The precise measurement of cell temperature and an in-depth understanding of thermogenic processes are critical in unraveling the complexities of cellular metabolism and its implications for health and disease. This review focuses on the mechanisms of local temperature generation within cells and the array of methods developed for accurate temperature assessment. The contact and noncontact techniques are introduced, including infrared thermography, fluorescence thermometry, and other innovative approaches to localized temperature measurement. The role of thermogenesis in cellular metabolism, highlighting the integral function of temperature regulation in cellular processes, environmental adaptation, and the implications of thermogenic dysregulation in diseases such as metabolic disorders and cancer are further discussed. The challenges and limitations in this field are critically analyzed while technological advancements and future directions are proposed to overcome these barriers. This review aims to provide a consolidated resource for current methodologies, stimulate discussion on the limitations and challenges, and inspire future innovations in the study of cellular thermodynamics.

• MeSH
• lidé MeSH
• teplota MeSH
• termogeneze * fyziologie   MeSH
• termografie * metody   MeSH
• termometrie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

The integration of 3D printing into the pharmaceutical sciences opens new possibilities for personalized medicine. Poly(lactide) (PLA), a biodegradable and biocompatible polymer, is highly suitable for biomedical applications, particularly in the context of 3D printing. However, its processability often requires the addition of plasticizers. This study investigates the use of phase diagram modeling as a tool to guide the rational selection of plasticizers and to assess their impact on the thermodynamic and kinetic stability of PLA-based amorphous solid dispersions (ASDs) containing active pharmaceutical ingredients (APIs). Thermodynamic stability against API recrystallization was predicted based on the API solubility in PLA and Plasticizer-PLA carriers using the Conductor-like Screening Model for Real Solvents (COSMO-RS), while the kinetic stability of the ASDs was evaluated by modeling the glass transition temperatures of the mixtures. Two APIs, indomethacin (IND) and naproxen (NAP), with differing glass-forming abilities (i.e., recrystallization tendencies), and three plasticizers, triacetin (TA), triethyl citrate (TEC), and poly(L-lactide-co-caprolactone) (PLCL), were selected for investigation. The physical stability of ASD formulations containing 9 wt% API and plasticizer to PLA in two ratios, 10:81 and 20:71 w/w %, was monitored over time using differential scanning calorimetry and X-ray powder diffraction and compared with phase diagram predictions. All formulations were predicted to be thermodynamically unstable; however, those containing no plasticizer or with TEC and TA at 10 wt% were predicted to exhibit some degree of kinetic stability. Long-term physical studies corroborated these predictions. The correlation between the predicted phase behavior and long-term physical stability highlights the potential of phase diagram modeling as a tool for the rational design of ASDs in pharmaceutical 3D printing.

• MeSH
• 3D tisk * MeSH
• citráty chemie   MeSH
• diferenciální skenovací kalorimetrie metody   MeSH
• farmaceutická chemie metody   MeSH
• farmaceutická technologie metody   MeSH
• indomethacin * chemie   MeSH
• krystalizace MeSH
• naproxen chemie   MeSH
• polyestery * chemie   MeSH
• rozpouštědla chemie   MeSH
• rozpustnost * MeSH
• stabilita léku MeSH
• termodynamika MeSH
• tranzitní teplota MeSH
• triacetin chemie   MeSH
• změkčovadla * chemie   MeSH
• Publikační typ
• časopisecké články MeSH

There is increasing pharmaceutical interest in deep eutectic solvents not only as a green alternative to organic solvents in drug manufacturing, but also as liquid formulation for drug delivery. The present work introduces a hydrophobic deep eutectic solvent (HDES) to the field of lipid-based formulations (LBF). Phase behavior of a mixture with 2:1 M ratio of decanoic- to dodecanoic acid was studied experimentally and described by thermodynamic modelling. Venetoclax was selected as a hydrophobic model drug and studied by atomistic molecular dynamics simulations of the mixtures. As a result, valuable molecular insights were gained into the interaction networks between the different components. Moreover, experimentally the HDES showed greatly enhanced drug solubilization compared to conventional glyceride-based vehicles, but aqueous dispersion behavior was limited. Hence surfactants were studied for their ability to improve aqueous dispersion and addition of Tween 80 resulted in lowest droplet sizes and high in vitro drug release. In conclusion, the combination of HDES with surfactant(s) provides a novel LBF with high pharmaceutical potential. However, the components must be finely balanced to keep the integrity of the solubilizing HDES, while enabling sufficient dispersion and drug release.

