Crystal Structures of AlCr2 and MoSi2 : Same Structure Type vs. Different Bonding Pattern.
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ABSTRACT:
SUBMITTER: Milosavljevic MD
PROVIDER: S-EPMC8596511 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A pair of tropinone reductases (TRs) share 64% of the same amino acid residues and belong to the short-chain dehydrogenase/reductase family. In the synthesis of tropane alkaloids in several medicinal plants, the TRs reduce a carbonyl group of an alkaloid intermediate, tropinone, to hydroxy groups with different diastereomeric configurations. To clarify the structural basis for their different reaction stereospecificities, we determined the crystal structures of the two enzymes at 2.4- and 2.3-A resolutions. The overall folding of the two enzymes was almost identical. The conservation was not confined within the core domains that are conserved within the protein family but extended outside the core domain where each family member has its characteristic structure. The binding sites for the cofactor and the positions of the active site residues were well conserved between the two TRs. The substrate binding site was composed mostly of hydrophobic amino acids in both TRs, but the presence of different charged residues conferred different electrostatic environments on the two enzymes. A modeling study indicated that these charged residues play a major role in controlling the binding orientation of tropinone within the substrate binding site, thereby determining the stereospecificity of the reaction product. The results obtained herein raise the possibility that in certain cases different stereospecificities can be acquired in enzymes by changing a few amino acid residues within substrate binding sites.
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Project description:The rack-induced bonding mechanism of metals to proteins is a useful concept for explaining the generation of metal sites in electron transfer proteins, such as the blue copper proteins, that are designed for rapid electron transfer. The trigonal pyramidal structure imposed by the protein with three strong equatorial ligands (one Cys and two His) provides a favorable geometry for both cuprous and cupric oxidation states. However, the crystal structures of the Met121His mutant of azurin from Alcaligenes denitrificans at pH 6.5 (1.89- and 1.91-A resolutions) and pH 3.5 (2.45-A resolution) show that the preformed metal binding cavity in the protein is more flexible than expected. At high pH (6.5), the Cu site retains the same three equatorial ligands as in the wild-type azurin and adds His121 as a fourth strong ligand, creating a tetrahedral copper site geometry with a green color referred to as 1.5 type. In the low pH (3.5) structure, the protonation of His121 causes a conformational change in residues 117-123, moving His121 away from the copper. The empty coordination site is occupied by an oxygen atom of a nitrate molecule of the buffer solution. This axial ligand is coordinated less strongly, generating a distorted tetrahedral copper geometry with a blue color and spectroscopic properties of a type-1 site. These crystal structures demonstrate that blue copper proteins are flexible enough to permit a range of movement of the Cu atom along the axial direction of the trigonal pyramid.
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Project description:The mechanism of the recently reported catalyzed asymmetric hydrogenation of enyne 1 catalyzed by the Co-(R,R)-QuinoxP* complex was studied by DFT. Conceivable pathways for the Co(I)-Co(III) mechanism were computed together with a Co(0)-Co(II) catalytic cycle. It is commonly assumed that the exact nature of the chemical transformations taking place along the actually operating catalytic pathway determine the sense and level of enantioselection of the catalytic reaction. In this work, two chemically different mechanisms reproduced the experimentally observed perfect stereoselection of the same handedness. Moreover, the relative stabilities of the transition states of the stereo induction stages were controlled via exactly the same weak disperse interactions between the catalyst and the substrate.
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Project description:In the crystal structure of the title compound, 5-fluoro-cytosinium picrate, C4H5FN3O+·C6H2N3O7-, one N heteroatom of the 5-fluoro-cytosine (5FC) ring is protonated. The 5FC ring forms a dihedral angle of 19.97 (11)° with the ring of the picrate (PA-) anion. In the crystal, the 5FC+ cation inter-acts with the PA- anion through three-centre N-H⋯O hydrogen bonds, forming two conjoined rings having R21(6) and R12(6) motifs, and is extended by N-H⋯O hydrogen bonds and C-H⋯O inter-actions into a two-dimensional sheet structure lying parallel to (001). Also present in the crystal structure are weak C-F⋯π inter-actions.
