Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase

Do "Newly Born" orphan proteins resemble "Never Born" proteins? A study using three deep learning algorithms

"Newly Born" proteins, devoid of detectable homology to any other proteins, known as orphan proteins, occur in a single species or within a taxonomically restricted gene family. They are generated by the expression of novel open reading frames, and appear throughout evolution. We were curious if three recently developed programs for predicting protein structures, namely, AlphaFold2, RoseTTAFold, and ESMFold, might be of value for comparison of such "Newly Born" proteins to random polypeptides with amino acid content similar to that of native proteins, which have been called "Never Born" proteins. The programs were used to compare the structures of two sets of "Never Born" proteins that had been expressed-Group 1, which had been shown experimentally to possess substantial secondary structure, and Group 3, which had been shown to be intrinsically disordered. Overall, although the models generated were scored as being of low quality, they nevertheless revealed some general principles. Specifically, all four members of Group 1 were predicted to be compact by all three algorithms, in agreement with the experimental data, whereas the members of Group 3 were predicted to be very extended, as would be expected for intrinsically disordered proteins, again consistent with the experimental data. These predicted differences were shown to be statistically significant by comparing their accessible surface areas. The three programs were then used to predict the structures of three orphan proteins whose crystal structures had been solved, two of which display novel folds. Surprisingly, only for the protein which did not have a novel fold, and was taxonomically restricted, rather than being a true orphan, did all three algorithms predict very similar, high-quality structures, closely resembling the crystal structure. Finally, they were used to predict the structures of seven orphan proteins with well-identified biological functions, whose 3D structures are not known. Two proteins, which were predicted to be disordered based on their sequences, are predicted by all three structure algorithms to be extended structures. The other five were predicted to be compact structures with only two exceptions in the case of AlphaFold2. All three prediction algorithms make remarkably similar and high-quality predictions for one large protein, HCO_11565, from a nematode. It is conjectured that this is due to many homologs in the taxonomically restricted family of which it is a member, and to the fact that the Dali server revealed several nonrelated proteins with similar folds. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Proteins:3.

Diagnostic role of urinary CA-2 in urinary stones and its prediction of complications

BACKGROUND

Carbonic anhydrase-2 (CA-2) is involved in the mineralization and calcification of organisms. Evidence suggests that CA-2 is associated with urolithiasis. However, the relationship between CA-2 and urinary stones remains unclear. The study aimed to assess the correlation of urinary CA-2 (uCA-2) level with the risk of urinary stones.

METHODS

A retrospective cohort study was conducted on patients with urinary stones and healthy subjects who presented to our hospital between March 2017 and November 2019 to determine the pretreatment uCA-2 level by enzyme linked immunosorbent assay (ELISA). Differences in uCA-2 levels between patients with urinary stones and healthy subjects were compared. Then, comparison between stone patients with complications and those without was carried out as well as correlation analysis to detect factors associated with biomarker expression.

RESULTS

Patients with urinary stones (n=118) were designated the urinary stones group and healthy subjects (n=42) were designated the healthy control group. The mean pretreatment uCA-2 level was significantly higher in cases than in controls (P=0.028). Furthermore, the uCA-2 level had a positive correlation with urinary stone-associated complications (R=0.379, P<0.001), especially pain (R=0.524, P<0.001) and hematuria (R=0.374, P<0.001). Receiver operating characteristic curve (ROC) analysis revealed that a uCA-2 level threshold of 10.94 ng/mL had 83.67% sensitivity and 68.12% specificity for predicting complications in patients with urinary stones.

CONCLUSION

Excessive uCA-2 excretion is a major risk factor for urinary stones. Our findings suggest that uCA-2 may be used as a novel biomarker for the diagnosis of urinary stones and the prediction of its complications.

Nitric oxide generation study of unsymmetrical β-diketiminato copper(II) nitrite complexes

The β-diketiminato copper(II) L1CuCl−L4CuCl and their nitrite complexes L1Cu(O2N) and L2Cu(O2N) has been synthesized and characterized. The X-ray structure of the L1CuCl−L4CuCl complexes clearly indicates towards the mononuclear structure with...

Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase

Inorganic anions inhibit the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) generally by coordinating to the active site metal ion. Cyanate was reported as a non-coordinating CA inhibitor but those erroneous results were subsequently corrected by another group. We review the anion CA inhibitors (CAIs) in the more general context of drug design studies and the discovery of a large number of inhibitor classes and inhibition mechanisms, including zinc binders (sulphonamides and isosteres, dithiocabamates and isosteres, thiols, selenols, benzoxaboroles, ninhydrins, etc.); inhibitors anchoring to the zinc-coordinated water molecule (phenols, polyamines, sulfocoumarins, thioxocoumarins, catechols); CAIs occluding the entrance to the active site (coumarins and derivatives, lacosamide), as well as compounds that bind outside the active site. All these new chemotypes integrated with a general procedure for obtaining isoform-selective compounds (the tail approach) has resulted, through the guidance of rigorous X-ray crystallography experiments, in the development of highly selective CAIs for all human CA isoforms with many pharmacological applications.

Mechanism of O-Atom Transfer from Nitrite: Nitric Oxide Release at Copper(II)

Nitric oxide (NO) is a key signaling molecule in health and disease. While nitrite acts as a reservoir of NO activity, mechanisms for NO release require further understanding. A series of electronically varied β-diketiminatocopper(II) nitrite complexes [Cu^II](κ²-O₂N) react with a range of electronically tuned triarylphosphines PAr^Z₃ that release NO with the formation of O═PAr^Z₃. Second-order rate constants are largest for electron-poor copper(II) nitrite and electron-rich phosphine pairs. Computational analysis reveals a transition-state structure energetically matched with experimentally determined activation barriers. The production of NO follows a pathway that involves nitrite isomerization at Cu^II from κ²-O₂N to κ¹-NO₂ followed by O-atom transfer (OAT) to form O═PAr^Z₃ and [Cu^I]-NO that releases NO upon PAr^Z₃ binding at Cu^I to form [Cu^I]-PAr^Z₃. These findings illustrate important mechanistic considerations involved in NO formation from nitrite via OAT.

Nitrous anhydrase activity of carbonic anhydrase II: cysteine is required for nitric oxide (NO) dependent phosphorylation of VASP in human platelets

The carbonic anhydrase (CA) family does not only catalyse the reversible hydration of CO₂ to bicarbonate, but it also possesses esterase and phosphatase activity. Recently, bovine CA II and human CA II have been reported to convert inorganic nitrite (O=N-O⁻) to nitric oxide (NO) and nitrous anhydride (N₂O₃). Given the ability of NO to mediate vasodilation and inhibit platelet aggregation, this CA II activity would represent a bioactivation of nitrite. There are contradictory reports in the literature and the physiological role of CA II nitrite bioactivation is still disputed. Here, we provide new experimental data in support of the nitrous anhydrase activity of CA II and the key role L-cysteine in the bioactivation of nitrite by CA II. Using washed human platelets and by measuring VASP phosphorylation we provide evidence that exogenous nitrite (10 µM) is bioactivated to NO in a manner strongly depending on L-cysteine (100 and 200 µM). The process is not inhibitable by acetazolamide, a potent CA inhibitor. The contradictory results of recently published studies in this area are thoroughly discussed.

Comment on the article Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase

The paper discusses a recent paper [Andring et al. (2020). IUCrJ, 7, 287-293] on the nitrite reductase and nitrous anhydrase activity of carbonic anhydrase.

Erratum: Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase. Corrigendum

[This corrects the article DOI: 10.1107/S2052252520000986.].

