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1.
Previously, a hypothetical protein (HP) termed Bleg1_2437 (currently named Bleg1_2478) from Bacillus lehensis G1 was discovered to be an evolutionary divergent B3 subclass metallo-β-lactamase (MBL). Due to the scarcity of clinical inhibitors for B3 MBLs and the divergent nature of Bleg1_2478, this study aimed to design and characterise peptides as inhibitors against Bleg1_2478. Through in silico docking, RSWPWH and SSWWDR peptides with comparable binding energy to ampicillin were obtained. In vitro assay results showed RSWPWH and SSWWDR inhibited the activity of Bleg1_2478 by 50% at concentrations as low as 0.90 µM and 0.50 µM, respectively. At 10 µM of RSWPWH and 20 µM of SSWWDR, the activity of Bleg1_2478 was almost completely inhibited. Isothermal titration calorimetry (ITC) analyses showed slightly improved binding properties of the peptides compared to ampicillin. Docked peptide–protein complexes revealed that RSWPWH bound near the vicinity of the Bleg1_2478 active site while SSWWDR bound at the center of the active site itself. We postulate that the peptides caused the inhibition of Bleg1_2478 by reducing or blocking the accessibility of its active site from ampicillin, thus hampering its catalytic function.  相似文献   

2.
In this work, we have calculated boron-, aluminum-, titanium-, and nickel-doped La13 clusters by DMOL method based on the density-functional theory. Two doping modes are employed: surface and center doping. The boron, aluminum, and nickel atoms prefer to occupy the surface sites while the titanium atom prefers to occupy the center site. The doped La13 clusters with these four kinds of atoms have lower binding energy than pure La13 clusters. The icosahedral isomers are of lower binding energy than cubotahedral and decahedral isomers for La12B(-1), La12Al(-1), and La12Ni, while doping makes the cubotahedral La12Ti stable with a binding energy a little lower than icosahedral La12Ti. There are electronic shell effects in icosahedral La12B(-1) and La12Al(-1). The icosahedral La12B(-1) is promising to be formed during the doped process experimentally. Furthermore, we have also discussed the distorted structures of center doping by bond lengths, density of states, and charge transfers.  相似文献   

3.
Compound [Re2(CH3COO)2Cl4((CH3)2NCOCH3)2] is synthesized. The influence of parameters of the hydrothermal synthesis under elevated pressure on the yield of a target product and its molecular structure and physicochemical properties is studied. In the neutral complex with cis-arrangement of the bridging acetate and terminal chloride ligands with respect to the multiply bonded Re2 6+ complex-forming center, the Re–Re bond length is 2.2418(3) Å. Dimethylacetamide molecules are in the axial positions, the Re–O bond lengths being 2.304(3) and 2.321(4) Å. The influence of the donor ability of the axial substituents in analogous structures of the rhenium(III) binuclear clusters on the Re–Re and Re–Lax bond lengths is analyzed.  相似文献   

4.
A dataset of 82 protein–ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein–ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the protein and the ligand, the size of the lipophilic contact surface, the flexibility of the ligand, the electrostatic potential in the binding site, water molecules in the binding site, cavities along the protein–ligand interface and specific interactions between aromatic rings. Based on these parameters, a new empirical scoring function is presented that estimates the free energy of binding for a protein–ligand complex of known 3D structure. The function distinguishes between buried and solvent accessible hydrogen bonds. It tolerates deviations in the hydrogen bond geometry of up to 0.25 Å in the length and up to 30 °Cs in the hydrogen bond angle without penalizing the score. The new energy function reproduces the binding constants (ranging from 3.7 × 10-2 M to 1 × 10-14 M, corresponding to binding energies between -8 and -80 kJ/mol) of the dataset with a standard deviation of 7.3 kJ/mol corresponding to 1.3 orders of magnitude in binding affinity. The function can be evaluated very fast and is therefore also suitable for the application in a 3D database search or de novo ligand design program such as LUDI. The physical significance of the individual contributions is discussed.  相似文献   

5.
Adsorption equilibrium constants and adsorption enthalpies have been calculated from kinetic data of cyclohexane dehydrogenation and ethane hydrogenolysis on metallic nickel. From these data the bond strength of hydrogen and carbon with the active sites of nickel and the activation barrier of C–H and H–H bond dissociation were calculated by the recently developed method of Shustorovich. The calculated data indicate that the active sites for dehydrogenation differ (or in part differ) from those of hydrogenolysis.  相似文献   

