Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

Analytical pyrolysis of carbohydrates: I. Chemical interpretation of matrix influences on pyrolysis-mass spectra of amylose using pyrolysis-gas chromatography-mass spectrometry

Inorganic additives, viz. Na₂CO₃, NaOH, HCl, ZnC₂, NaH₂PO₄, Na₂HPO₄, NaCl. MgSO₄ and sea salt, to the pyrolysis matrix change the pyrolysis-mass spectrum of amylose significantly. Carbonyl compounds, acids and their lactones, furans, pyranones anhydrosugars and aromatic substances are found in different ratios under the various conditions, as determined by pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS).Carbonyl compounds, acids and lactones are released from alkaline and neutral matrices. Furans and anhydrohexoses are particularly formed under neutral and acidic conditions. Pyranones are specific for phosphate matrices. Unsaturated hydrocarbons and aromatic substances arise from strongly alkaline or dehydrating matrices. Degradation pathways are proposed for various compound categories.The results of pyrolysis-mass spectrometry and Py-GC-MS are highly compatible.     

Synthesis and derivatization of daptomycin: a chemoenzymatic route to acidic lipopeptide antibiotics

Daptomycin is a branched cyclic nonribosomally assembled acidic lipopeptide, which is the first clinically approved antibiotic of this class. Here we show that the recombinant cyclization domain of the Streptomyces coelicolor calcium-dependent antibiotic (CDA) nonribosomal peptide synthetase (NRPS) is a versatile tool for the chemoenzymatic generation of daptomycin derivatives. Linear CDA undecapeptide thioesters with single exchanges at six daptomycin-specific residues were successfully cyclized by CDA cyclase. Simultaneous incorporation of all six of these residues into the peptide backbone and elongation of the N-terminus of CDA by two residues yielded a daptomycin derivative that lacked only the beta-methyl group of l-3-methylglutamate. Bioactivity studies with several substrate analogues revealed a significant role of nonproteinogenic constituents for antibacterial potency. In accordance with acidic lipopeptides, the bioactivity of the chemoenzymatic assembled daptomycin analogue is dependent on the concentration of calcium ions. Single deletions of the four acidic residues in the peptide backbone suggest that only two aspartic acid residues are essential for antimicrobial potency. These two residues are strictly conserved among other nonribosomal acidic lipopeptides and the EF-motif of ribosomally assembled calmodulin. Based on these findings CDA cyclase is a versatile catalyst that can be used to generate novel daptomycin derivatives that are otherwise difficult to obtain by chemical modification of the parental tridecapeptide to improve further its therapeutic activity.     

Effect of protonation exothermicity on the chemical ionization mass spectra of some alkylbenzenes

The H₂, N₂/H₂, CO₂/H₂, N₂O/H₂, CO/H₂ and CH₄ chemical ionization mass spectra of thirteen C₈ to C₁₁ alkylbenzenes are reported. Characteristic hydride and alkide ion abstraction reactions are observed with all reagent gases. The major fragmentation reactions of [MH]⁺ are olefin elimination to form a protonated arene and arene elimination to form an alkyl ion. From the effect of structure and protonation exothermicity it is concluded that rearrangement of primary alkyl groups to the more stable secondary or tertiary structure occurs prior to alkyl ion formation. A detailed fragmentation mechanism for protonated arenes is proposed. The ‘effective’ proton affinity of the methane-derived reagent system is estimated to be ～556 kJ mol^?1.     

The reactivity of 1,4-dihydronicotinamides towards reduction of 1,1′,1″-trifluoro-acetophenone : influence of methyl substitution on the pyridine ring.

In a series of methyl substituted 1-(2′,6′-dichlorobenzyl)-1,4-dihydronicotinamides those compounds with the methyl α to the pyridine nitrogen are at least one order of magnitude more reactive than the analogues without methyl or methyl on the 5-position.     

Time-resolved intraband electronic relaxation dynamics of Hg(n) (-) clusters (n=7-13,15,18) excited at 1.0 eV

Time-resolved photoelectron imaging has been used to study the relaxation dynamics of small Hg(n) (-) clusters (n=7-13,15,18) following intraband electronic excitation at 1250 nm (1.0 eV). This study furthers our previous investigation of single electron, intraband relaxation dynamics in Hg(n) (-) clusters at 790 nm by exploring the dynamics of smaller clusters (n=7-10), as well as those of larger clusters (n=11-13,15,18) at a lower excitation energy. We measure relaxation time scales of 2-9 ps, two to three times faster than seen previously after 790 nm excitation of Hg(n) (-), n=11-18. These results, along with size-dependent trends in the absorption cross-section and photoelectron angular distribution anisotropy, suggest significant evolution of the cluster anion electronic structure in the size range studied here. Furthermore, the smallest clusters studied here exhibit 35-45 cm(-1) oscillations in pump-probe signal at earliest temporal delays that are interpreted as early coherent nuclear motion on the excited potential energy surfaces of these clusters. Evidence for evaporation of one or two Hg atoms is seen on a time scale of tens of picoseconds.     