Tuning the redox potential of the primary electron donor in bacterial reaction centers by manganese binding and light-induced structural changes

The influence of transition metal binding on the charge storage ability of native bacterial reaction centers (BRCs) was investigated. Binding of manganous ions uniquely prevented the light-induced conformational changes that would yield to long lifetimes of the charge separated state and the drop of the redox potential of the primary electron donor (P). The lifetimes of the stable charge pair in the terminal conformations were shortened by 50-fold and 7-fold upon manganous and cupric ion binding, respectively. Nickel and zinc binding had only marginal effects. Binding of manganese not only prevented the drop of the potential of P/P⁺ but also elevated it by up to 117 mV depending on where the metal was binding. With variable conditions, facilitating either manganese binding or light-induced structural changes a controlled tuning of the potential of P/P⁺ in multiple steps was demonstrated in a range of ~200 mV without the need of a mutation or synthesis. Under the selected conditions, manganese binding was achieved without its photochemical oxidation thus, the energized but still native BRCs can be utilized in photochemistry that is not reachable with regular BRCs. A 42 Å long hydrophobic tunnel was identified that became obstructed upon manganese binding and its likely role is to deliver protons from the hydrophobic core to the surface during conformational changes.

The Active Site of a Prototypical "Rigid" Drug Target is Marked by Extensive Conformational Dynamics

Drug discovery, in particular optimization of candidates using medicinal chemistry, is generally guided by structural biology. However, for optimizing binding kinetics, relevant for efficacy and off-target effects, information on protein motion is important. Herein, we demonstrate for the prototypical textbook example of an allegedly "rigid protein" that substantial active-site dynamics have generally remained unrecognized, despite thousands of medicinal-chemistry studies on this model over decades. Comparing cryogenic X-ray structures, solid-state NMR on micro-crystalline protein at room temperature, and solution NMR structure and dynamics, supported by MD simulations, we show that under physiologically relevant conditions the pocket is in fact shaped by pronounced open/close conformational-exchange dynamics. The study, which is of general significance for pharmacological research, evinces a generic pitfall in drug discovery routines.

Elucidating the role of metal ions in carbonic anhydrase catalysis

Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn²⁺, tetrahedral to octahedral conversion for Co²⁺, octahedral for Ni²⁺, and trigonal bipyramidal for Cu²⁺) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.

Carbonic Anhydrases: Versatile and Useful Biocatalysts in Chemistry and Biochemistry

Metalloenzymes such as the carbonic anhydrases (CAs, EC 4.2.1.1) possess highly specialized active sites that promote fast reaction rates and high substrate selectivity for the physiologic reaction that they catalyze, hydration of CO2 to bicarbonate and a proton. Among the eight genetic CA macrofamilies, α-CAs possess rather spacious active sites and show catalytic promiscuity, being esterases with many types of esters, but also acting on diverse small molecules such as cyanamide, carbonyl sulfide (COS), CS2, etc. Although artificial CAs have been developed with the intent to efficiently catalyse non-biologically related chemical transformations with high control of stereoselectivity, the activities of these enzymes were much lower when compared to natural CAs. Here, we report an overview on the catalytic activities of α-CAs as well as of enzymes which were mutated or artificially designed by incorporation of transition metal ions. In particular, the distinct catalytic mechanisms of the reductase, oxidase and metatheses-ase such as de novo designed CAs are discussed.

Perspectives on the Classical Enzyme Carbonic Anhydrase and the Search for Inhibitors

Carbonic anhydrase (CA) is a thoroughly studied enzyme. Its primary role is the rapid interconversion of carbon dioxide and bicarbonate in the cells, where carbon dioxide is produced, and in the lungs, where it is released from the blood. At the same time, it regulates pH homeostasis. The inhibitory function of sulfonamides on CA was discovered some 80 years ago. There are numerous physiological-therapeutic conditions in which inhibitors of carbonic anhydrase have a positive effect, such as glaucoma, or act as diuretics. With the realization that several isoenzymes of carbonic anhydrase are associated with the development of several types of cancer, such as brain and breast cancer, the development of inhibitor drugs specific to those enzyme forms has exploded. We would like to highlight the breadth of research on the enzyme as well as draw the attention to some problems in recent published work on inhibitor discovery.

An enzyme in disguise

The enzyme carbonic anhydrase binds its zinc ion by three histidine residues in a similar manner to the way copper is bound to nitrite reductase. This remote similarity has now been shown to be real [Andring et al. (2020). IUCrJ, 7, 287-293]. A carbonic anhydrase with two bound copper ions is also a nitrite reductase.