Structure-function relationship
Dotaz
Zobrazit nápovědu
Quantitative structure-function relationships (QSFR) and quantitative structure-stability relationships (QSSR) analyses are described here. The objective of these analyses is to investigate and quantitatively describe the effect of the changes in structure of protein on its function or stability. During the analysis, the structural and physico-chemical properties of the amino acid residues are related to activity or stability data derived for the group of proteins containing systematic substitutions at certain positions. Four examples of the application of these analyses on the data obtained with proteins modified by site-directed mutagenesis experiments are provided. Structure-function relationships were studied for 15 mutants in position 172 of the haloalkane dehalogenase and 19 mutants in position 222 of the subtilisin, while the structure-stability relationships were investigated for 13 mutants in position 157 of phage T4 lysozyme and 18 mutants in position 49 of alpha-subunits tryptophan synthase. A total of 402 molecular descriptors derived from AAindex database were used to quantify amino acid properties and the multivariate statistical technique--partial least squares projections to latent structures--was used to identify those of them which are important for explanation of the activity and stability data. Quantitative models were developed and internally validated for every data set. The possibilities for further development of both analyses and their application for predictive and analytical purposes in protein engineering research are discussed.
The main lipid compounds of the outermost layer of human skin are ceramides (CERs), free fatty acids, and cholesterol. Although numerous studies performed in the past could demonstrate the importance of these lipids for an intact skin barrier function, knowledge about the impact of each single component on the lamellar lipid films is still lacking. Especially, the CERs are a very heterogeneous group with high relevance for a proper barrier. It was found that the reason for the high stability of the lamellae is related to the lipid structure and function, with the type and extent of interactions between the head groups of the individual CER subspecies being particularly important. Elucidating these at the molecular level could help us to understand CER phase behavior in general. Using grazing incidence X-ray diffraction and measurements of Langmuir isotherms, the current work investigated the lateral packing of the monolayers of different subclasses of C18:0 CERs at air-water interfaces, including phytosphingosine, sphingosine, and dihydrosphingosine CERs, all with either α-hydroxy and nonhydroxy N-acylated fatty acyl. We were able to observe clear effects of the minimal differences in the polar headgroup structures of the sphingoid bases, with respect to the number and position of hydroxyl groups and double bonds, on the CER arrangement regarding the compressibility and structure of the films they formed, revealing that the hydroxyl group at the C4 of the phytosphingosine CERs leads not only to the formation of a hydrogen bond network but also to a stable suprastructure, which might be of high benefit for the barrier properties of intact skin.
- MeSH
- ceramidy * chemie MeSH
- difrakce rentgenového záření MeSH
- lidé MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- ceramidy * MeSH
The FOXO subgroup of forkhead transcription factors plays a central role in cell-cycle control, differentiation, metabolism control, stress response and apoptosis. Therefore, the function of these important molecules is tightly controlled by a wide range of protein-protein interactions and posttranslational modifications including phosphorylation, acetylation and ubiquitination. The mechanisms by which these processes regulate FOXO activity are mostly elusive. This review focuses on recent advances in structural studies of forkhead transcription factors and the insights they provide into the mechanism of DNA recognition. On the basis of these data, we discuss structural aspects of protein-protein interactions and posttranslational modifications that target the forkhead domain and the nuclear localization signal of FOXO proteins.
- MeSH
- acetylace MeSH
- forkhead transkripční faktory chemie fyziologie MeSH
- fosforylace MeSH
- konformace proteinů MeSH
- lidé MeSH
- posttranslační úpravy proteinů MeSH
- ubikvitin metabolismus MeSH
- vztahy mezi strukturou a aktivitou MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- forkhead transkripční faktory MeSH
- ubikvitin MeSH
The TERT (telomerase reverse transcriptase) subunit of telomerase is an intensively studied macromolecule due to its key importance in maintaining genome integrity and role in cellular aging and cancer. In an effort to provide an up-to-date overview of the topic, we discuss the structure of TERT genes, their alternative splicing products and their functions. Nucleotide databases contain more than 90 full-length cDNA sequences of telomerase protein subunits. Numerous in silico, in vitro and in vivo experimental techniques have revealed a great deal of structural and functional data describing particular features of the telomerase subunit in various model organisms. We explore whether particular findings are generally applicable to telomerases or species-specific. We also discuss in an evolutionary context the role of identified functional TERT subdomains.
- MeSH
- alternativní sestřih MeSH
- eukaryotické buňky chemie enzymologie MeSH
- lidé MeSH
- molekulární evoluce MeSH
- molekulární sekvence - údaje MeSH
- prokaryotické buňky chemie enzymologie MeSH
- telomerasa chemie genetika metabolismus MeSH
- telomery metabolismus MeSH
- vazba proteinů MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- telomerasa MeSH
G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.
- Klíčová slova
- DNA:RNA hybrid, G-quadruplex, R-loop, dimer, multimer, oligomer, promoter, telomere, tetramer,
- MeSH
- DNA chemie MeSH
- G-kvadruplexy * MeSH
- konformace nukleové kyseliny * MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- RNA chemie MeSH
- telomery MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- DNA MeSH
- RNA MeSH
Membrane proteins are a large, diverse group of proteins, serving a multitude of cellular functions. They are difficult to study because of their requirement of a lipid membrane for function. Here we show that two-photon polarization microscopy can take advantage of the cell membrane requirement to yield insights into membrane protein structure and function, in living cells and organisms. The technique allows sensitive imaging of G-protein activation, changes in intracellular calcium concentration and other processes, and is not limited to membrane proteins. Conveniently, many suitable probes for two-photon polarization microscopy already exist.
- MeSH
- buněčná membrána metabolismus ultrastruktura MeSH
- konformace proteinů MeSH
- membránové proteiny metabolismus ultrastruktura MeSH
- mikroskopie fluorescenční multifotonová metody MeSH
- polarizační mikroskopie metody MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- membránové proteiny MeSH
Sarcoplasmic reticulum (SR) is a specialized tubular network, which not only maintains the intracellular concentration of Ca2+ at a low level but is also known to release and accumulate Ca2+ for the occurrence of cardiac contraction and relaxation, respectively. This subcellular organelle is composed of several phospholipids and different Ca2+-cycling, Ca2+-binding and regulatory proteins, which work in a coordinated manner to determine its function in cardiomyocytes. Some of the major proteins in the cardiac SR membrane include Ca2+-pump ATPase (SERCA2), Ca2+-release protein (ryanodine receptor), calsequestrin (Ca2+-binding protein) and phospholamban (regulatory protein). The phosphorylation of SR Ca2+-cycling proteins by protein kinase A or Ca2+-calmodulin kinase (directly or indirectly) has been demonstrated to augment SR Ca2+-release and Ca2+-uptake activities and promote cardiac contraction and relaxation functions. The activation of phospholipases and proteases as well as changes in different gene expressions under different pathological conditions have been shown to alter the SR composition and produce Ca2+-handling abnormalities in cardiomyocytes for the development of cardiac dysfunction. The post-translational modifications of SR Ca2+ cycling proteins by processes such as oxidation, nitrosylation, glycosylation, lipidation, acetylation, sumoylation, and O GlcNacylation have also been reported to affect the SR Ca2+ release and uptake activities as well as cardiac contractile activity. The SR function in the heart is also influenced in association with changes in cardiac performance by several hormones including thyroid hormones and adiponectin as well as by exercise-training. On the basis of such observations, it is suggested that both Ca2+-cycling and regulatory proteins in the SR membranes are intimately involved in determining the status of cardiac function and are thus excellent targets for drug development for the treatment of heart disease.
- MeSH
- myokard metabolismus MeSH
- sarkoplazmatické retikulum * metabolismus MeSH
- srdce fyziologie MeSH
- vápník * metabolismus MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- vápník * MeSH
NMDA receptors have received much attention over the last few decades, due to their role in many types of neural plasticity on the one hand, and their involvement in excitotoxicity on the other hand. There is great interest in developing clinically relevant NMDA receptor antagonists that would block excitotoxic NMDA receptor activation, without interfering with NMDA receptor function needed for normal synaptic transmission and plasticity. This review summarizes current understanding of the structure of NMDA receptors and the mechanisms of NMDA receptor activation and modulation, with special attention given to data describing the properties of various types of NMDA receptor inhibition. Our recent analyses point to certain neurosteroids as NMDA receptor inhibitors with desirable properties. Specifically, these compounds show use-dependent but voltage-independent block, that is predicted to preferentially target excessive tonic NMDA receptor activation. Importantly, neurosteroids are also characterized by use-independent unblock, compatible with minimal disruption of normal synaptic transmission. Thus, neurosteroids are a promising class of NMDA receptor modulators that may lead to the development of neuroprotective drugs with optimal therapeutic profiles.
- MeSH
- gating iontového kanálu účinky léků MeSH
- konformace proteinů MeSH
- lidé MeSH
- mozek účinky léků metabolismus MeSH
- nemoci mozku farmakoterapie metabolismus MeSH
- nervový přenos účinky léků MeSH
- neurony účinky léků metabolismus MeSH
- neuroprotektivní látky terapeutické užití MeSH
- receptory N-methyl-D-aspartátu chemie účinky léků metabolismus ultrastruktura MeSH
- vztahy mezi strukturou a aktivitou MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- neuroprotektivní látky MeSH
- receptory N-methyl-D-aspartátu MeSH
Although telomerase (EC 2.7.7.49) is important for genome stability and totipotency of plant cells, the principles of its regulation are not well understood. Therefore, we studied subcellular localization and function of the full-length and truncated variants of the catalytic subunit of Arabidopsis thaliana telomerase, AtTERT, in planta. Our results show that multiple sites in AtTERT may serve as nuclear localization signals, as all the studied individual domains of the AtTERT were targeted to the nucleus and/or the nucleolus. Although the introduced genomic or cDNA AtTERT transgenes display expression at transcript and protein levels, they are not able to fully complement the lack of telomerase functions in tert -/- mutants. The failure to reconstitute telomerase function in planta suggests a more complex telomerase regulation in plant cells than would be expected based on results of similar experiments in mammalian model systems.
- MeSH
- Arabidopsis enzymologie genetika MeSH
- buněčné jadérko enzymologie genetika MeSH
- buněčné jádro enzymologie genetika MeSH
- geneticky modifikované rostliny MeSH
- jaderné lokalizační signály genetika MeSH
- katalytická doména genetika MeSH
- listy rostlin genetika MeSH
- proteiny huseníčku genetika metabolismus MeSH
- proteosyntéza MeSH
- regulace genové exprese u rostlin MeSH
- sestřih RNA MeSH
- tabák genetika MeSH
- telomerasa chemie genetika metabolismus MeSH
- terciární struktura proteinů MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- jaderné lokalizační signály MeSH
- proteiny huseníčku MeSH
- telomerasa MeSH
Coronaviral methyltransferases (MTases), nsp10/16 and nsp14, catalyze the last two steps of viral RNA-cap creation that takes place in cytoplasm. This cap is essential for the stability of viral RNA and, most importantly, for the evasion of innate immune system. Non-capped RNA is recognized by innate immunity which leads to its degradation and the activation of antiviral immunity. As a result, both coronaviral MTases are in the center of scientific scrutiny. Recently, X-ray and cryo-EM structures of both enzymes were solved even in complex with other parts of the viral replication complex. High-throughput screening as well as structure-guided inhibitor design have led to the discovery of their potent inhibitors. Here, we critically summarize the tremendous advancement of the coronaviral MTase field since the beginning of COVID pandemic.
- MeSH
- aminokyseliny chemie MeSH
- Coronavirus účinky léků enzymologie genetika MeSH
- lidé MeSH
- methyltransferasy antagonisté a inhibitory chemie metabolismus MeSH
- metylace MeSH
- molekulární konformace MeSH
- molekulární modely MeSH
- molekulární struktura MeSH
- objevování léků MeSH
- RNA virová chemie genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- aminokyseliny MeSH
- methyltransferasy MeSH
- RNA virová MeSH
