Vysokoškolská učebnice, která se zaměřuje na biochemii.

• MeSH
• biochemie MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• Učební osnovy. Vyučovací předměty. Učebnice
• NLK Obory
• biochemie
• NLK Publikační typ
• učebnice vysokých škol

Předkládaná učebnice přináší netradičním způsobem zpracované základy biochemie, nepřetížené nadbytkem faktografických údajů. Je určena pro vysokoškolské studenty, kteří již zvládli základy obecné, organické a analytické chemie. Ve dvanácti kapitolách postupuje výklad přes základní stavební struktury biologických systémů (aminokyseliny, peptidy, proteiny, lipidy, nukleové kyseliny a sacharidy), membránové děje a molekulovou genetiku až k nejdůležitějším metabolickým procesům. Nakladatelská anotace; Základy biochemie pro vysokoškolské studenty.

• MeSH
• biochemie MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• Učební osnovy. Vyučovací předměty. Učebnice
• NLK Obory
• biochemie
• NLK Publikační typ
• učebnice vysokých škol

Předkládaná učebnice přináší netradičním způsobem zpracované základy biochemie, nepřetížené nadbytkem faktografických údajů. Je určena pro vysokoškolské studenty, kteří již zvládli základy obecné, organické a analytické chemie. Ve dvanácti kapitolách postupuje výklad přes základní stavební struktury biologických systémů (aminokyseliny, peptidy, proteiny, lipidy, nukleové kyseliny a sacharidy), membránové děje a molekulovou genetiku až k nejdůležitějším metabolickým procesům. Mimořádná pozornost je věnována enzymologii a bioenergetice, jejichž pochopení umožňuje propojit metabolismus jako jediný systém chemických reakcí. Text výkladu je doplněn četnými zajímavostmi a nadhledovými úvahami., jednotlivé kapitoly obsahují řadu otázek s uvedeným řešením, průřezovým otázkám a odpovědím je věnována i celá závěrečná kapitola.

• MeSH
• biochemie MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• Učební osnovy. Vyučovací předměty. Učebnice
• NLK Obory
• biochemie
• NLK Publikační typ
• učebnice vysokých škol

Oil bodies, lipid-storage organelles, are stabilized by a number of specific proteins. These proteins are very hydrophobic, which complicates their identification by "classical" proteomic protocols using trypsin digestion. Due to the lack of trypsin cleavage sites, the achievable protein coverage is limited or even insufficient for reliable protein identification. To identify such proteins and to enhance their coverage, we introduced a modified method comprising standard three-step procedure (SDS-PAGE, in-gel digestion, and LC-MS/MS analysis). In this method, chymotrypsin, single or in combination with trypsin, was used, which enabled to obtain proteolytic peptides from the hydrophobic regions and to identify new oil bodies' proteins. Our method can be easily applied to identification of other hydrophobic proteins.

• MeSH
• Arabidopsis metabolismus   MeSH
• chromatografie kapalinová MeSH
• chymotrypsin metabolismus   MeSH
• elektroforéza v polyakrylamidovém gelu MeSH
• hmotnostní spektrometrie MeSH
• hydrofobní a hydrofilní interakce * MeSH
• lipidy * MeSH
• organely metabolismus   MeSH
• proteiny huseníčku metabolismus   MeSH
• proteomika metody   MeSH
• trypsin metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH

Biofysikální chemie je interdisciplinární obor zabývající se aplikací fysikálně-chemických přístupů při řešení biologických problémů. Probíraná látka je v knize rozdělena do tří oblastí. První z nich zahrnuje analysu biologicky významných jevů, pro jejichž chápání je fysikálně-chemický přístup rozhodující. Řadíme sem celý soubor problémů spojených s bioenergetikou, nekovalentními interakcemi, strukturou vody, kinetickou analysou biologických procesů a ději na membránách. Druhým okruhem je využití fysikálních metod v biologii, podrobněji jsou vysvětleny principy a aplikace spektrofotometrie, fluorimetrie, kalorimetrie, cirkulárního dichroismu, rentgenové krystalografie, nukleární magnetické resonance, radiometrie a výpočetních metod, používaných při určování prostorové struktury biomakromolekul.