BRCA1 mutation screening using restriction endonuclease fingerprinting-single-strand conformation polymorphism in an automated capillary electrophoresis system

Efficient mutation scanning techniques are needed for the rapid detection of novel disease-associated mutations and rare-sequence variants of putative importance. The large size of the breast cancer 1 gene (BRCA1) and the many mutations found throughout its entire coding sequence make screening for mutations in this gene particularly challenging. We have developed a method for screening exon 11 of the BRCA1 gene based on restriction enzyme digestion of fluorescence-labeled polymerase chain reaction (PCR) products followed by single-strand conformation polymorphism (SSCP) using an automated capillary electrophoresis system, denoted capillary restriction endonuclease fingerprinting (REF)-SSCP electrophoresis. Using this strategy on a control set of samples, we were able to detect 17 of 18 known sequence alterations. The method was then applied to screen 73 Norwegian females with family histories of breast and/or ovarian cancer. A total of 172 sequence alterations were detected, including substitutions, insertions, and deletions. One novel substitution of unknown function was identified. Sequencing of all samples negative in the capillary REF-SSCP system gave no additional mutations confirming the high sensitivity of the described methodology. Capillary REF-SSCP electrophoresis appeared as a technically convenient technique, requiring amplification of fewer PCR fragments than traditional SSCP. The novel strategy allows high-throughput mutation scanning without radioactive labeling and polyacrylamide gel electrophoresis (PAGE).     

Bicyclic [b]-heteroannulated pyridazine derivatives. 4. Cyclization reactions of 4-aryltetrahydropyridazine-3,6-dione 3-hydrazones with some keto esters

Ethoxycarbonylalkylidene derivatives 2 and 6 of the title hydrazones were obtained in the reaction with ethyl pyruvate or ethyl aroylformate and ethyl acetoacetate, respectively, in methanol. Both compounds were mixtures of geometric isomers with high predominance of one of them. Nmr spectroscopy revealed an unexpected magnetic non-equivalence of the CH₂ protons in the ester ethyl group of the major isomer of 6 . On heating (?200°) in an inert medium or on refluxing in ethanolic sodium ethoxide 2 cyclized to the corresponding pyridazino[6,1-c]-triazines 4 , whereas 6 formed pyrazolylpyridazines 7 . The structure of the latter was unambigously established by X-ray analysis. Alkylation of 4a with benzyl bromide in the presence of tetrabutylammonium bromide occurred selectively on the pyridazine N atom.     

Capillary isoelectric focusing-mass spectrometry for shotgun approach in proteomics

We report on capillary isoelectric focusing-mass spectrometry (CIEF-MS) of complex peptide mixtures in the absence of carrier ampholytes. Furthermore, the use of low concentrations of carrier ampholytes as mere spacers is investigated. Carrier ampholytes are complex mixtures of amphoteric compounds with high buffering capacity. Since all peptides are amphoteric compounds by themselves, the use of carrier ampholytes may be superfluous to establish a stable pH gradient in CIEF analysis of protein digests. Our research showed that when carrier ampholytes are omitted, the analyte ions are not focused at their isoelectric point. The analytes are charged, leading to electrophoretic mobility uncharacteristic for CIEF. The method was tested for a five-protein-mixture at 0.02 mg/mL per protein and 0.05 mg/mL per protein. At the lower concentration, the analytes were stacked during the focusing process in only a limited length of the capillary. Therefore, the higher concentration led to better separation efficiency. It was found that at low concentration (0.20%) the carrier ampholytes could work as spacers. Though it led to sensitivity losses of 15-45%, this was compensated by the higher separation efficiencies seen. The method was evaluated with an eight-protein-mixture, of which all could be identified after performing MS/MS.     

Susceptibility to Effects of UVB Irradiation on Induction of Contact Sensitivity, Relevance of Number and Function of Langerhans Cells and Epidermal Macrophages

Sensitization on skin exposed to acute low-dose UVB irradiation separates normal humans into two phenotypically distinct groups: One group, following sensitization on UVB-irradiated skin, develops contact sensitivity, designated UVB resistant (UVB-R) and the second group, following sensitization on UVB-irradiated skin, fails to develop contact sensitivity, designated UVB susceptible (UVB-S). To investigate whether UVB susceptibility in humans is related to antigen-presenting activity in the skin we studied the effect of UVB irradiation on the number and function of the epidermal antigen-presenting cells in volunteers identified as UVB-R and UVB-S. Single cell suspensions of epidermal cells from control skin and skin exposed to 3 minimal erythema doses (MED) of UVB 3 days previously were stained for Langerhans cells (CD1a+HLA-DR+) and epidermal macrophages (CD1a-HLA-DR+). The UVB exposure of the skin significantly decreased the percentage of Langerhans cells (UVB-R: n = 7, P < 0.02, UVB-S: n = 6, P < 0.03) and increased the percentage of epidermal macrophages (UVB-R: n = 7, P < 0.03, UVB-S: n = 6, P < 0.03) however to the same degree in both the UVBR and the UVB-S group. To study the effect on Langerhans cell alloreactivity, epidermal cells were harvested immediately after UVB irradiation. However, in both UVB-R and UVB-S subjects the Langerhans cell alloreactivity was blocked to the same degree immediately after UVB irradiation compared to nonirradiated epidermal cells. To determine the effect of UVB irradiation on epidermal macrophages, epidermal cells were harvested 3 days after UVB irradiation. Irradiated epidermal cells from both UVB-R and UVB-S subjects demonstrated a strong antigen-presenting capacity compared to epidermal cells from control skin leading to activation of T cells that mainly secrete interferon (1FN)-γ and not interleukin (IL)-4. In conclusion we found that UVB susceptibility was not correlated with the number of Langerhans cells or epidermal macrophages in the skin at the same time of sensitization. Neither was it correlated with the capacity of Langerhans cells nor UVB-induced epidermal macrophages to activate T cells in vitro.