Lymeská borrelióza (LB) je klíšťaty nejčastěji přenášenou infekcí v České republice. Diagnostika LB může být komplikovaná. Doporučená léčba je vždy antibiotická a obvykle vede k vymizení příznaků a snížení rizika persistence borrelií v organismu. LB nezpůsobuje úmrtí, ale jde o multisystémové onemocnění, které svými akutními i následnými příznaky může významně a dlouhodobě snižovat kvalitu života pacientů. Článek popisuje zkušenosti pacientů v průběhu celého onemocnění, včetně vlivu nemoci na další aspekty jejich života. Hlavním výstupem výzkumu je publikování zkušeností pacientů s onemocněním LB na webových stránkách www.hovoryozdravi.cz, jež mohou být přínosné nejen praktickým a dalším lékařům.
Lyme disease (LB) is the most commonly transmitted tick-borne infection in the Czech Republic. The diagnosis of LB can be complicated. The recommended treatment is antibiotic and usually leads to the disappearance of symptoms and a reduced risk of persistence of Borrelia in the organism. LB does not cause death, but its acute and subsequent symptoms can significantly reduce the quality of life of patients in the long term. The article describes the experience of patients throughout the course of the disease, including the impact of the disease on other aspects of patients' lives. The main output of the research is the publication of the experience of patients with LB on the website www.hovoryozdravi.cz, which can be beneficial not only to general practitioners and other physicians.
- MeSH
- dospělí MeSH
- kvalita života MeSH
- lidé středního věku MeSH
- lidé MeSH
- lymeská nemoc * diagnóza patologie psychologie MeSH
- lymská neuroborelióza diagnóza patologie MeSH
- příznaky a symptomy MeSH
- průzkumy a dotazníky MeSH
- senioři MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)-a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz .
Secondary structure elements (SSEs) are inherent parts of protein structures, and their arrangement is characteristic for each protein family. Therefore, annotation of SSEs can facilitate orientation in the vast number of homologous structures which is now available for many protein families. It also provides a way to identify and annotate the key regions, like active sites and channels, and subsequently answer the key research questions, such as understanding of molecular function and its variability.This chapter introduces the concept of SSE annotation and describes the workflow for obtaining SSE annotation for the members of a selected protein family using program SecStrAnnotator.
MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.
Mammalian cytochromes P450 are an important class of enzymes involved in the biotransformation of many endo- and exogenous compounds. Cytochrome P450 isoforms are attached to the membrane of the endoplasmic reticulum or mitochondria, and their catalytic domains move along the membrane surface while being partially immersed in the membrane environment. Their active sites are connected to both the membrane and cytosolic environments via a complex network of access channels. Consequently, they can accept substrates from both environments. The membrane also supports the interactions of cytochromes P450 with their redox partners. In this review, we provide an overview of current knowledge of the structure, flexibility, and interactions with substrates and redox partners of cytochrome P450 on membranes, amalgamating information derived from both experiments and simulations.
ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.
- MeSH
- aminokyseliny chemie metabolismus MeSH
- cytochrom P-450 CYP2D6 chemie genetika metabolismus MeSH
- databáze proteinů * MeSH
- eukaryotické buňky cytologie enzymologie MeSH
- exprese genu MeSH
- hydrofobní a hydrofilní interakce MeSH
- iontové kanály chemie genetika metabolismus MeSH
- jaderný pór chemie genetika metabolismus MeSH
- katalytická doména MeSH
- koenzymy chemie metabolismus MeSH
- lidé MeSH
- mutace MeSH
- prokaryotické buňky cytologie enzymologie MeSH
- software * MeSH
- statická elektřina MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Cytochromes P450 are major drug-metabolizing enzymes involved in the biotransformation of diverse xenobiotics and endogenous chemicals. Persistent organic pollutants (POPs) are toxic hydrophobic compounds that cause serious environmental problems because of their poor degradability. This calls for rational design of enzymes capable of catalyzing their biotransformation. Cytochrome P450 1A1 isoforms catalyze the biotransformation of some POPs, and constitute good starting points for the design of biocatalysts with tailored substrate specificity. METHODS: We rationalized the activities of wild type and mutant forms of rat cytochrome P450 1A1 towards 2,3,7,8-tetrachloro-dibenzo-p-dioxin (TCDD) and 3,3',4,4'-tetrachlorobiphenyl (PCB77) using experiments and molecular dynamics simulations. RESULTS: We showed that the enhanced activity of the CYP1A1 mutant towards TCDD was due to more efficient binding of the substrate in the active site even though the mutated site was over 2.5nm away from the catalytic center. Moreover, this mutation reduced activity towards PCB77. GENERAL SIGNIFICANCE: Amino acids that affect substrate access channels can be viable targets for rational enzyme design even if they are located far from the catalytic site.
- MeSH
- adukty DNA účinky léků MeSH
- biotransformace účinky léků MeSH
- cytochrom P-450 CYP1A1 chemie genetika MeSH
- katalytická doména účinky léků MeSH
- katalýza * MeSH
- krysa rodu rattus MeSH
- látky znečišťující životní prostředí chemie toxicita MeSH
- lidé MeSH
- metabolická inaktivace účinky léků genetika MeSH
- mutace MeSH
- polychlorované bifenyly chemie toxicita MeSH
- polychlorované dibenzodioxiny chemie toxicita MeSH
- substrátová specifita MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
This symposium summary, sponsored by the ASPET, was held at Experimental Biology 2015 on March 29, 2015, in Boston, Massachusetts. The symposium focused on: 1) the interactions of cytochrome P450s (P450s) with their redox partners; and 2) the role of the lipid membrane in their orientation and stabilization. Two presentations discussed the interactions of P450s with NADPH-P450 reductase (CPR) and cytochrome b5. First, solution nuclear magnetic resonance was used to compare the protein interactions that facilitated either the hydroxylase or lyase activities of CYP17A1. The lyase interaction was stimulated by the presence of b5 and 17α-hydroxypregnenolone, whereas the hydroxylase reaction was predominant in the absence of b5. The role of b5 was also shown in vivo by selective hepatic knockout of b5 from mice expressing CYP3A4 and CYP2D6; the lack of b5 caused a decrease in the clearance of several substrates. The role of the membrane on P450 orientation was examined using computational methods, showing that the proximal region of the P450 molecule faced the aqueous phase. The distal region, containing the substrate-access channel, was associated with the membrane. The interaction of NADPH-P450 reductase (CPR) with the membrane was also described, showing the ability of CPR to "helicopter" above the membrane. Finally, the endoplasmic reticulum (ER) was shown to be heterogeneous, having ordered membrane regions containing cholesterol and more disordered regions. Interestingly, two closely related P450s, CYP1A1 and CYP1A2, resided in different regions of the ER. The structural characteristics of their localization were examined. These studies emphasize the importance of P450 protein organization to their function.
- MeSH
- buněčná membrána metabolismus MeSH
- endoplazmatické retikulum metabolismus MeSH
- interakční proteinové domény a motivy fyziologie MeSH
- jaterní mikrozomy metabolismus MeSH
- lidé MeSH
- sekundární struktura proteinů MeSH
- systém (enzymů) cytochromů P-450 chemie fyziologie MeSH
- výzkumná zpráva * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Research Support, N.I.H., Extramural MeSH
Cholesterol is a widely researched component of biological membranes that significantly influences membrane properties. Human cytochrome P450 3A4 (CYP3A4) is an important drug-metabolizing enzyme, wherein the catalytic domain is attached to a membrane by an N-terminal α-helical transmembrane anchor. We analyzed the behavior of CYP3A4 immersed in a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) membrane with various amounts of cholesterol. The presence of cholesterol caused ordering and thickening of the membrane and led to greater immersion and inclination of CYP3A4 toward the membrane. Cholesterol also lowered the flexibility of and tended to concentrate around membrane-immersed parts of CYP3A4. Further, the pattern of the CYP3A4 active-site access channels was altered in the presence of cholesterol. In summary, cholesterol in the membrane affected the positioning and structural features of CYP3A4, which in turn may have implications for the activity of this enzyme in various membranes and membrane parts with different cholesterol content.
- MeSH
- buněčná membrána chemie metabolismus MeSH
- cholesterol chemie metabolismus MeSH
- cytochrom P-450 CYP3A chemie metabolismus MeSH
- fosfatidylcholiny chemie MeSH
- katalytická doména MeSH
- konformace proteinů MeSH
- lidé MeSH
- simulace molekulární dynamiky MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