• MeSH
• biofyzikální jevy MeSH
• fyzikální chemie MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• biochemie
• NLK Publikační typ
• učebnice vysokých škol

Winter barley is an economically important cereal crop grown in higher latitudes and altitudes where low temperatures represent an important environmental constraint limiting crop productivity. In this study changes in proteome of leaves and crowns in a frost tolerant winter barley cv. Luxor in relation to short and long term periods of cold followed by a brief frost treatment were studied in order to disclose proteins responsible for the cold hardening process in distinct plant tissues. The mentioned changes have been monitored using two dimensional difference gel electrophoresis (2D-DIGE) with subsequent peptide-mapping protein identification. Regarding approximately 600-700 distinct protein spots detected on 2D gels, there has been found at least a two-fold change after exposure to low temperatures in about 10% of proteins in leaves and 13% of proteins in crowns. Protein and nitrogen metabolic processes have been influenced by low temperature to a similar extent in both tissues while catabolism, carbohydrate metabolism and proteins involved in stress response have been more affected in crowns than in leaves. The range of changes in protein abundance was generally higher in leaves and chloroplast proteins were frequently affected which suggests a priority to protect photosynthetic apparatus. Overall, our data proved existence of slightly different response strategies to low temperature stress in crowns and leaves, i.e., tissues with different biological role. Moreover, there have been found several proteins with large increase in accumulation, e.g., 33 kDa oxygen evolving protein of photosystem II in leaves and "enhanced disease susceptibility 1" in crowns; these proteins might have potential to indicate an enhanced level of frost tolerance in barley.

• Publikační typ
• časopisecké články MeSH

Protein misfolding due to missense mutations is a common pathogenic mechanism in cystathionine β-synthase (CBS) deficiency. In our previous studies, we successfully expressed, purified, and characterized nine CBS mutant enzymes containing the following patient mutations: P49L, P78R, A114V, R125Q, E176K, R266K, P422L, I435T, and S466L. These purified mutants exhibited full heme saturation, normal tetrameric assembly, and high catalytic activity. In this work, we used several spectroscopic and proteolytic techniques to provide a more thorough insight into the conformation of these mutant enzymes. Far-UV circular dichroism, fluorescence, and second-derivative UV spectroscopy revealed that the spatial arrangement of these CBS mutants is similar to that of the wild type, although the microenvironment of the chromophores may be slightly altered. Using proteolysis with thermolysin under native conditions, we found that the majority of the studied mutants is more susceptible to cleavage, suggesting their increased local flexibility or propensity for local unfolding. Interestingly, the presence of the CBS allosteric activator, S-adenosylmethionine (AdoMet), increased the rate of cleavage of the wild type and the AdoMet-responsive mutants, while the proteolytic rate of the AdoMet-unresponsive mutants was not significantly changed. Pulse proteolysis analysis suggested that the protein structure of the R125Q and E176K mutants is significantly less stable than that of the wild type and the other mutants. Taken together, the proteolytic data shows that the conformation of the pathogenic mutants is altered despite retained catalytic activity and normal tetrameric assembly. This study demonstrates that the proteolytic techniques are useful tools for the assessment of the biochemical penalty of missense mutations in CBS.

• MeSH
• cirkulární dichroismus MeSH
• cystathionin-beta-synthasa nedostatek   genetika   metabolismus   MeSH
• Escherichia coli metabolismus   MeSH
• konformace proteinů MeSH
• lidé MeSH
• missense mutace MeSH
• molekulární modely MeSH
• proteolýza MeSH
• S-adenosylmethionin MeSH
• sbalování proteinů MeSH
• spektrofotometrie ultrafialová MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

Plant seed oil bodies, subcellular lipoprotein inclusions providing storage reserves, are composed of a neutral lipid core surrounded by a phospholipid monolayer with several integrated proteins that play a significant role in stabilization of the particles and probably also in lipid mobilization. Oil bodies' proteins are generally very hydrophobic, due to the long uncharged sequences anchoring them into the lipid core, which makes them extremely difficult to handle and to digest successfully. Although oil bodies have been intensively studied during last decades, not all their proteins have been identified yet. To overcome the problems connected with their identification, a method based on SDS-PAGE, in-gel digestion and LC-MS/MS analysis was used. Digestion was carried out with trypsin and chymotrypsin, single or in combination, which increased significantly the number of identified peptides, namely the hydrophobic ones. Thanks to this methodology it was possible to achieve an extensive coverage of proteins studied, to analyze their N-terminal modifications and moreover, to detect four new oil bodies' protein isoforms, which demonstrates the complexity of oil bodies' protein composition.

• MeSH
• Arabidopsis chemie   metabolismus   MeSH
• chromatografie kapalinová MeSH
• chymotrypsin chemie   MeSH
• elektroforéza v polyakrylamidovém gelu MeSH
• hmotnostní spektrometrie MeSH
• molekulární sekvence - údaje MeSH
• oleje rostlin chemie   MeSH
• peptidové fragmenty analýza   chemie   MeSH
• protein - isoformy chemie   klasifikace   izolace a purifikace   MeSH
• proteiny huseníčku chemie   izolace a purifikace   metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza proteinů MeSH
• semena rostlinná chemie   metabolismus   MeSH
• trypsin chemie   MeSH
• vakuoly chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In our laboratory, we have been studying the reductive processes that occur during matrix-assisted laser desorption/ionization (MALDI) experiments. Recently, we have finished an analysis of the DHB matrix effect on the azo group in cyclic peptides. However, deep understanding of disulfide bond behaviour during a mass spectrometry (MS) experiment is much more important in proteomics as its reduction can cause serious errors in protein spectra interpretation. Therefore, we have focused on intra- and intermolecular disulfide bonds as well as disulfide bonds connecting cysteine and 2-thio-5-nitrobenzoic acid (TNB, Ellman's reagent modification) in model peptides during MALDI MS measurements. While the reduction was not observed for intra- and intermolecular cysteine-cysteine disulfide bonds, the disulfide connection between cysteine and TNB was always affected. It was proved that TNB and Ellman's reagent can act as a matrix itself. The results obtained enabled us to propose a reaction mechanism model which is able to describe the phenomena observed during the desorption/ionization process of disulfide-containing molecules.

• MeSH
• cystein chemie   MeSH
• disulfidy chemie   MeSH
• ionty chemie   MeSH
• kyselina dithionitrobenzoová chemie   MeSH
• molekulární sekvence - údaje MeSH
• nitrobenzoany chemie   MeSH
• peptidy chemie   MeSH
• sekvence aminokyselin MeSH
• spektrometrie hmotnostní - ionizace laserem za účasti matrice metody   MeSH
• sulfhydrylové sloučeniny chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Some time ago, we published an announcement that the azo group that closes model cyclic peptides is often reduced in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) in the presence of 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix. In this work, we demonstrate that these peptides are ionized in all DHB matrix isomers, although threshold ionization laser energies as well as the reduction ratios differ in each matrix. Using a NALDI plate, we confirmed that their reduction depends on the presence of DHB matrix and that the hydrogen atoms participating in the reaction come from the DHB matrix hydroxyl group. We show that the reduction ratio is affected by the overall covalent structure of the peptide, by the presence of a free carboxyl group in DHB matrix, by the mutual position of the hydroxyl and carboxyl groups, as well as the laser beam intensity. Based on these results, it can be concluded that the azo-group reduction in cyclic peptides is a very complex process and we are far from fully understanding its nature. We hope that our experimental results will help to shed some light on the MALDI process that still remains mysterious in some of its aspects.

• MeSH
• azosloučeniny chemie   metabolismus   MeSH
• cyklické peptidy chemie   metabolismus   MeSH
• gentisáty chemie   MeSH
• hydroxylový radikál chemie   MeSH
• isomerie MeSH
• oxidace-redukce MeSH
• spektrometrie hmotnostní - ionizace laserem za účasti matrice metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH