Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) -based identification of bacteria and fungi significantly changed the diagnostic process in clinical microbiology. We describe here a novel technique for bacterial and yeast deposition on MALDI target using an automated workflow resulting in an increase of the microbes' score of MALDI identification. We also provide a comparison of four different sample preparation methods. In the first step of the study, 100 Gram-negative bacteria, 100 Gram-positive bacteria, 20 anaerobic bacteria and 20 yeasts were spotted on the MALDI target using manual deposition, semi-extraction, wet deposition onto 70% formic acid and by automatic deposition using MALDI Colonyst. The lowest scores were obtained by manual toothpick spotting which significantly differ from other methods. Identification score of semi-extraction, wet deposition and automatic wet deposition did not significantly differ using calculated relative standard deviation (RSD). Nevertheless, the best results with low error rate have been observed using MALDI Colonyst robot. The second step of validation included processing of 542 clinical isolates in routine microbiological laboratory by a toothpick direct spotting, on-plate formic acid extraction (for yeasts) and automatic deposition using MALDI Colonyst. Validation in routine laboratory process showed significantly higher identification scores obtained using automated process compared with standard manual deposition in all tested microbial groups (Gram-positive, Gram-negative, anaerobes, and yeasts). As shown by our data, automatic colony deposition on MALDI target results in an increase of MALDI-TOF MS identification scores and reproducibility.
A method for discriminating malting barley varieties based on direct matrix-assisted laser desorption-ionisation - time-of-flight mass spectrometry (MALDI-TOF MS) fingerprinting of proteins was developed. Signals corresponding to hordeins were obtained by simple mixing of powdered barley grain with a MALDI matrix solution containing 12.5mgmL(-1) of ferulic acid in an acetonitrile:water:formic acid 50:33:17 v/v/v mixture. Compared to previous attempts at MALDI-TOF mass spectrometric analysis of barley proteins, the extraction and fractionation steps were practically omitted, resulting in a significant reduction in analytical time and costs. The discriminatory power was examined on twenty malting barley varieties and the practicability of the method was tested on sixty barley samples acquired from Pilsner Urquell Brewery. The method is proposed as a rapid tool for variety assignment and purity determination of malting barley that may replace gel electrophoresis currently used for this purpose.
- Klíčová slova
- Barley, MALDI-TOF MS, Malting, Proteins,
- MeSH
- gluteny analýza MeSH
- ječmen (rod) chemie klasifikace metabolismus MeSH
- pivo MeSH
- průmysl zpracování potravin metody MeSH
- semenáček chemie klasifikace metabolismus MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- gluteny MeSH
The statistical evaluation of triacylglycerol profiles in plant oils based on high-performance liquid chromatography mass spectrometry (HPLC/MS) analysis enables the differentiation of various plant oils on the basis of the multidimensional data matrix. A data set of 93 oil samples from 60 varieties of plants composed from 355 triacylglycerols is evaluated using the principal component analysis. Analyzed samples are resolved in the principal component analysis plot, and similarities among some types of plant oils are visualized by the formation of clusters. The authentication of plant oils is tested with model samples of olive oil adulterated with sunflower oil at different concentration levels. Our HPLC/MS method using the statistical multivariate data analysis of a large data matrix enables a clear identification of adulterated olive oils already from 1% of added sunflower oil as an adulterant.
We evaluate the applicability of automated molecular docking techniques and quantum mechanical calculations to the construction of a set of structures of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis to obtain 3D structure-activity relationships. The data set studied consists of the complexes of eighteen substrates docked within the active site of haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJ10. The results of the COMBINE analysis are compared with previously reported data obtained for the same dataset from modelled complexes that were based on an experimentally determined structure of the DhlA-dichloroethane complex. The quality of fit and the internal predictive power of the two COMBINE models are comparable, but better external predictions are obtained with the new approach. Both models show a similar composition of the principal components. Small differences in the relative contributions that are assigned to important residues for explaining binding affinity differences can be directly linked to structural differences in the modelled enzyme-substrate complexes: (i) rotation of all substrates in the active site about their longitudinal axis, (ii) repositioning of the ring of epihalohydrines and the halogen substituents of 1,2-dihalopropanes, and (iii) altered conformation of the long-chain molecules (halobutanes and halohexanes). For external validation, both a novel substrate not included in the training series and two different mutant proteins were used. The results obtained can be useful in the future to guide the rational engineering of substrate specificity in DhlA and other related enzymes.
- MeSH
- analýza hlavních komponent MeSH
- chemické modely MeSH
- databáze proteinů MeSH
- halogenované uhlovodíky chemie metabolismus MeSH
- hydrolasy chemie metabolismus MeSH
- konformace proteinů MeSH
- kvantitativní vztahy mezi strukturou a aktivitou MeSH
- metoda nejmenších čtverců MeSH
- molekulární konformace MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- počítačová simulace MeSH
- statická elektřina MeSH
- substrátová specifita MeSH
- termodynamika MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Xanthobacter enzymologie MeSH
- zobrazování trojrozměrné MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- haloalkane dehalogenase MeSH Prohlížeč
- halogenované uhlovodíky MeSH
- hydrolasy MeSH
Haloalkane dehalogenases catalyze cleavage of the carbon-halogen bond in halogenated aliphatic compounds, resulting in the formation of an alcohol, a halide, and a proton as the reaction products. Three structural features of haloalkane dehalogenases are essential for their catalytic performance: (i) a catalytic triad, (ii) an oxyanion hole, and (iii) the halide-stabilizing residues. Halide-stabilizing residues are not structurally conserved among different haloalkane dehalogenases. The level of stabilization of the transition state structure of S(N)2 reaction and halide ion provided by each of the active site residues in the enzymes DhlA, LinB, and DhaA was quantified by quantum mechanic calculations. The residues that significantly stabilize the halide ion were assigned as the primary (essential) or the secondary (less important) halide-stabilizing residues. Site-directed mutagenesis was conducted with LinB enzyme to confirm location of its primary halide-stabilizing residues. Asn38Asp, Asn38Glu, Asn38Phe, Asn38Gln, Trp109Leu, Phe151Leu, Phe151Trp, Phe151Tyr, and Phe169Leu mutants of LinB were constructed, purified, and kinetically characterized. The following active site residues were classified as the primary halide-stabilizing residues: Trp125 and Trp175 of DhlA; Asn38 and Trp109 of LinB; and Asn41 and Trp107 of DhaA. All these residues make a hydrogen bond with the halide ion released from the substrate molecule, and their substitution results in enzymes with significantly modified catalytic properties. The following active site residues were classified as the secondary halide-stabilizing residues: Phe172, Pro223, and Val226 of DhlA; Trp207, Pro208, and Ile211 of LinB; and Phe205, Pro206, and Ile209 of DhaA. The differences in the halide stabilizing residues of three haloalkane dehalogenases are discussed in the light of molecular adaptation of these enzymes to their substrates.
- MeSH
- aminokyseliny chemie genetika MeSH
- anionty chemie MeSH
- asparagin genetika MeSH
- chemické modely MeSH
- fenylalanin genetika MeSH
- halogeny chemie MeSH
- histidin genetika MeSH
- hydrolasy chemie genetika MeSH
- isoleucin genetika MeSH
- kvantová teorie * MeSH
- kyselina glutamová genetika MeSH
- leucin genetika MeSH
- matematické výpočty počítačové MeSH
- mutageneze cílená * MeSH
- prolin genetika MeSH
- statická elektřina MeSH
- tryptofan genetika MeSH
- valin genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- validační studie MeSH
- Názvy látek
- aminokyseliny MeSH
- anionty MeSH
- asparagin MeSH
- fenylalanin MeSH
- haloalcohol dehalogenase MeSH Prohlížeč
- haloalkane dehalogenase MeSH Prohlížeč
- halogeny MeSH
- histidin MeSH
- hydrolasy MeSH
- isoleucin MeSH
- kyselina glutamová MeSH
- leucin MeSH
- prolin MeSH
- tryptofan MeSH
- valin MeSH