• MeSH
• farmaceutická chemie metody   MeSH
• hydrofobní a hydrofilní interakce * MeSH
• kyseliny laurové chemie   MeSH
• lipidy * chemie   MeSH
• oleje chemie   MeSH
• polysorbáty chemie   MeSH
• povrchově aktivní látky * chemie   MeSH
• příprava léků * metody   MeSH
• rozpouštědla * chemie   MeSH
• rozpustnost * MeSH
• simulace molekulární dynamiky * MeSH
• sulfonamidy chemie   aplikace a dávkování   MeSH
• uvolňování léčiv * MeSH
• Publikační typ
• časopisecké články MeSH

Self-balancing diffusion is a theoretical concept that restricts the introduction of extents of reactions. This concept is analyzed in detail for general mass- and molar-based balances of reaction-diffusion mixtures, in relation to non-self-balancing cases, and with respect to its practical consequences. Self-balancing is a mathematical restriction on the divergences of diffusion fluxes. Fulfilling this condition enables the proper introduction of the extents of (independent) reactions that reduce the number of independent variables in thermodynamic descriptions. A note on a recent generalization of the concept of reaction and diffusion extents is also included. Even in the case of self-balancing diffusion, such extents do not directly replace reaction rates. Concentration changes caused by reactions (not by diffusion) are properly described by rates of independent reactions, which are instantaneous descriptors. If an overall descriptor is needed, the traditional extents of reactions can be used, bearing in mind that they include diffusion-caused changes. On the other hand, rates of independent reactions integrated with respect to time provide another overall, but reaction-only-related descriptor.

• MeSH
• difuze * MeSH
• kinetika MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH

PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.

• MeSH
• benchmarking MeSH
• datové soubory jako téma MeSH
• interakční proteinové domény a motivy MeSH
• internet MeSH
• konformace proteinů, alfa-helix MeSH
• konformace proteinů, beta-řetězec MeSH
• lidé MeSH
• ligandy MeSH
• proteiny chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• software * MeSH
• strojové učení * MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

G protein-coupled receptors (GPCRs) control cellular signaling and responses. Many of these GPCRs are modulated by cholesterol and polyunsaturated fatty acids (PUFAs) which have been shown to co-exist with saturated lipids in ordered membrane domains. However, the lipid compositions of such domains extracted from the brain cortex tissue of individuals suffering from GPCR-associated neurological disorders show drastically lowered levels of PUFAs. Here, using free energy techniques and multiscale simulations of numerous membrane proteins, we show that the presence of the PUFA DHA helps helical multi-pass proteins such as GPCRs partition into ordered membrane domains. The mechanism is based on hybrid lipids, whose PUFA chains coat the rough protein surface, while the saturated chains face the raft environment, thus minimizing perturbations therein. Our findings suggest that the reduction of GPCR partitioning to their native ordered environments due to PUFA depletion might affect the function of these receptors in numerous neurodegenerative diseases, where the membrane PUFA levels in the brain are decreased. We hope that this work inspires experimental studies on the connection between membrane PUFA levels and GPCR signaling.

• MeSH
• cholesterol metabolismus   MeSH
• konformace proteinů MeSH
• kyseliny dokosahexaenové chemie   metabolismus   MeSH
• lidé MeSH
• membránové mikrodomény chemie   metabolismus   MeSH
• membránové proteiny chemie   metabolismus   MeSH
• modely neurologické MeSH
• molekulární modely MeSH
• mozek metabolismus   MeSH
• nenasycené mastné kyseliny metabolismus   MeSH
• nervové receptory chemie   metabolismus   MeSH
• počítačová simulace MeSH
• receptor adenosinový A2A chemie   metabolismus   MeSH
• receptory spřažené s G-proteiny chemie   metabolismus   MeSH
• signální transdukce MeSH
• termodynamika MeSH
• výpočetní biologie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• Klíčová slova
• Lékařské obory,
• MeSH
• biofyzika MeSH

