The role of the correlated motion(s) of the chromophore in photoswitching of green and red forms of the photoconvertible fluorescent protein mSAASoti.

Wild-type SAASoti and its monomeric variant mSAASoti can undergo phototransformations, including reversible photoswitching of the green form to a nonfluorescent state and irreversible green-to-red photoconversion. In this study, we extend the photochemistry of mSAASoti variants to enable reversible photoswitching of the red form. This result is achieved by rational and site-saturated mutagenesis of the M163 and F177 residues. In the case of mSAASoti it is M163T substitution that leads to the fastest switching and the most photostable variant, and reversible photoswitching can be observed for both green and red forms when expressed in eukaryotic cells. We obtained a 13-fold increase in the switching efficiency with the maximum switching contrast of the green form and the appearance of comparable switching of the red form for the C21N/M163T mSAASoti variant. The crystal structure of the C21N mSAASoti in its green on-state was obtained for the first time at 3.0 Å resolution, and it is in good agreement with previously calculated 3D-model. Dynamic network analysis reveals that efficient photoswitching occurs if motions of the 66H residue and phenyl fragment of chromophore are correlated and these moieties belong to the same community.

Multifunctionality of arginine residues in the active sites of non-canonical d-amino acid transaminases.

Structure-function relationships are key to understanding enzyme mechanisms, controlling enzyme activities, and designing biocatalysts. Here, we investigate the functions of arginine residues in the active sites of pyridoxal-5'-phosphate (PLP)-dependent non-canonical d-amino acid transaminases, focusing on the analysis of a transaminase from Haliscomenobacter hydrossis. Our results show that the tandem of arginine residues R28* and R90, which form the conserved R-[RK] motif in non-canonical d-amino acid transaminases, not only facilitates effective substrate binding but also regulates the catalytic properties of PLP. Non-covalent interactions between residues R28*, R90, and Y147 strengthen the hydrogen bond between Y147 and PLP, thereby maintaining the reactivity of the cofactor. Next, the R90 residue contributes to the stability of the holoenzyme. Finally, the R90I substitution induces structural changes that lead to substrate promiscuity, as evidenced by the effective binding of substrates with and without the α-carboxylate group. This study sheds light on the structural determinants of the activity of non-canonical d-amino acid transaminases. Understanding the structural basis of the active site plasticity in the non-canonical transaminase from H. hydrossis, which is characterized by effective conversion of d-amino acids and α-keto acids, may help to tailor it for industrial applications.

Tridentate Nitrogen Ligand as a Tool for the Construction of Well-Defined Rare Earth Trichloride Complexes.

LnCl3(THF)3 (Ln = Y, La ÷ Nd, Sm ÷ Lu) readily react with the tridentate 1,3,5-trimethyl-1,3,5-triazacyclohexane (Me3tach) ligand to form mono- or binuclear lanthanide trichloride complexes, depending on the stoichiometry of the reaction and the ionic radius of the metal: mononuclear pseudosandwich [LnCl3(Me3tach)2], (Ln = Y, La ÷ Ho) or binuclear complexes [Ln2Cl6(Me3tach)3], or [LnCl3(Me3tach)(THF)]2 (Ln = Sm, Tb). Detailed analysis of the NMR data of [LnCl3(Me3tach)2] complexes with paramagnetic lanthanide ions showed that their structures remained unchanged in the toluene solution. A series of isomorphous complexes [LnCl3(Me3tach)(Py)2] (Ln = La, Sm, Tb, Er, Lu; Py = pyridine) have been obtained by the recrystallization of either mononuclear or binuclear complexes from pyridine. Complexes of terbium and europium ions with the Me3tach ligand exhibit relatively high quantum yields of metal-centered luminescence (0.39 and 0.32, respectively).

Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens.

Enzymes with expanded substrate specificity are good starting points for the design of biocatalysts for target reactions. However, the structural basis of the expanded substrate specificity is still elusive, especially in the superfamily of pyridoxal-5'-phosphate-dependent transaminases, which are characterized by a conserved organization of both the active site and functional dimer. Here, we analyze the structure-function relationships in a non-canonical D-amino acid transaminase from Blastococcus saxobsidens, which is active towards D-amino acids and primary (R)-amines. A detailed study of the enzyme includes a kinetic analysis of its substrate scope and a structural analysis of the holoenzyme and its complex with phenylhydrazine-a reversible inhibitor and analogue of (R)-1-phenylethylamine-a benchmark substrate of (R)-selective amine transaminases. We suggest that the features of the active site of transaminase from B. saxobsidens, such as the flexibility of the R34 and R96 residues, the lack of bulky residues in the ß-turn at the entrance to the active site, and the short O-pocket loop, facilitate the binding of substrates with and without α-carboxylate groups. The proposed structural determinants of the expanded substrate specificity can be used for the design of transaminases for the stereoselective amination of keto compounds.

Crystal structure reveals canonical recognition of the phosphorylated cytoplasmic loop of human alpha7 nicotinic acetylcholine receptor by 14-3-3 protein.

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels composed of five homologous subunits. The homopentameric α7-nAChR, abundantly expressed in the brain, is involved in the regulation of the neuronal plasticity and memory and undergoes phosphorylation by protein kinase A (PKA). Here, we extracted native α7-nAChR from murine brain, validated its assembly by cryo-EM and showed that phosphorylation by PKA in vitro enables its interaction with the abundant human brain protein 14-3-3ζ. Bioinformatic analysis narrowed the putative 14-3-3-binding site down to the fragment of the intracellular loop (ICL) containing Ser365 (Q361RRCSLASVEMS372), known to be phosphorylated in vivo. We reconstructed the 14-3-3ζ/ICL peptide complex and determined its structure by X-ray crystallography, which confirmed the Ser365 phosphorylation-dependent canonical recognition of the ICL by 14-3-3. A common mechanism of nAChRs' regulation by ICL phosphorylation and 14-3-3 binding that potentially affects nAChR activity, stoichiometry, and surface expression is suggested.

In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.

The development of biocatalysts requires reorganization of the enzyme's active site to facilitate the productive binding of the target substrate and improve turnover number at desired conditions. Pyridoxal-5'-phosphate (PLP) - dependent transaminases are highly efficient biocatalysts for asymmetric amination of ketones and keto acids. However, transaminases, being stereoselective enzymes, have a narrow substrate specificity due to the ordered structure of the active site and work only in neutral-alkaline media. Here, we investigated the d-amino acid transaminase from Aminobacterium colombiense, with the active site organized differently from that of the canonical d-amino acid transaminase from Bacillus sp. YM-1. Using a combination of site-directed mutagenesis, kinetic analysis, molecular modeling, and structural analysis we determined the active site residues responsible for substrate binding, substrate differentiation, thermostability of a functional dimer, and affecting the pH optimum. We demonstrated that the high specificity toward d-glutamate/α-ketoglutarate is due to the interactions of a γ-carboxylate group with K237 residue, while binding of other substrates stems from the effectiveness of their accommodation in the active site optimized for d-glutamate/α-ketoglutarate binding. Furthermore, we showed that the K237A substitution shifts the catalytic activity optimum to acidic pH. Our findings are useful for achieving target substrate specificity and demonstrate the potential for developing and optimizing transaminases for various applications.

New class of RSO2-NHC ligands and Pd/RSO2-NHC complexes with tailored electronic properties and high performance in catalytic C-C and C-N bonds formation.

Imidazolium salts have found ubiquitous applications as N-heterocyclic carbene precursors and metal nanoparticle stabilizers in catalysis and metallodrug research. Substituents directly attached to the imidazole ring can have a significant influence on the electronic, steric, and other properties of NHC-proligands as well as their metal complexes. In the present study, for the first time, a new type of Pd/NHC complex with the RSO2 group directly attached to the imidazol-2-ylidene ligand core was designed and synthesized. The electronic properties as well as structural features of the new ligands were evaluated by means of experimental and computational methods. Interestingly, the introduction of a 4-aryl(alkyl)sulfonyl group only slightly decreased the electron donation, but it significantly increased the π-acceptance and slightly enhanced the buried volume (%Vbur) of new imidazol-2-ylidenes. New Pd/NHC complexes were obtained through selective C(2)H-palladation of some of the synthesized 4-RSO2-functionalized imidazolium salts under mild conditions. Several complexes demonstrated good activity in the catalysis of model cross-coupling reactions, outperforming the activity of similar complexes with non-substituted NHC ligands.

Synthesis of substituted 8H-benzo[h]pyrano[2,3-f]quinazolin-8-ones via photochemical 6π-electrocyclization of pyrimidines containing an allomaltol fragment.

For the first time, we elaborated a method for the synthesis of pyrimidines containing an allomaltol unit. The suggested approach is based on the reaction of 2-(1-(dimethylamino)-3-oxo-3-arylprop-1-en-2-yl)-3-hydroxy-6-methyl-4H-pyran-4-ones with cyanamide. The photochemical behavior of the obtained pyrimidines was investigated. It was shown that for the hydroxy derivatives the main pathway of phototransformation is a 6π-electrocyclization of the 1,3,5-hexatriene system and subsequent [1,9]-H sigmatropic shift leading to dihydrobenzo[h]pyrano[2,3-f]quinazolines. At the same time, for methylated analogues the photoreaction proceeds in two directions resulting in the formation of a mixture of the corresponding dihydrobenzo[h]pyrano[2,3-f]quinazolines and polyaromatic products. The obtained dihydro derivatives are stable compounds and do not undergo aromatization upon further UV irradiation. The structures of two of the dihydrobenzo[h]pyrano[2,3-f]quinazolines were confirmed by X-ray diffraction analysis. Based on the performed studies, a two-stage telescopic method for the synthesis of polyaromatic benzo[h]pyrano[2,3-f]quinazolines including the initial photocyclization of the starting pyrimidines and the final dehydration was proposed.

Synthesis of N,N'-Unsymmetrical 9-Amino-5,7-dimethyl-bispidines.

A new approach to the preparation of N,N'-unsymmetrically substituted 9-aminobispidines through aminal bridge removal reaction has been developed, the principal feature of which is the ability to selectively functionalize all three nitrogen atoms. The intermediates of 1,3-diazaadamantane's aminal bridge removal reaction are characterized, and the mechanism of this reaction is proposed based on the analysis of their structures. Representatives of the previously unknown saturated heterocyclic 1,5,9-triazatricyclo[5.3.1.03,8]undecane system were obtained and structurally characterized. Thus, it was possible for the first time to obtain 3,7,9-trisubstituted bispidines containing acetyl, Boc, and benzyl groups at nitrogen atoms, which can be independently removed (orthogonal protective groups).

To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense.

Pyridoxal-5'-phosphate (PLP)-dependent transaminases are highly efficient biocatalysts for stereoselective amination. D-amino acid transaminases can catalyze stereoselective transamination producing optically pure D-amino acids. The knowledge of substrate binding mode and substrate differentiation mechanism in D-amino acid transaminases comes down to the analysis of the transaminase from Bacillus subtilis. However, at least two groups of D-amino acid transaminases differing in the active site organization are known today. Here, we present a detailed study of D-amino acid transaminase from the gram-negative bacterium Aminobacterium colombiense with a substrate binding mode different from that for the transaminase from B. subtilis. We study the enzyme using kinetic analysis, molecular modeling, and structural analysis of holoenzyme and its complex with D-glutamate. We compare the multipoint binding of D-glutamate with the binding of other substrates, D-aspartate and D-ornithine. QM/MM MD simulation reveals that the substrate can act as a base and its proton can be transferred from the amino group to the α-carboxylate group. This process occurs simultaneously with the nucleophilic attack of the PLP carbon atom by the nitrogen atom of the substrate forming gem-diamine at the transimination step. This explains the absence of the catalytic activity toward (R)-amines that lack an α-carboxylate group. The obtained results clarify another substrate binding mode in D-amino acid transaminases and underpinned the substrate activation mechanism.

Synthesis and a combined experimental/theoretical structural study of a comprehensive set of Pd/NHC complexes with o-, m-, and p-halogen-substituted aryl groups (X = F, Cl, Br, CF3).

Pd/NHC complexes (NHCs - N-heterocyclic carbenes) with electron-withdrawing halogen groups were prepared by developing an optimized synthetic procedure to access imidazolium salts and the corresponding metal complexes. Structural X-ray analysis and computational studies have been carried out to evaluate the effect of halogen and CF3 substituents on the Pd-NHC bond and have provided insight into the possible electronic effects on the molecular structure. The introduction of electron-withdrawing substituents changes the ratio of σ-/π-contributions to the Pd-NHC bond but does not affect the Pd-NHC bond energy. Here, we report the first optimized synthetic approach to access a comprehensive range of o-, m-, and p-XC6H4-substituted NHC ligands, including incorporation into Pd complexes (X = F, Cl, Br, CF3). The catalytic activity of the obtained Pd/NHC complexes was compared in the Mizoroki-Heck reaction. For substitution with halogen atoms, the following relative trend was observed: X = Br > F > Cl, and for all halogen atoms, the catalytic activity changed in the following order: m-X, p-X > o-X. Evaluation of the relative catalytic activity showed a significant increase in the catalyst performance in the case of Br and CF3 substituents compared to the unsubstituted Pd/NHC complex.

Straightforward and Efficient Protocol for the Synthesis of Pyrazolo [4,3-b]pyridines and Indazoles.

An efficient method for the synthesis of pyrazolo [4,3-b]pyridines has been developed on the basis of readily available 2-chloro-3-nitropyridines via a sequence of SNAr and modified Japp-Klingemann reactions. The method offers a number of advantages including utilization of stable arenediazonium tosylates, operational simplicity as well as combining the azo-coupling, deacylation and pyrazole ring annulation steps in a one-pot manner. An unusual rearrangement (C-N-migration of the acetyl group) was observed and a plausible mechanism was proposed based on the isolated intermediates and NMR experiments. In addition, the developed protocol was successfully applied to the synthesis of 1-arylindazoles combining the Japp-Klingemann reaction and cyclization of the resulting hydrazone as a one-pot procedure.

Structure-Functional Examination of Novel Ribonucleoside Hydrolase C (RihC) from Limosilactobacillus reuteri LR1.

Ribonucleoside hydrolase C (RihC, EC 3.2.2.1, 3.2.2.2, 3.2.2.3, 3.2.2.7, 3.2.2.8) belongs to the family of ribonucleoside hydrolases Rih and catalyzes the cleavage of ribonucleosides to nitrogenous bases and ribose. RihC is one of the enzymes that are synthesized by lactobacilli in response to the presence of Klebsiella. To characterize this protein from Limosilactobacillus reuteri LR1, we cloned and expressed it. The activity of the enzyme was studied towards a wide range of substrates, including ribonucleosides, deoxyribonucleosides as well as an arabinoside. It was shown that the enzyme is active only with ribonucleosides and arabinoside, with the best substrate being uridine. The thermal stability of this enzyme was studied, and its crystal structure was obtained, which demonstrated the tetrameric architecture of the enzyme and allowed to shed light on a correlation between its structure and enzymatic activity. Comprehensive comparisons of all known RihC structures, both existing crystal structures and computed model structures from various species, were made, allowing for the identification of structural motifs important for enzyme functioning.

New Aspects of the Reaction of Thioacetamide and N-Substituted Maleimides.

N-Arylmaleimides are universal substrates for the synthesis of various heterocyclic compounds with a wide spectrum of biological activity. However, their reactions with thioacetamides have not been comprehensively studied. We studied the reactions of thioacetamide with N-arylmaleimides under various conditions. We established for the first time that three types of products: epithiopyrrolo[3,4-c]pyridines, pyrrolo[3,4-c]pyridines and 3,3'-thiobis(1-arylpyrrolidine-2,5-diones) can be obtained in different conditions. In all cases, two maleimide molecules are involved in the reaction. 3,3'-Thiobis(1-arylpyrrolidine-2,5-diones) are the major products when the reaction is conducted at boiling in acetic acid. When thioacetamide and N-arylmaleimide are kept in dioxane at 50 °C, epithiopyrrolo[3,4-c]pyridines can be isolated, which, when heated in dioxane, in acetic acid or in methanol in the presence of catalytic amounts of sodium methoxide, are converted into pyrrolo[3,4-c]pyridines by eliminating hydrogen sulfide. The reaction of thioacetamide and N-arylmaleimide in dioxane at boiling temperature with the portioned addition of N-arylmaleimide leads predominantly to the formation of pyrrolo[3,4-c]pyridines. The reaction of thioacetamide with N-alkylmaleimides under all the above conditions leads predominantly to the formation of the corresponding sulfides. The structure of the compounds obtained was characterized by a set of spectral analysis methods and X-ray diffraction (XRD) data.

Coordination Polymers of Polyphenyl-Substituted Potassium Cyclopentadienides.

A series of potassium salts of di- and tri-arylsubstituted cyclopentadienes has been obtained by the metalation of the corresponding cyclopentadienes with benzylpotassium in THF media. Crystals of all compounds, afforded by recrystallization from THF/hexane, diglyme-THF/hexane and toluene/hexane mixtures, have been studied by X-ray diffraction. All studied potassium cyclopentadienides exhibit the luminescence at room temperature and overall quantum yield of photoluminescence for potassium salt of diarylsubstituted cyclopentadiene is 18%.

Structural basis for the carotenoid binding and transport function of a START domain.

STARD3, a steroidogenic acute regulatory lipid transfer protein, was identified as a key xanthophyll-binding protein in the human retina. STARD3 and its homologs in invertebrates are known to bind and transport carotenoids, but this lacks structural elucidation. Here, we report high-resolution crystal structures of the apo- and zeaxanthin (ZEA)-bound carotenoid-binding protein from silkworm Bombyx mori (BmCBP). Having a STARD3-like fold, BmCBP features novel elements, including the Ω1-loop that, in the apoform, is uniquely fixed on the α4-helix by an R173-D279 salt bridge. We exploit absorbance, Raman and dichroism spectroscopy, and calorimetry to describe how ZEA and BmCBP mutually affect each other in the complex. We identify key carotenoid-binding residues, confirm their roles by ZEA-binding capacity and X-ray structures of BmCBP mutants, and also demonstrate that markedly different carotenoid-binding capacities of BmCBP and human STARD3 stem from differences in the structural organization of their carotenoid-binding cavity.

Yellow to blue switching of fluorescence by the tuning of the pentaphenylphosphole structure: phosphorus electronic state vs. ring conjugation.

