Several small-molecule ligands specifically bind and stabilize G-quadruplex (G4) nucleic acid structures, which are considered to be promising therapeutic targets. G4s are polymorphic structures of varying stability, and their formation is dynamic. Here, we investigate the mechanisms of ligand binding to dynamically populated human telomere G4 DNA by using the bisquinolinium based ligand Phen-DC3 and a combination of single-molecule FRET microscopy, ensemble FRET and CD spectroscopies. Different cations are used to tune G4 polymorphism and folding dynamics. We find that ligand binding occurs to pre-folded G4 structures and that Phen-DC3 also induces G4 formation in unfolded single strands. Following ligand binding to dynamically populated G4s, the DNA undergoes pronounced conformational redistributions that do not involve direct ligand-induced G4 conformational interconversion. On the contrary, the redistribution is driven by ligand-induced G4 folding and trapping of dynamically populated short-lived conformation states. Thus, ligand-induced stabilization does not necessarily require the initial presence of stably folded G4s.

• Klíčová slova
• G-quadruplex, Phen-DC3, dynamics, ligand binding, smFRET,
• MeSH
• chinoliny chemie   metabolismus   MeSH
• G-kvadruplexy * MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• ligandy * MeSH
• rezonanční přenos fluorescenční energie MeSH
• simulace molekulární dynamiky MeSH
• telomery chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chinoliny MeSH
• ligandy * MeSH

MOTIVATION: Structure-based methods for detecting protein-ligand binding sites play a crucial role in various domains, from fundamental research to biomedical applications. However, current prediction methodologies often rely on holo (ligand-bound) protein conformations for training and evaluation, overlooking the significance of the apo (ligand-free) states. This oversight is particularly problematic in the case of cryptic binding sites (CBSs) where holo-based assessment yields unrealistic performance expectations. RESULTS: To advance the development in this domain, we introduce CryptoBench, a benchmark dataset tailored for training and evaluating novel CBS prediction methodologies. CryptoBench is constructed upon a large collection of apo-holo protein pairs, grouped by UniProtID, clustered by sequence identity, and filtered to contain only structures with substantial structural change in the binding site. CryptoBench comprises 1107 structures with predefined cross-validation splits, making it the most extensive CBS dataset to date. To establish a performance baseline, we measured the predictive power of sequence- and structure-based CBS residue prediction methods using the benchmark. We selected PocketMiner as the state-of-the-art representative of the structure-based methods for CBS detection, and P2Rank, a widely-used structure-based method for general binding site prediction that is not specifically tailored for cryptic sites. For sequence-based approaches, we trained a neural network to classify binding residues using protein language model embeddings. Our sequence-based approach outperformed PocketMiner and P2Rank across key metrics, including area under the curve, area under the precision-recall curve, Matthew's correlation coefficient, and F1 scores. These results provide baseline benchmark results for future CBS and potentially also non-CBS prediction endeavors, leveraging CryptoBench as the foundational platform for further advancements in the field. AVAILABILITY AND IMPLEMENTATION: The CryptoBench dataset, including the benchmark model, is available on Open Science Framework-https://osf.io/pz4a9/. The code and tutorial are available at the GitHub repository-https://github.com/skrhakv/CryptoBench/.

• MeSH
• benchmarking * MeSH
• databáze proteinů * MeSH
• konformace proteinů MeSH
• ligandy MeSH
• proteiny * chemie   metabolismus   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ligandy MeSH
• proteiny * MeSH

UNLABELLED: The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein-ligand binding mechanisms or simply to dock any ligand to a protein. AVAILABILITY: Executable files of TRITON are available free of charge for academic users at http://ncbr.chemi.muni.cz/triton/

• MeSH
• algoritmy MeSH
• chemické modely * MeSH
• ligandy MeSH
• molekulární modely * MeSH
• počítačová grafika * MeSH
• počítačová simulace MeSH
• proteinové inženýrství metody   MeSH
• proteiny chemie   ultrastruktura   MeSH
• racionální návrh léčiv MeSH
• software * MeSH
• uživatelské rozhraní počítače MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ligandy MeSH
• proteiny MeSH