• NLK Obory
• fyzika, biofyzika

The coarse-grained Martini model is employed extensively to study membrane protein oligomerization. While this approach is exceptionally promising given its computational efficiency, it is alarming that a significant fraction of these studies demonstrate unrealistic protein clusters, whose formation is essentially an irreversible process. This suggests that the protein-protein interactions are exaggerated in the Martini model. If this held true, then it would limit the applicability of Martini to study multi-protein complexes, as the rapidly clustering proteins would not be able to properly sample the correct dimerization conformations. In this work we first demonstrate the excessive protein aggregation by comparing the dimerization free energies of helical transmembrane peptides obtained with the Martini model to those determined from FRET experiments. Second, we show that the predictions provided by the Martini model for the structures of transmembrane domain dimers are in poor agreement with the corresponding structures resolved using NMR. Next, we demonstrate that the first issue can be overcome by slightly scaling down the Martini protein-protein interactions in a manner, which does not interfere with the other Martini interaction parameters. By preventing excessive, irreversible, and non-selective aggregation of membrane proteins, this approach renders the consideration of lateral dynamics and protein-lipid interactions in crowded membranes by the Martini model more realistic. However, this adjusted model does not lead to an improvement in the predicted dimer structures. This implicates that the poor agreement between the Martini model and NMR structures cannot be cured by simply uniformly reducing the interactions between all protein beads. Instead, a careful amino-acid specific adjustment of the protein-protein interactions is likely required.

• MeSH
• chemické modely * MeSH
• dimerizace MeSH
• konformace proteinů MeSH
• mapy interakcí proteinů MeSH
• membránové proteiny chemie   metabolismus   MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• rezonanční přenos fluorescenční energie MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH

• MeSH
• biofyzika MeSH

• Konspekt
• Lékařské vědy. Lékařství
• Učební osnovy. Vyučovací předměty. Učebnice
• NLK Obory
• fyzika, biofyzika
• NLK Publikační typ
• učebnice vysokých škol

Numerous cellular functions including respiration require iron. Plants and phytoplankton must also maintain the iron-rich photosynthetic electron transport chain, which most likely evolved in the iron-replete reducing environments of the Proterozoic ocean [1]. Iron bioavailability has drastically decreased in the contemporary ocean [1], most likely selecting for the evolution of efficient iron acquisition mechanisms among modern phytoplankton. Mesoscale iron fertilization experiments often result in blooms dominated by diatoms [2], indicating that diatoms have adaptations that allow survival in iron-limited waters and rapid multiplication when iron becomes available. Yet the genetic and molecular bases are unclear, as very few iron uptake genes have been functionally characterized from marine eukaryotic phytoplankton, and large portions of diatom iron starvation transcriptomes are genes encoding unknown functions [3-5]. Here we show that the marine diatom Phaeodactylum tricornutum utilizes ISIP2a to concentrate Fe(III) at the cell surface as part of a novel, copper-independent and thermodynamically controlled iron uptake system. ISIP2a is expressed in response to iron limitation several days prior to the induction of ferrireductase activity, and it facilitates significant Fe(III) uptake during the initial response to Fe limitation. ISIP2a is able to directly bind Fe(III) and increase iron uptake when heterologously expressed, whereas knockdown of ISIP2a in P. tricornutum decreases iron uptake, resulting in impaired growth and chlorosis during iron limitation. ISIP2a is expressed by diverse marine phytoplankton, indicating that it is an ecologically significant adaptation to the unique nutrient composition of marine environments.

• MeSH
• druhová specificita MeSH
• fytoplankton metabolismus   MeSH
• membránové proteiny metabolismus   MeSH
• mořská biologie MeSH
• mořská voda chemie   MeSH
• rozsivky metabolismus   MeSH
• stanovení celkové genové exprese MeSH
• terciární struktura proteinů MeSH
• železo metabolismus   farmakokinetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH