Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Synthesis and photochromic properties of 4-[2-(anthracen-9-yl)-5-methyloxazolyl] fulgide

New photochromic fulgide, viz., 4-{1-[2-(anthracen-9-yl)-5-methyloxazol-4-yl]ethylidene}-3-isopropylidenetetrahydrofuran-2,5-dione, with fluorescent properties was synthesized. Studies by electronic, IR, and ¹H NMR spectroscopy and X-ray diffraction demonstrated that this fulgide exists in the Z form. Light irradiation of its solutions at a wavelength of 365 nm causes Z/E isomerization giving rise to the thermally stable cyclic form. The latter is transformed into the starting E isomer under light irradiation at λ = 436 nm. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 97–101, January, 2006.     

Folding, conformational changes, and dynamics of cytochromes C probed by NMR spectroscopy

NMR spectroscopy has become a vital tool for studies of protein conformational changes and dynamics. Oxidized Fe(III)cytochromes c are a particularly attractive target for NMR analysis because their paramagnetism (S = (1)/(2)) leads to high (1)H chemical shift dispersion, even for unfolded or otherwise disordered states. In addition, analysis of shifts induced by the hyperfine interaction reveals details of the structure of the heme and its ligands for native and nonnative protein conformational states. The use of NMR spectroscopy to investigate the folding and dynamics of paramagnetic cytochromes c is reviewed here. Studies of nonnative conformations formed by denaturation and by anomalous in vivo maturation (heme attachment) are facilitated by the paramagnetic, low-spin nature of native and nonnative forms of cytochromes c. Investigation of the dynamics of folded cytochromes c also are aided by their paramagnetism. As an example of this analysis, the expression in Escherichia coli of cytochrome c(552) from Nitrosomonas europaea is reported here, along with analysis of its unusual heme hyperfine shifts. The results are suggestive of heme axial methionine fluxion in N. europaea ferricytochrome c(552). The application of NMR spectroscopy to investigate paramagnetic cytochrome c folding and dynamics has advanced our understanding of the structure and dynamics of both native and nonnative states of heme proteins.     

Fluorine containing coordination compounds of Cr(III)

Trans-[Cr(NH₃)₄F₂]I·H₂O (A) has monoclinic P2_l/m (No. 11) space group witha=5.033 (3),b=16.333 (10),c=5.539 (3) Å and =98.47 (3)°,Z=2.Cis-[Cr(NH₃)₄F₂]ClO₄ (B) has tetragonal space group I4_lmd (No. 109) witha=7.417 (1),c=16.610 (2) Å,Z=4. Cr–F and Cr–N bonding distances are 1.894 (3); 2.087 and 2.083 (5) Å for A and 1.887 (6); 2.062 (5) and 2.051 (7) Å for B. Octahedral angles within the cations are close to 90° for both compounds. Cr–N bondtrans to Cr–F bond in thecis compound is shorter. Structures were refined toR ₂ values of 0.072 (A) and 0.058 (B).Trans-[Cr(NH₃)₄F₂]I·H₂O has weak N–H–F hydrogen bonds between the cations. None such interactions were found incis-[Cr(NH₃)₄F₂]ClO₄.

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Fluorhältige Komplexe des Cr(III), 2. Mitt.: Kristall- und Molekülstruktur von trans-[Cr(NH₃)₄F₂]I·H₂O und cis-[Cr(NH₃)₄F₂]ClO₄

Zusammenfassung Trans-[Cr(NH₃)₄F₂]I·H₂O (A) kristallisiert in der Raumgruppe P2_l/m (No. 11) mitZ=2 unda=5,033 (3),b=16,333 (10),c=5,539 (3) Å und =98,47 (3)°.Cis-[Cr(NH₃)₄F₂]ClO₄ (B) kristallisiert in der Raumgruppe I4_lmd (No. 109) mitZ=4,a=7,417 (1) undc=16,610 (2) Å. Die Cr–F- und Cr–N-Abstände sind 1,894 (3); 2,087 (6), 2,083 (5) Å für A und 1,887 (6); 2,062 (5), 2,051 (7) Å für B. Die octaedrischen Bindungswinkel innerhalb der Kationen weichen nicht viel von 90° ab. Der Cr–N-Abstand intrans-Position der Cr–F-Bindung ist kürzer. Die Strukturen wurden bis zu GütefaktorenR ₂ 0,072 (A) und 0,058 (B) verfeinert. Bei der Verbindung A wurden schwache N–H ... F-Wasserstoff-Bindungen zwischen verschiedenen Kationen beobachtet, während bei der Verbindung B keine Wasserstoff-Bindungen vorhanden sind.

     

Structure and photochromism of 2-(<Emphasis Type="Italic">N</Emphasis>-acyl-<Emphasis Type="Italic">N</Emphasis>-arylaminomethylene)benzo[<Emphasis Type="Italic">b</Emphasis>]thiophen-3(2<Emphasis Type="Italic">H</Emphasis>)-ones

It was shown by electron absorption spectroscopy and X-ray diffraction analysis that steric strains in photochromic 2-(N-acyl-N-arylaminomethylene) benzo[b]thiophen-3(2H)-one molecules ortho-substituted in the N-phenyl ring increase the quantum yield of the N→O photoinduced rearrangement in accord with an increase in the steric constant of the ortho-substituent.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2151–2155, October, 2004.     

Benzoid-quinoid tautomerism of Schiff bases and their structural analogs: LV. Crown-containing N-phenylimines derived from ortho-hydroxycarbaldehydes of the coumarin series

Schiff bases were synthesized from 3-hydroxy-6-oxo-6H-benzo[c]chromene-4-carbaldehyde, 5-hydroxy-4,7-dimethyl-2-oxo-2H-chromene-6-carbaldehyde, 6,7-dihydroxy-4-methyl-2-oxo-2H-chromene-8-carbaldehyde, 5,7-dihydroxy-4-methyl-2-oxo-2H-chromene-6,8-dicarbaldehyde, and 5-hydroxy-4,7-dimethyl-2-oxo-2H-chromene-6,8-dicarbaldehyde and (¹⁵N)aniline or aminobenzo-15-crown-5 (2,3,5,6,8,9,11,12-octahydrobenzo[b][1,4,7,10,13]pentaoxacyclopentadecin-15-amine), and tautomeric equilibrium between the hydroxy enimino and keto enamino forms of the 4- and 8-iminomethyl derivatives in solution was revealed by 1H NMR and electronic spectroscopy. Addition of alkaline earth cations to their solutions in acetonitrile displaced the tautomeric equilibrium toward the hydroxy enimino structure due to complex formation with the crown ether fragment.     

Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors

SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CL^pro or M^pro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CL^pro active site. These compounds will facilitate further 3CL^pro inhibitor design.     

Basicities and transformations of pyrylium and pyridinium salts containing p-aminophenyl substituents

On the basis of the measured basicity constants of pyrylium and pyridinium salts containing p-aminophenyl substituents it is shown that the positive charge in the pyrylium cation is considerably higher than in the pyridinium cation. The constants of the pyrylium and pyridinium substituents, which show that the magnitude of the electronic effect of the pyrylium ring is considerably higher than that of the pyrydinium ring, were calculated. The reaction of the indicated pyrylium salts with some electrophilic and nucleophilic reagents was examined.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1025–1028, August, 1976.