6.
An exhaustive survey of crystal structure data on simple amides and metal complexes containing monodentate amide ligands has been performed. Statistical analysis of structural features are reported as a function of the degree of alkylation of the amide functional group, the type of metal ion in the amide complex, and the type of binding to the metal ion. Average values are reported for bond lengths, bond angles, and torsional angles. Orientational preferences of the coordinated amide ligand are discussed in terms of M–O–C bond angles and M–O–C–N torsion angles.  相似文献   

7.
Hydrolytic reactions between cis-[Pd( -Ala-N,O)Cl2] and cis-[Pd( -Ala-N,O)(H2O)2]+, in which -Ala is alanine coordinated through N and O atoms, and N-acetylated peptides -histidylglycine (MeCO-His-Gly), glycyl- -histidine (MeCO-Gly-His), glycylglycyl- -histidine (MeCO-Gly-Gly-His) and glycyl- -histidylglycine (MeCO-Gly-His-Gly) were studied by 1H NMR spectroscopy. All reactions were carried out in the pH range 2.0–2.5 and two different temperatures, 22 and 60°C. In the reactions of these two palladium(II) complexes with MeCO-His-Gly, complete hydrolysis of the amide bond involving carboxylic group of histidine occurs in less than 24 h. The cleavage is regioselective. With peptides containing free a carboxylic group of histidine, MeCO-Gly-His and MeCO-Gly-Gly-His, palladium(II) complex promote the cleavage of the MeCO–Gly and Gly–Gly amide bonds. No cleavage of the Gly–His amide bond was observed. The mechanism of these hydrolytic reactions involves release of -Ala ligand and aquation of the palladium(II) complex chelated to the substrate through the imidazole N-3 atom and deprotonated nitrogen atom of the amide bond involving amino group of histidine. This aqua complex represents a catalytically active form different from the initially added catalytically inactive complex. In the reactions of palladium(II) complexes with tripeptide MeCO-Gly-His-Gly, two amide bonds, MeCO–Gly and His–Gly, were cleaved. The mechanism of the cleavage of these amide bonds is correlated with two different palladium(II)–substrate catalytically active forms. These findings contribute to the better understanding of selective cleavage of peptides and proteins and must be taken into consideration in designing new reagents for this purpose.  相似文献   

8.
IR studies were preformed to determine possible transition metal ion binding sites of penicillin. the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M–L complexes with engagement of –COO and/or –CONH– functional groups. The small shift of νC=O towards higher frequencies rules out direct M–L interaction via β-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic β-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and C=O stretching frequencies were discussed to determine the β-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.  相似文献   

9.
The structures and energies of axial and equatorial conformers and rotamers of 4-substituted tetrahydro-2H-thiopyran-1,1-dioxides (tetrahydrothiopyran-1,1-dioxides, thiacyclohexane-1,1-dioxides, thiane-1,1-dioxides, and 1,1-dioxothianes; CH3, CH2OH, CHO, COCH3, CN, F, Cl, Br, and OCOCH3) were calculated using the hybrid density functionals B3LYP, B3P86, and B3PW91, as well as MP2 and the 6-31G(d), 6-31G(2d), 6-31G(3d), 6-31G(d,p), and 6-31+G(d) basis sets. MP2/6-31+G(d)/ /HF/6-31+G(d) [–G° = 1.73 kcal/mol], B3P86/6-31G(d) [–G° = 1.75 kcal/mol], and B3PW91/6-31G(d) [–G° = 1.85 kcal/mol] gave conformational free energy (G°) values at 180 K for 4-methyltetrahydro-2H-thiopyran-1,1-dioxide which were similar to the reported experimental values for methylcyclohexane (–G° = 1.80 kcal/mol), 4-methyltetrahydro-2H-thiopyran (–G° = 1.80 kcal/mol), and other 4-methyl-substituted heterocycles. All levels of theory showed that the conformational preferences of the 4-methanoyl (4-formyl), 4-ethanoyl (4-acetyl), and 4-cyano substituents were small. The HF calculations gave conformational free energy (G°) values for 4-chlorotetrahydro-2H-thiopyran-1,1dioxide which were closer to the experimental value than the MP2 and density functional methods. The best agreement with available experimental data for 4-bromotetrahydro-2H-thiopyran-1,1-dioxide was obtained from the HF/6-31G(2d), HF/6-31G(3d), and B3LYP/6-31G(2d) calculations, and, for 4-acetoxytetrahydro-2H-thiopyran-1,1-dioxide, from the HF/6–31G(3d) calculations. The conformational free energies (G°) and relative energies (E) of the conformers and rotamers have been compared with the correspondingly substituted cyclohexanes and tetrahydro-2H-thiopyrans and are discussed in terms of dipole–dipole (electrostatic) interactions and repulsive nonbonded interactions (steric) in the most stable axial and equatorial conformers. The axial S=O bond lengths are shorter than the equatorial S=O bond lengths and the C2–C3 bond lengths in the substituents with carbon-bonded to the ring are shorter than the C3–C4 and C4–C-5 bond lengths. In contrast, the C2–C3 bond lengths in the 4-halogen and 4-acetoxy substituents are longer than the C3–C4 and C4–C-5 bond lengths.  相似文献   