We have investigated the effect of the binding of glutamine on the conformational dynamics of the recombinant glutamine binding protein (GlnBP) from Escherichia coli by steady-state and time-resolved fluorescence techniques. The structural stability of the protein was also studied by far-UV circular dichroism spectroscopy in the range of temperature between 25 and 80 degrees C. The results showed that the interaction of the protein with the ligand resulted in a marked change of the structural and conformational dynamics features of the protein. In particular, the fluorescence and circular dichroism data showed that the presence of glutamine resulted in a dramatic increase of the protein thermal stability of about 10 degrees C. In addition, the fluorescence time-resolved data pointed out that both in the absence and in the presence of glutamine the protein structure was highly rigid with small amplitude of segmental motion up to 65 degrees C and a low accessibility of the protein tryptophan residues to acrylamide. The obtained results on the structural properties of the recombinant glutamine-binding protein in the absence and in the presence of glutamine can contribute to a better understanding of the transport-related functions of the protein and structurally similar periplasmic transport proteins, as well as to the design and development of new biotechnological applications of this class of proteins.

• MeSH
• Escherichia coli genetika   metabolismus   MeSH
• glutamin chemie   MeSH
• kinetika MeSH
• konformace proteinů MeSH
• ligandy MeSH
• rekombinantní proteiny chemie   MeSH
• teplota MeSH
• transportní proteiny chemie   genetika   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• glutamin MeSH
• glutamine transport proteins MeSH Prohlížeč
• ligandy MeSH
• rekombinantní proteiny MeSH
• transportní proteiny MeSH

Human phosphoglycerate kinase 1(hPGK1) is a key glycolytic enzyme that regulates the balance between ADP and ATP concentrations inside the cell. Phosphorylation of hPGK1 at S203 and S256 has been associated with enzyme import from the cytosol to the mitochondria and the nucleus respectively. These changes in subcellular locations drive tumorigenesis and are likely associated with site-specific changes in protein stability. In this work, we investigate the effects of site-specific phosphorylation on thermal and kinetic stability and protein structural dynamics by hydrogen-deuterium exchange (HDX) and molecular dynamics (MD) simulations. We also investigate the binding of 3-phosphoglycerate and Mg-ADP using these approaches. We show that the phosphomimetic mutation S256D reduces hPGK1 kinetic stability by 50-fold, with no effect of the mutation S203D. Calorimetric studies of ligand binding show a large decrease in affinity for Mg-ADP in the S256D variant, whereas Mg-ADP binding to the WT and S203D can be accurately investigated using protein kinetic stability and binding thermodynamic models. HDX and MD simulations confirmed the destabilization caused by the mutation S256D (with some long-range effects on stability) and its reduced affinity for Mg-ADP due to the strong destabilization of its binding site (particularly in the apo-state). Our research provides evidence suggesting that modifications in protein stability could potentially enhance the translocation of hPGK1 to the nucleus in cancer. While the structural and energetic basis of its mitochondrial import remain unknown.

• Klíčová slova
• cancer, ligand binding, phosphoglycerate kinase, protein phosphorylation, protein stability,
• MeSH
• adenosindifosfát metabolismus   MeSH
• cytosol * metabolismus   MeSH
• fosfoglycerátkinasa * metabolismus   genetika   chemie   MeSH
• fosforylace MeSH
• kinetika MeSH
• lidé MeSH
• ligandy MeSH
• mutace MeSH
• nádory * genetika   metabolismus   patologie   MeSH
• simulace molekulární dynamiky * MeSH
• stabilita proteinů MeSH
• termodynamika MeSH
• vazba proteinů * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenosindifosfát MeSH
• fosfoglycerátkinasa * MeSH
• ligandy MeSH

BACKGROUND: Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. RESULTS: We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. CONCLUSIONS: The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.