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Project description:ImportancePerforming elective upper and lower endoscopic procedures on the same day is a patient-centered and less costly approach than a 2-stage approach performed on different days, when clinically appropriate. Whether this practice pattern varies based on practice setting has not been studied.ObjectivesTo estimate the rate of different-day upper and lower endoscopic procedures in 3 types of outpatient settings and investigate the factors associated with the performance of these procedures on different days.Design, setting, and participantsA retrospective analysis was conducted of Medicare claims between January 1, 2011, and June 30, 2018, for Medicare beneficiaries who underwent a pair of upper and lower endoscopic procedures performed within 90 days of each other at hospital outpatient departments (HOPDs), freestanding ambulatory surgery centers (ASCs), and physician offices.Main outcomes and measuresUndergoing an upper and a lower endoscopic procedure on different days, adjusted for patient characteristics (age, sex, race/ethnicity, residence location and region, comorbidity, and procedure indication) and physician characteristics (sex, years in practice, procedure volume, and primary specialty). Adjusted odds ratios (aORs) and 95% CIs were calculated.ResultsA total of 4 028 587 procedure pairs were identified, of which 52.5% were performed in HOPDs, 43.3% in ASCs, and 4.2% in physician offices. The rate of different-day procedures was 13.6% in HOPDs, 22.2% in ASCs, and 47.7% in physician offices. For the 7564 physicians who practiced at both HOPDs and ASCs, their different-day procedure rate changed from 14.1% at HOPDs to 19.4% at ASCs. For the 993 physicians who practiced at both HOPDs and physician offices, their different-day procedure rate changed from 15.8% at HOPDs to 37.4% at physician offices. Patients were more likely to undergo different-day procedures at physician offices and ASCs compared with HOPDs, even after adjusting for patient and physician characteristics (physician office vs HOPD: aOR, 2.02; 95% CI, 1.85-2.20; ASC vs HOPD: aOR, 1.27; 95% CI, 1.23-1.32). Older age (85-94 years vs 65-74 years: aOR, 1.10; 95% CI, 1.08-1.11; 95 years or older vs 65-74 years: aOR, 1.14; 95% CI, 1.03-1.26), black and Hispanic race/ethnicity (black: aOR, 1.15; 95% CI, 1.12-1.17; Hispanic: aOR, 1.12; 95% CI, 1.10-1.14), and residing in the Northeast region (adjusted OR, 1.32; 95% CI, 1.28-1.36) were risk factors for undergoing different-day procedures. Micropolitan location (aOR, 0.94; 95% CI, 0.92-0.96) and rural location (aOR, 0.91; 95% CI, 0.89-0.93), more comorbidities (≥5: aOR, 0.75; 95% CI, 0.74-0.76), physician's fewer years in practice (aOR, 0.84; 95% CI, 0.81-0.87), physician's higher procedure volume (aOR, 0.65; 95% CI, 0.62-0.68), and physician's specialty of general surgery (aOR, 0.86; 95% CI, 0.80-0.91) were protective factors.Conclusions and relevancePhysician offices and ASCs had much higher different-day procedure rates compared with HOPDs. This disparity may represent an opportunity for quality improvement and financial savings for common endoscopic procedures.
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Project description:Native cytochrome c6 was purified from an extract of strain BP-1 of the thermophilic cyanobacterium Thermosynechococcus elongatus. The protein was crystallized, and with only slight modifications of the buffer and vapour-diffusion conditions two different space groups were observed, namely H3 and C2. Both crystal structures were solved; they contained three and six molecules per asymmetric unit and were refined to 1.7 and 2.25 Å resolution, respectively. To date, the structure of native cytochrome c6 from T. elongatus has only been reported as a monomer using NMR spectroscopy, i.e. without addressing putative oligomerization, and related structures have only previously been solved using X-ray crystallography after recombinant gene overexpression in Escherichia coli. The reported space groups of related cyanobacterial cytochrome c6 structures differ from those reported here. Interestingly, the protein-protein interfaces that were observed utilizing X-ray crystallography could also explain homo-oligomerization in solution; specifically, trimerization is indicated by infra-red dynamic light scattering and blue native gel electrophoresis in solution. Trimers were also detected by mass spectrometry. Furthermore, there is an indication of post-translational methylation in the crystal structure. Additionally, the possibility of modifying the crystal size and the redox activity in the context of photosynthesis is shaping the investigated cytochrome as a highly suitable model protein for advanced serial crystallography at highly brilliant X-ray free-electron laser sources.
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Project description:Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28 A resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cytochrome b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density, the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alphaA helix.
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Project description:The nature of halogen-bond interactions was scrutinized from the perspective of astatine, potentially the strongest halogen-bond donor atom. In addition to its remarkable electronic properties (e.g., its higher aromaticity compared to benzene), C6At6 can be involved as a halogen-bond donor and acceptor. Two-component relativistic calculations and quantum chemical topology analyses were performed on C6At6 and its complexes as well as on their iodinated analogues for comparative purposes. The relativistic spin-orbit interaction was used as a tool to disclose the bonding patterns and the mechanisms that contribute to halogen-bond interactions. Despite the stronger polarizability of astatine, halogen bonds formed by C6At6 can be comparable or weaker than those of C6I6. This unexpected finding comes from the charge-shift bonding character of the C-At bonds. Because charge-shift bonding is connected to the Pauli repulsion between the bonding σ electrons and the σ lone-pair of astatine, it weakens the astatine electrophilicity at its σ-hole (reducing the charge transfer contribution to halogen bonding). These two antinomic characters, charge-shift bonding and halogen bonding, can result in weaker At-mediated interactions than their iodinated counterparts.
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Project description:Single crystals of KScP2O7, potassium scandium diphosphate, were grown in a borate flux. The title compound crystallizes isotypically with KAlP2O7 in space-group type P21/c, Z = 4. The main building block is an {ScP2O11}9- unit, forming layers parallel to (001). These layers are stacked along [001] via common corners of octa-hedral and tetra-hedral units to span up large hepta-gonal cavities that host the potassium cations with a coordination number of 10. The P-O-P bridging angle increases with increasing size of the octa-hedrally coordinated M III cation, as do the K-O distances within a series of KM IIIP2O7 compounds (M III = Al to Y with ionic radii r = 0.538 to 0.90 Å).
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Project description:The reaction of 1,5-di-bromo-pentane with urotropine results in crystals of the title mol-ecular salt, 5-bromo-urotropinium bromide [systematic name: 1-(5-bro-mo-pent-yl)-3,5,7-tri-aza-1-azoniatri-cyclo-[3.3.1.13,7]decane bromide], C11H22BrN4 +·Br- (1), crystallizing in space group P21/n. The packing in compound 1 is directed mainly by H⋯H van der Waals inter-actions and C-H⋯Br hydrogen bonds, as revealed by Hirshfeld surface analysis. Comparison with literature examples of alkyl-urotropinium halides shows that the inter-actions in 1 are consistent with those in other bromides and simple chloride and iodide species.
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