10.
The purpose of this report is to quantitatively find the cause for the elongation of the R-C bond in R-COO (R = H, CH3 and C2H5) and the shortening of the C-O bond in CH3-O upon deprotonation in the gas phase. These elongations and shortenings result from the contributions of R---CO2 and H---CH2=O as resonance structures to the systems. Because these structures must make only a small contribution in the crystal, the R-C bond lengths of R-COO (R= H and CH3) in the crystal structure are shorter than those in the gas phase.  相似文献   

11.
The structure of 4-hydroxy-4-[1-n-butyl-2-phenyl-2-(diphenylphosphino)ethenyl]-2-methyl-5,5-di-(n-butyl)-1-tert-butyl-1-aza-3-azonia-4-boratacyclopent-2-ene (I), the product of the reaction of the title compounds, has been established by X-ray structure analysis. The heterocycle has an envelope conformation, with the B atom deviating from the plane of four atoms. The distribution of bond lengths in the heterocycle is indicative of a delocalization in the N–C–N fragment. In the crystal, the molecules I form centrosymmetric dimers with the help of the H-bonds N–H...O. The hydroxyl group has a short intramolecular contact to the phosphorus atom, which can be interpreted as the hydrogen bond of the O–H...P type.A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 3, pp. 91–95, May–June 1993.Translated by T. Yudanova.  相似文献   

12.
Understanding binding site preferences in biological systems as well as affinities to binding partners is a crucial aspect in metallodrug development. We here present a mass spectrometry-based method to compare relative stabilities of metal-peptide adducts in the gas phase. Angiotensin 1 and substance P were used as model peptides. Incubation with isostructural N-heterocyclic carbene (NHC) complexes of RuII, OsII, RhIII, and IrIII led to the formation of various adducts, which were subsequently studied by energy-resolved fragmentation experiments. The gas-phase stability of the metal-peptide bonds depended on the metal and the binding partner. Of the four complexes used, the OsII derivative bound strongest to Met, while RuII formed the most stable coordination bond with His. RhIII was identified as the weakest peptide binder and IrIII formed peptide adducts with intermediate stability. Probing these intrinsic gas-phase properties can help in the interpretation of biological activities and the design of site-specific protein binding metal complexes.  相似文献   

13.
R67 dihydrofolate reductase (DHFR) is a novel enzyme that confers resistance to the antibiotic trimethoprim. The crystal structure of R67 DHFR displays a toroidal structure with a central active-site pore. This homotetrameric protein exhibits 222 symmetry, with only a few residues from each chain contributing to the active site, so related sites must be used to bind both substrate (dihydrofolate) and cofactor (NADPH) in the productive R67 DHFR?NADPH?dihydrofolate complex. Whereas the site of folate binding has been partially resolved crystallographically, an interesting question remains: how can the highly symmetrical active site also bind and orient NADPH for catalysis? To model this ternary complex, we employed DOCK and SLIDE, two methods for docking flexible ligands into proteins using quite different algorithms. The bound pteridine ring of folate (Fol I) from the crystal structure of R67 DHFR was used as the basis for docking the nicotinamide-ribose-Pi (NMN) moiety of NADPH. NMN was positioned by both DOCK and SLIDE on the opposite side of the pore from Fol I, where it interacts with Fol I at the pore's center. Numerous residues serve dual roles in binding. For example, Gln 67 from both the B and D subunits has several contacts with the pteridine ring, while the same residue from the A and C subunits has several contacts with the nicotinamide ring. The residues involved in dual roles are generally amphipathic, allowing them to make both hydrophobic and hydrophilic contacts with the ligands. The result is a `hot spot' binding surface allowing the same residues to co-optimize the binding of two ligands, and orient them for catalysis.  相似文献   

14.
The MutT pyrophosphohydrolase from E. coli (129 residues) catalyzes the hydrolysis of nucleoside triphosphates (NTP), including 8-oxo-dGTP, by substitution at Pβ, to yield NMP and pyrophosphate. The product, 8-oxo-dGMP is an unusually tight binding, slowly exchanging inhibitor with a KD=52 nM, (ΔG°=−9.8 kcal/mol) which is 6.1 kcal/mol tighter than the binding of dGMP (ΔG°=−3.7 kcal/mol). The higher affinity for 8-oxo-dGMP results from a more favorable ΔHbinding (−32 kcal/mol) despite an unfavorable −TΔS°binding (+22 kcal/mol). The solution structure of the MutT–Mg2+-8-oxo-dGMP complex shows a narrowed, hydrophobic nucleotide-binding cleft with Asn-119 and Arg-78 among the few polar residues. The N119A, N119D, R78K and R78A single mutations, and the R78K+N119A double mutant all showed largely intact active sites, on the basis of small changes in the kinetic parameters of dGTP hydrolysis and in 1H–15N HSQC spectra. However, the N119A mutation profoundly weakened the active site binding of 8-oxo-dGMP by 4.3 kcal/mol (1650-fold). The N119D mutation also weakened 8-oxo-dGMP binding but only by 2.1 kcal/mol (37-fold), suggesting that Asn-119 functioned both as a hydrogen bond donor to C8=O, and a hydrogen bond acceptor from N7H of 8-oxo-dGMP, while aspartate at position −119 functioned as an acceptor of a single hydrogen bond. Much smaller weakening effects (0.3–0.4 kcal/mol) on the binding of dGMP and dAMP were found, indicating specific hydrogen bonding of Asn-119 to 8-oxo-dGMP. While formation of the wild type MutT–Mg2+-8-oxo-dGMP complex slowed the backbone NH exchange rates of 45 residues distributed throughout the protein, the same complex of the N119A mutant slowed the exchange rates of only 11 residues at or near the active site, indicating an increase in conformational flexibility of the N119A mutant. The R78K and R78A mutations weakened the binding of 8-oxo-dGMP by 1.7 and 1.1 kcal/mol, respectively, indicating a lesser role of Arg-78 than of Asn-119 in the selective binding of 8-oxo-dGMP, likely donating a single hydrogen bond to its C6=O. The R78K+N119A double mutant weakened the binding of 8-oxo-dGMP (KIslope=3.1 mM) by 6.5±0.2 kcal/mol which overlaps, within error with the sum of the effects of the two single mutants (6.0±0.3 kcal/mol). Such additive effects of the two single mutants in the double mutant are most simply explained by the independent functioning of Asn-119 and Arg-78 in the binding of 8-oxo-dGMP. Independent functioning of these two residues in nucleotide binding is consistent with their locations in the MutT–Mg2+-8-oxo-dGMP complex, on opposite sides of the active site cleft, with a distance of 8.4±0.5 Å between their side chain nitrogens.  相似文献   

15.
Using the unity bond index–quadratic exponential potential (UBI–QEP) formalism and the Monte Carlo method, functions are obtained that describe the dependence of the binding energies of atomic adsorbates on the single crystal surface coverage for the models of random adsorption, models with a site choice and site preference, models with neighbor exclusion, and models with diffusion assistance.  相似文献   

16.
Cyclodextrins and antibodies have been used as affinity agents to improve relative recovery during microdialysis sampling. Two neuropeptides, methionine-enkephalin (ME) and leucine-enkephalin (LE), were chosen to compare the use of cyclodextrins and antibodies as possible affinity agents for improving their relative recovery across polycarbonate and polyethersulfone membranes during in vitro sampling. Cyclodextrins (CD) including β-CD, 2-hydroxypropyl-β-cyclodextrin (2HPβ-CD), and γ-CD gave improvements of relative recovery for both peptides of less than 2-fold as compared to controls. Comparisons of relative recovery between tyrosine–glycine–glycine, tyrosine, and phenylalanine using different cyclodextrins in the perfusion fluid were also obtained. Inclusion of an antibody against met-enkephalin in the microdialysis perfusion fluid resulted in relative recovery increases of up to 2.5-fold. These results show that using antibodies as affinity agents during microdialysis sampling may be more effective agents to improve the relative recovery of these opioid neuropeptides.  相似文献   