The interaction between diphenylacetylene and dichlorophenylphosphine under various conditions is a simple method for the preparation of pentaphenylphosphole derivatives exhibiting fluorescence properties. Depending on the electronic state of the various centers of the phospholic structure, it was possible to obtain molecules with fluorescence, as in the blue area for 1,2,3,4,5-pentaphenyl-2,5-dihydro-phosphole-1-oxide (H2PPPO), in the yellow area for 1,2,3,4,5-pentaphenylphosphole-1-oxide (PPPO) and in the cyan area for 1,2,3,4,5-pentaphenylphosphole (PPP). The effect of the structure and π-conjugation on the optical properties of these compounds was studied using PPP derivatives as examples. Unusual changes in the optical properties of PPP derivatives in solution and in the crystalline state are explained. In the case of agglomeration of PPPO and PPP molecules, the effect of aggregation-induced emission (AIE) was observed to have weak fluorescence in solution and strong fluorescence in the aggregated state. However, for H2PPPO, the AIE effect remains mild. With the help of experimental studies, supported by theoretical calculations, the main mechanism of the optical properties of pentaphenylphosphole derivatives has been revealed. It was observed that the intramolecular motions of PPPO and PPP are more limited in the solid state than the motions of H2PPPO, which is associated with less conjugation of the phenyl rotors of H2PPPO. The analysis of the structure and distribution of electron density showed why hydrogenation of the phosphole ring leads to a sharp change in the optical properties of pentaphenylphosphole derivatives, while the oxidation of phosphorus does not lead to the disappearance of the AIE effect and to a lesser extent affects the change in the fluorescence wavelength. Thus, it was shown how the regulation of various structural features of the phospholic ring helps to control the optical properties of such compounds.

Nucleophilic Functionalization of 2-R-3-Nitropyridines as a Versatile Approach to Novel Fluorescent Molecules.

A number of new 2-methyl- and 2-arylvinyl-3-nitropyridines were synthesized and their reactions with thiols were studied. It was found that 3-NO2 tends to be selectively substituted under the action of sulfur nucleophiles in the presence of another nucleofuge in position 5. Correlations between the substitution pattern and regioselectivity as well as photophysical properties were established. Some synthesized compounds possessed a large Stokes shift.

Tetrahydropyridines' Stereoselective Formation, How Lockdown Assisted in the Identification of the Features of Its Mechanism.

The multicomponent reaction of aldehydes, cyano-containing C-H acids, esters of 3-oxocarboxylic acid and ammonium acetate led to unexpected results. The boiling of starting materials in methanol for one to two hours resulted in the formation of polysubstituted 1,4,5,6-tetrahydropyridines with two or three stereogenic centers. During the 2020 lockdown, we obtained key intermediates of this six-step domino reaction. A number of fast and slow reactions occurred during the prolonged stirring of the reaction mass at rt. Sequence: 1. Knoevenagel condensation; 2. Michael addition; 3. Mannich reaction; 4. cyclization-fast reactions and cyclization of the product polysubstituted 2-hydroxypiperidine-was isolated after 40 min stirring at rt. Further monitoring proved the slow dehydration of 2-hydroxypiperidine to obtain 3,4,5,6-tetrahydropyridine after 7 days. Then, four-month isomerization occurred with 1,4,5,6-tetrahydropyridine formation. All reactions were stereoselective. Key intermediates and products structures were verified by X-ray diffraction analysis. Additionally, we specified conditions for the selective intermediates' preparation.

Synthesis and characterization of Pd/NHCF complexes with fluorinated aryl groups.

The key problem of the instability of fluorine-containing diazadienes was addressed to perform the efficient synthesis of imidazolium salts containing fluorine substituents in the aryl groups. The subsequent reaction of fluorine-containing imidazolium compounds (NHCF) with palladium salts under simple conditions afforded new Pd/NHCF complexes. Computational and structural studies were performed to assess the effect of fluorine on the Pd-NHC bond and gave insight into the electronic effects in the molecule. The introduction of fluorine substituents into the aryl rings of the NHC ligands leads to a slight decrease in their σ-donor properties. At the same time, there is a slight increase in the π-acceptor capacity of NHCF. These two effects compensate for each other, so that the Pd-NHC bonding energy remains virtually unchanged. Another observed effect is associated with a slight weakening of the trans influence of the NHCF ligands, which is expressed in the strengthening of the Pd-Solv bond in (NHC)Pd(Solv) complexes. For the first time, a series of novel Pd/NHCF complexes were synthesized via a straightforward approach from fluorine-containing anilines.