• Klíčová slova
• Deorphanization, Functional evolution, HEK293 cells, Odorant receptor, Pest insect, Pheromone receptor, Xenopus oocyte,
• MeSH
• hmyzí proteiny chemie   genetika   MeSH
• ligandy MeSH
• nosatcovití chemie   genetika   MeSH
• receptory pachové chemie   genetika   MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hmyzí proteiny MeSH
• ligandy MeSH
• receptory pachové 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
• Názvy látek
• ligandy MeSH
• proteiny MeSH

Knowledge of protein-ligand binding sites (LBSs) enables research ranging from protein function annotation to structure-based drug design. To this end, we have previously developed a stand-alone tool, P2Rank, and the web server PrankWeb (https://prankweb.cz/) for fast and accurate LBS prediction. Here, we present significant enhancements to PrankWeb. First, a new, more accurate evolutionary conservation estimation pipeline based on the UniRef50 sequence database and the HMMER3 package is introduced. Second, PrankWeb now allows users to enter UniProt ID to carry out LBS predictions in situations where no experimental structure is available by utilizing the AlphaFold model database. Additionally, a range of minor improvements has been implemented. These include the ability to deploy PrankWeb and P2Rank as Docker containers, support for the mmCIF file format, improved public REST API access, or the ability to batch download the LBS predictions for the whole PDB archive and parts of the AlphaFold database.

• MeSH
• databáze proteinů MeSH
• internet MeSH
• ligandy MeSH
• proteinové domény MeSH
• proteiny * chemie   MeSH
• software * MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• ligandy MeSH
• proteiny * MeSH

After short preincubations with N-[(3)H]methylscopolamine ([(3)H]NMS) or R(-)-[(3)H]quinuclidinyl benzilate ([(3)H]QNB), radioligand dissociation from muscarinic M(1) receptors in Chinese hamster ovary cell membranes was fast, monoexponential, and independent of the concentration of unlabeled NMS or QNB added to reveal dissociation. After long preincubations, the dissociation was slow, not monoexponential, and inversely related to the concentration of the unlabeled ligand. Apparently, the unlabeled ligand becomes able to associate with the receptor simultaneously with the already bound radioligand if the preincubation lasts for a long period, and to hinder radioligand dissociation. When the membranes were preincubated with [(3)H]NMS and then exposed to benzilylcholine mustard (covalently binding specific ligand), [(3)H]NMS dissociation was blocked in wild-type receptors, but not in mutated (D99N) M(1) receptors. Covalently binding [(3)H]propylbenzilylcholine mustard detected substantially more binding sites than [(3)H]NMS. The observations support a model in which the receptor binding domain has two tandemly arranged subsites for classical ligands, a peripheral one and a central one. Ligands bind to the peripheral subsite first (binding with lower affinity) and translocate to the central subsite (binding with higher affinity). The peripheral subsite of M(1) receptors may include Asp-99. Experimental data on [(3)H]NMS and [(3)H]QNB association and dissociation perfectly agree with the predictions of the tandem two-site model.

• MeSH
• chinuklidinylbenzilát metabolismus   MeSH
• CHO buňky MeSH
• křečci praví MeSH
• ligandy MeSH
• N-methylskopolamin metabolismus   MeSH
• propylbenzilylcholinový yperit metabolismus   MeSH
• radioligandová zkouška MeSH
• receptory muskarinové metabolismus   MeSH
• tritium MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• křečci praví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Názvy látek
• chinuklidinylbenzilát MeSH
• ligandy MeSH
• N-methylskopolamin MeSH
• propylbenzilylcholinový yperit MeSH
• receptory muskarinové MeSH
• tritium MeSH

Accurate estimation of protein-ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms. To validate it rigorously, we have compiled and made available the PL-REX benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets. Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more expensive DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R2 = 0.69) and exhibits consistent performance across all targets. In contrast to DFT, SQM2.20 provides affinity predictions in minutes, making it suitable for practical applications in hit identification or lead optimization.

• MeSH
• ligandy MeSH
• proteiny * metabolismus   MeSH
• racionální návrh léčiv * MeSH
• termodynamika MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• ligandy MeSH
• proteiny * MeSH