17.
Density functional theory (DFT) using the finite cluster approach is utilized to compute binding energies, bond geometries, and vibrational properties of carbon monoxide adsorbed on Pt(111) as a function of the external interfacial field, focusing attention on the metal–CO bond itself. Comparison with electrode potential-dependent frequencies for the metal–CO (νM–CO) as well as the much-studied intramolecular C---O (νCO) vibration, as measured by in-situ Raman and infrared spectroscopy, facilitate their interpretation in terms of metal-chemisorbate bonding for this archetypal electrochemical system. Decomposing the calculated metal–CO binding energy and vibrational frequencies into individual orbital and steric repulsion components enables the role of such quantum-chemical interactions to the field- (and hence potential-) dependent bonding to be assessed. No simple relationship between the field(F)-dependent binding energies and the νM–CO frequencies is evident. While the DFT νM–COF slopes are negative at positive and small–moderate negative fields, reflecting the prevailing influence of back-donation, a νM–COF maximum is obtained at larger negative fields for atop CO, and a plateau for hollow-site CO. This Stark-tuning behavior reflects largely offsetting field-dependent contributions from π and σ surface bonding, and can also be rationalized on the basis of changes in the electrostatic component of νM–CO from increasing M–CO charge polarization. A rough correlation between the field-dependent νM–CO frequencies and the corresponding bond distances, rM–CO, is observed for hollow and atop CO in that rM–CO shortens towards less positive fields, but becomes near-constant at moderate–large negative fields. A more quantitative correlation between the field-dependent C---O frequencies and bond lengths is also evident. In harmony with earlier findings (and unlike the νM–COF behavior), the νCOF dependence is due chiefly to changes in the back-donation bonding component. The overall vibrational frequency-field behavior predicted by DFT is also in semi-quantitative concordance with experimental potential-dependent spectra.  相似文献   

18.
Electrostatic interactions and other weak interactions between amino acid side chains on protein surfaces play important roles in molecular recognition, and the mechanism of their intermolecular interactions has gained much interest. We established that charged peptides are useful for investigating the molecular recognition character of proteins and their molecular interaction induced structural changes. Positively charged lysine peptides competitively inhibited electron transfer from reduced cytochrome f (cyt f or cytochrome c (cyt c) to oxidized plastocyanin (PC), due to neutralization of the negatively charged site of PC by formation of PC-lysine peptide complexes. Lysine peptides also inhibited electron transfer from cyt c to cytochrome c peroxidase. Likewise, negatively charged aspartic acid peptides interacted with the positively charged sites of cytfand cyt c, and competitively inhibited electron transfer from reduced cytfor cyt c to oxidized PC and from [Fe(CN)6]4- to oxidized cyt c. Changes in the geometry and a shift to a higher redox potential of the active site Cu of PC on oligolysine binding were detected by spectroscopic and electrochemical measurements, owing to the absence of absorption in the visible region for lysine peptides. Structural and redox potential changes were also observed for cyt f and cyt c by interaction with aspartic acid peptides.  相似文献   

19.
The geometries of the dipeptides -Pro- -Ala, -Pro- -Ala and -Pro-Gly were investigated by a grid scan ab initio calculation. The 6-31G basis set was used to estimate the effect of the alanyl side-chain on the conformation of the peptide backbone and to provide a computational basis for the interpretation of known physical-chemical properties of larger peptides that contain these dipeptides. These calculations furnish a direct quantum mechanical assessment of the energetic consequences of a methyl side-chain in the i + 2 position of a turn. The results of the calculation support the current view that the presence of a -Ala residue in the i + 2 position favors a type II β-turn over a type I β-turn conformation, while -Ala has the opposite effect. Total and relative energies for all the optimized conformations identified by the grid search are given and geometric parameters (bond lengths, bond angles and dihedral angles) and net atomic charges have been calculated.  相似文献   

20.
An x-ray structural investigation of four permethylcyclocarbosilanes, whose heterocycles are formed by –Si–CH2–CH2–, –Si–CH=CH–, and –Si–CC– fragments, has been carried out. Strong distortions of some bond lengths and bond angles (caused by the shortness of the Si...Si distances between the neighboring Si atoms and the absence of intermolecular contancts with the participation of atoms of the heterocycles), which attest to statistical disordering of the molecules in the crystals, whose character could be established unequivocally for three of the compounds, have been observed in all the structures.For part LXIII, see [1].A. N. Nesmeyanov Institute of Organometallic Compounds, Academy of Sciences of the USSR. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 2, pp. 116–124, March–April, 1991.  相似文献   

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