Protein stability
Dotaz
Zobrazit nápovědu
sv.
Cold Spring Harbor symposia on quantitative biology ; Vol. 60
[1st ed.] xxiv, 843 s. : il.
Cíl: Informace o preanalytických podmínkách pro stanovení cystatinu C jsou rozporuplné a často si protiřečí. Snažili jsme se proto ověřit stabilitu cystatinu C ve vzorcích moče za různých podmínek. Metodika: Analyzováno bylo 15 vzorků ranní moče. Bezprostředně po odběru a označení byl každý vzorek rozdělen na 4 díly, přičemž vzorek 1 byl ponechán bez úpravy (bez přídavku stabilizačního činidla), vzorek 2 byl stabilizován Tencerovým činidlem, vzorek 3 byl stabilizován stabilizačním činidlem připraveným podle vlastního návrhu a vzorek 4 byl stabilizován komerčním činidlem StabilZyme Select. Každý z těchto 4 vzorků byl dále ještě rozdělen na 3 díly (A–C), které byly různým způsobem zatíženy. První byl bezprostředně zmražen při -80 °C (A), druhý byl zatížen 5 cykly zmražení a rozmražení (B) a třetí inkubován 15 dnů při laboratorní teplotě a následně zmražen při -80 °C (C). Od každého pacienta bylo tak připraveno 12 různě upravených a/nebo zatížených vzorků, ve kterých byl následně stanoven cystatin C. Výsledky: Bylo provedeno 171 měření v dubletu, průměrný variační koeficient stanovení činil 5,6 %, přičemž jeho hodnota se mezi jednotlivými testovanými skupinami (1–4, A–C) nelišila. Přestože bylo možné sledovat po několikatýdenním skladování vzorku při laboratorní teplotě pokles koncentrací cystatinu C, nebyly změny ve srovnání s koncentrací cystatinu C ve vzorku zamraženém při -80 °C statisticky významné. Také opakované zmražení a rozmražení vzorku nemělo na hodnoty cystatinu C v moči významný vliv. I když změřené rozdíly nebyly statisticky významné, lze při individuálním hodnocení pacientů usuzovat, že nejvhodnější postup pro uskladnění vzorků po jejich příjmu do laboratoře je jejich zmražení. Závěr: Bezprostřední zmražení vzorku moče určeného pro analýzu cystatinu C při teplotě -80 °C bez přidání stabilizačního činidla lze považovat za dostatečné preanalytické opatření. Použití Tencerova nebo jiného stabilizačního koktejlu nepřineslo žádné podstatné výhody.
Objective: Information about pre-analytical preparation for urine cystatin C measurement is often contradictory; verification of cystatin C stability in urine samples. Methods: Each urine sample collected from 15 individuals was divided into 4 parts and 3 parts were treated with various stabilizers: 1-sample without stabilizer; 2-sample stabilized with Tencer reagent; 3-sample stabilized with reagent according to our own design (thimerosal-anitimicrobial agent; benzamidin-serine proteases inhibitor; aminocapronic acid-lysine proteases inhibitor, citrate buffer-modulator of pH value; BSA-suppressor of non-specific adsorption and protective colloid effect); 4-sample stabilized with StabilZyme Select. All parts were further divided into 3 aliquots and frozen at -80 °C, or treated by 5 cycles of freezing and thawing, or incubated at room temperature for 15 days. Cystatin C was subsequently determined in all samples. Results: We did not observe any significant change in samples after 5 cycles of freezing and thawing, or incubation at room temperature in samples without as well with stabilizing agent. However, storage at room temperature led to a nonsignificant reduction in cystatin C level by 13% in samples without stabiliser, by 18% with Tencer stabilizer, by 13% with our own designed stabilizer, and by 3% with StabilZyme. Conclusion: Urine samples may be frozen at -80 °C without lost of cystatin C level in that kind of sample and it may be a convenient pre-analytical precaution. Application of Tencer or other tested stabilizers does not significantly improve sample handling.
... Craik -- 2 Protein Conformation 33 -- Fred E. Cohen and David P. ... ... Hearst -- 3 Predicting the Conformation of Proteins from Sequence Data 71 -- Steven A. ... ... on Protein Folding: Methodology, Application, and Interpretation 249 -- Mark R. ... ... -- VII -- • • • -- Vili -- Contents -- 11 Protein Engineering for Stability 299 -- Scott Braxton -- 12 ... ... Structure-Function Relationships for Protein Design 317 -- Craig S. ...
x, 518 s. : il.
The determination of a suitable buffer environment for a protein of interest is not an easy task. The requirements of advanced techniques, the demands on the biological material and the researcher time needed for buffer optimization, as well as personal inflexibility, lead frequently to the use of sub-optimal buffers. Here, we demonstrate the design of a 48-condition buffer screen that can be used to determine an appropriate environment for downstream studies. By the combination of several techniques (differential scanning fluorimetry, dynamic light scattering, and bio-layer interferometry), we are able to assess the protein stability, homogeneity and binding activity across the screen with less than half a milligram of protein in 1 day. The application of this screen helps to avoid unsuitable conditions, to explain problems observed upon protein analysis and to choose the most suitable buffers for further research. The screen can be routinely used as a primary screen for buffer optimization in labs and facilities.
- MeSH
- dynamický rozptyl světla MeSH
- fluorometrie MeSH
- proteiny MeSH
- pufry MeSH
- stabilita proteinů * MeSH
- Publikační typ
- časopisecké články MeSH
p53 is an intrinsically disordered protein with a large number of post-translational modifications and interacting partners. The hierarchical order and subcellular location of these events are still poorly understood. The activation of p53 during the DNA damage response (DDR) requires a switch in the activity of the E3 ubiquitin ligase MDM2 from a negative to a positive regulator of p53. This is mediated by the ATM kinase that regulates the binding of MDM2 to the p53 mRNA facilitating an increase in p53 synthesis. Here we show that the binding of MDM2 to the p53 mRNA brings ATM to the p53 polysome where it phosphorylates the nascent p53 at serine 15 and prevents MDM2-mediated degradation of p53. A single synonymous mutation in p53 codon 22 (L22L) prevents the phosphorylation of the nascent p53 protein and the stabilization of p53 following genotoxic stress. The ATM trafficking from the nucleus to the p53 polysome is mediated by MDM2, which requires its interaction with the ribosomal proteins RPL5 and RPL11. These results show how the ATM kinase phosphorylates the p53 protein while it is being synthesized and offer a novel mechanism whereby a single synonymous mutation controls the stability and activity of the encoded protein.
- MeSH
- ATM protein genetika metabolismus MeSH
- buňky A549 MeSH
- ELISA MeSH
- fosforylace genetika fyziologie MeSH
- lidé MeSH
- malá interferující RNA metabolismus MeSH
- messenger RNA metabolismus MeSH
- mutace genetika MeSH
- nádorové buněčné linie MeSH
- nádorový supresorový protein p53 genetika metabolismus MeSH
- polyribozomy metabolismus MeSH
- protoonkogenní proteiny c-mdm2 genetika metabolismus MeSH
- stabilita proteinů MeSH
- vnitřně neuspořádané proteiny genetika metabolismus MeSH
- western blotting MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
- MeSH
- cystein chemie genetika metabolismus MeSH
- hydrofobní a hydrofilní interakce MeSH
- kinetika MeSH
- konformace proteinů MeSH
- lidé MeSH
- molekulární modely MeSH
- multimerizace proteinu * MeSH
- mutace MeSH
- počítačová simulace MeSH
- proteiny 14-3-3 chemie genetika metabolismus MeSH
- stabilita proteinů MeSH
- termodynamika * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevated temperatures or in the presence of salts. Since experimental screening for stabilizing mutations is typically laborious and expensive, in silico predictors are often used for narrowing down the mutational landscape. The recent advances in machine learning and artificial intelligence further facilitate the development of such computational tools. However, the accuracy of these predictors strongly depends on the quality and amount of data used for training and testing, which have often been reported as the current bottleneck of the approach. To address this problem, we present a novel database of experimental thermostability data for single-point mutants FireProtDB. The database combines the published datasets, data extracted manually from the recent literature, and the data collected in our laboratory. Its user interface is designed to facilitate both types of the expected use: (i) the interactive explorations of individual entries on the level of a protein or mutation and (ii) the construction of highly customized and machine learning-friendly datasets using advanced searching and filtering. The database is freely available at https://loschmidt.chemi.muni.cz/fireprotdb.
- MeSH
- anotace sekvence MeSH
- bodová mutace * MeSH
- databáze proteinů * MeSH
- datové soubory jako téma MeSH
- internet MeSH
- molekulární modely MeSH
- proteiny chemie genetika MeSH
- software MeSH
- stabilita proteinů MeSH
- strojové učení statistika a číselné údaje MeSH
- výpočetní biologie metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
