gamma class; Iron; Mechanism; Archaea; Methane


Carboxysomal carbonic anhydrases: Structure and role in microbial CO2 fixation by Gordon C. Cannon; Sabine Heinhorst; Cheryl A. Kerfeld (pp. 382-392).
Cyanobacteria and some chemoautotrophic bacteria are able to grow in environments with limiting CO2 concentrations by employing a CO2- concentrating mechanism (CCM) that allows them to accumulate inorganic carbon in their cytoplasm to concentrations several orders of magnitude higher than that on the outside. The final step of this process takes place in polyhedral protein microcompartments known as carboxysomes, which contain the majority of the CO2-fixing enzyme, RubisCO. The efficiency of CO2 fixation by the sequestered RubisCO is enhanced by co-localization with a specialized carbonic anhydrase that catalyzes dehydration of the cytoplasmic bicarbonate and ensures saturation of RubisCO with its substrate, CO2. There are two genetically distinct carboxysome types that differ in their protein composition and in the carbonic anhydrase(s) they employ. Here we review the existing information concerning the genomics, structure and enzymology of these uniquely adapted carbonic anhydrases, which are of fundamental importance in the global carbon cycle.

Keywords: Carboxysome; Carbonic anhydrase; CO; 2; -concentrating mechanism; Cyanobacteria; Chemoautotrophs


Carbonic anhydrase II-based metal ion sensing: Advances and new perspectives by Tamiika K. Hurst; Da Wang; Richard B. Thompson; Carol A. Fierke (pp. 393-403).
Carbonic anhydrases are archetypical zinc metalloenzymes and as such, they have been developed as the recognition element of a family of fluorescent indicators (sensors) to detect metal ions, particularly Zn2+ and Cu2+. Subtle modification of the structure of human carbonic anhydrase II isozyme (CAII) alters the selectivity, sensitivity, and response time for these sensors. Sensors using CAII variants coupled with zinc-dependent fluorescent ligands demonstrate picomolar sensitivity, unmatched selectivity, ratiometric fluorescence signal, and near diffusion-controlled response times. Recently, these sensors have been applied to measuring the readily exchangeable concentrations of zinc in the cytosol and nucleus of mammalian tissue culture cells and concentrations of free Cu2+ in seawater.

Keywords: Abbreviations; AF594; AlexaFluor 594; CAII; carbonic anhydrase isozyme II; DNSA; dansylamide; FRET; Förster resonance energy transfer; ICP-MS; inductively coupled plasma mass spectrometry; NTA; nitrilotriacetic acid; TSQ; N; -6-methoxy-8-quinolyl)-; p; -toluenesulfonamide; XRF; X-ray fluorescence spectrometryCarbonic anhydrase; Zinc; Copper; Biosensor; Fluorescence


Carbonic anhydrase IX: Biochemical and crystallographic characterization of a novel antitumor target by Giuseppina De Simone; Claudiu T. Supuran (pp. 404-409).
Isoform IX of the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1), CA IX, is a transmembrane protein involved in solid tumor acidification through the HIF-1α activation cascade. CA IX has a very high catalytic activity for the hydration of carbon dioxide to bicarbonate and protons, even at acidic pH values (of around 6.5), typical of solid, hypoxic tumors, which are largely unresponsive to classical chemo- and radiotherapy. Thus, CA IX is used as a marker of tumor hypoxia and as a prognostic factor for many human cancers. CA IX is involved in tumorigenesis through many pathways, such as pH regulation and cell adhesion control. The X-ray structure of the catalytic domain of CA IX has been recently reported, being shown that CA IX has a typical α-CA fold. However, the CA IX structure differs significantly from the other CA isozymes when the protein quaternary structure is considered. Thus, two catalytic domains of CA IX associate to form a dimer, which is stabilized by the formation of an intermolecular disulfide bond. The active site clefts and the proteoglycan (PG) domains are located on one face of the dimer, while the C-termini are located on the opposite face to facilitate protein anchoring to the cell membrane. As all mammalian CAs, CA IX is inhibited by several main classes of inhibitors, such as the inorganic anions, the sulfonamides and their bioisosteres (sulfamates, sulfamides, etc.), the phenols, and the coumarins. The mechanism of inhibition with all these classes of compounds is understood at the molecular level, but the sulfonamides and their congeners have important applications. It has been recently shown that both in vitro, in cell cultures, as well as in animals with transplanted tumors, CA IX inhibition with sulfonamides lead to a return of the extracellular pH to more normal values, which leads to a delay in tumor growth. As a consequence, CA IX represents a promising antitumor target for the development of anticancer agents with an alternative mechanism of action.

Keywords: Carbonic anhydrase IX; Drug design; X-ray crystallography; CO2 hydration; Sulfonamide inhibitor


Evaluating the role of carbonic anhydrases in the transport of HCO3-related species by Walter F. Boron (pp. 410-421).
The soluble enzyme carbonic anhydrase II (CAII) plays an important role in CO2 influx and efflux by red blood cells (RBCs), a process initiated by changes in the extracellular [CO2] (CO2-initiated CO2 transport). Evidence suggests that CAII may be part of a macromolecular complex at the inner surface of the RBC membrane. Some have suggested CAII specifically binds to a motif on the cytoplasmic C terminus (Ct) of the Cl–HCO3 exchanger AE1 and some other members of the SLC4 family of HCO3 transporters, a transport metabolon. Moreover, others have suggested that this bound CAII enhances the transport of HCO3-related species—HCO3, CO3, or CO3 ion pairs—when the process is initiated by altering the activity of the transporter (HCO3-initiated HCO3 transport). In this review, I assess the theoretical roles of CAs in the transport of CO2 and HCO3-related species, concluding that although the effect of bound CAII on CO2-initiated CO2 transport is expected to be substantial, the effect of bound CAs on HCO3-initiated HCO3 transport is expected to be modest at best. I also assess the experimental evidence for CAII binding to AE1 and other transporters, and the effects of this binding on HCO3-initiated HCO3 transport. The early conclusion that CAII binds to the Ct of AE1 appears to be the result of unpredictable effects of GST in the GST fusion proteins used in the studies. The early conclusion that bound CAII speeds HCO3-initiated HCO3 transport appears to be the result of CAII accelerating the pH changes used as a read-out of transport. Thus, it appears that CAII does not bind directly to AE1 or other SLC4 proteins, and that bound CAII does not substantially accelerate HCO3-initiated HCO3 transport.

Keywords: Metabolon; carbon dioxide; SLC4 family; Erythrocyte; ELISA; Glutathione S-transferase


Proton transfer in catalysis and the role of proton shuttles in carbonic anhydrase by Rose L. Mikulski; David N. Silverman (pp. 422-426).
The undisputed role of His64 in proton transfer during catalysis by carbonic anhydrases in the α class has raised questions concerning the details of its mechanism. The highly conserved residues Tyr7, Asn62, and Asn67 in the active-site cavity function to fine tune the properties of proton transfer by human carbonic anhydrase II (HCA II). For example, hydrophobic residues at these positions favor an inward orientation of His64 and a low p Ka for its imidazole side chain. It appears that the predominant manner in which this fine tuning is achieved in rate constants for proton transfer is through the difference in p Ka between His64 and the zinc-bound solvent molecule. Other properties of the active-site cavity, such as inward and outward conformers of His64, appear associated with the change in Δp Ka; however, there is no strong evidence to date that the inward and outward orientations of His64 are in themselves requirements for facile proton transfer in carbonic anhydrase.

Keywords: Abbreviations; HCA II; human carbonic anhydrase isozyme II; 4-MI; 4-methylimidazoleCarbonic anhydrase; Proton transfer; Carbon dioxide; Bicarbonate; Hydration

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