Journal of molecular graphics & modelling最新文献

{"title":"Expression of Concern: Metalloporphyrin reduced C70 fullerenes as adsorbents and detectors of ethenone; A DFT, NBO, and TD-DFT study.","authors":"","doi":"10.1016/j.jmgm.2024.108865","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108865","url":null,"abstract":"","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"134 ","pages":"108865"},"PeriodicalIF":2.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new type of two-dimensional carbon-based monolayers namely irida-graphene as an anode material for magnesium-ion batteries.","authors":"Maher Ali Rusho, Abdulrahman T Ahmed, Ahmed Salman Jasim, Prakash Kanjariya, Asha Rajiv, Aman Shankhyan, Pushpa Negi Bhakuni, Hashim Elshafie","doi":"10.1016/j.jmgm.2024.108934","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108934","url":null,"abstract":"<p><p>The DFT was employed to assess the ion-storage capability of an irida-graphene monolayer (IGM) in Mg-ion batteries (MIBs). The IGM had a mechanically stable structure. The IGM also exhibited great conductance based on the DOS calculations. The energy density of the IGM for MIBs was 3139.60 mWh g^-1 and its storage capacity was 1643.21 mAh g^-1. Moreover, the Mg ions migrated easily across the IGM surface throughout cycle, as indicated by the increased rate of diffusion (1.58 x 10^-5 cm²s^-1) and the small energy barrier (0.068 eV). In addition, the obtained OCV for MIBs was 0.18 V, which was in line with the requirements for commercial designing. The current theoretical study demonstrated the possibility of using the IGM as an electrode in future MIBs.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108934"},"PeriodicalIF":2.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the molecular mechanism of temperature-induced destabilization in the PqsE-RhlR complex of Pseudomonas aeruginosa at mammalian body temperature through classical molecular dynamics and metadynamics.","authors":"Meryam Magri, Rachid Eljaoudi, Lahcen Belyamani, Azeddine Ibrahimi, El Mehdi Bouricha","doi":"10.1016/j.jmgm.2024.108931","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108931","url":null,"abstract":"<p><p>PqsE and RhlR, key regulators of the Pseudomonas aeruginosa quorum sensing (QS) system, form a hetero-tetrameric complex essential for controlling the expression of virulence factors such as pyocyanin. The interaction between the PqsE homodimer and the RhlR homodimer bound to C4-HSL, enables RhlR to bind low-affinity promoters, thereby influencing gene regulation. Recent studies suggest that RhlR transcriptional activity is modulated by temperature, exhibiting higher activity at environmental temperatures (25 °C) compared to mammalian body temperature (37 °C). However, the molecular mechanisms underlying this temperature-dependent regulation remain unclear. This study aims to explore how temperature influences the structural stability of the PqsE/RhlR/C4-HSL complex using molecular dynamics (MD) simulations at 25 °C and 37 °C. The results demonstrate that the overall stability of the complex decreases at 37 °C, with global RMSD analysis indicating greater fluctuations compared to 25 °C. Further RMSD analysis of PqsE and RhlR separately revealed that the destabilization is more pronounced in RhlR, particularly in its DNA-binding domain (DBD), where significant flexibility and destabilization were observed at 37 °C, as indicated by the higher RMSF values. Free energy landscape analysis confirmed increased conformational flexibility in the RhlR at higher temperatures, potentially impairing its DNA-binding ability. To further investigate this, metadynamics simulations were performed for PqsE/RhlR/C4-HSL bound to DNA, revealing a remarkable increase in the distance between RhlR and DNA at 37 °C, potentially leading to a faster separation. These findings indicate that temperature-induced destabilization of RhlR, especially in the DBD, may explain the reduced RhlR transcriptional activity observed at mammalian body temperature.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108931"},"PeriodicalIF":2.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing of new trans-stilbene derivative: An entry barrier of Zika virus in host cell.","authors":"Pawan, Sonia Devi","doi":"10.1016/j.jmgm.2024.108935","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108935","url":null,"abstract":"<p><p>A large population in the world lives in tropical and subtropical regions, showing a high risk of Zika viral infection which leads to a situation of global health emergency and demands extensive research to create effective antiviral medicines. Herein, we introduce the design of a new derivatized trans-stilbene molecule to investigate the inhibition of Zika virus entry into the host cell by molecular docking approach. The synthesized compound has been characterized by different analytical techniques such as FTIR, ¹H NMR,¹³C NMR and UV-visible spectroscopy as well as Mass spectrometry (MS). Moreover, the complete structure elucidation was achieved via X-ray crystallography and DFT analysis. The article describes the life cycle and genome of the Zika virus along with its mechanism of entry inhibition by illustrating the structure and function of the ZIKV envelop (E) protein. The docking studies disclosed that the newly synthesized stilbene compound confers an excellent inhibitory response towards the entry of Zika virus in host cells as supported by calculated docking score and its binding conformation with Zika virus E-protein. Further, the normal mode analysis (NMA) simulation technique is used to predict the conformational states of the target E-protein, which explains the potency of the compound to bind with the Zika virus E-protein. We hope that the present study will help and encourage researchers in the field of medicinal chemistry to develop potential drugs against the Zika virus.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108935"},"PeriodicalIF":2.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Base-catalyzed thiol-epoxy reactions: Energetic and kinetic evaluations.","authors":"Belma Gjergjizi Nallbani, Memet Vezir Kahraman, Isa Degirmenci","doi":"10.1016/j.jmgm.2024.108933","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108933","url":null,"abstract":"<p><p>The mechanism of the base-catalyzed thiol-epoxide stage of the thiol-ene/thiol-epoxide curing process was investigated using quantum chemical tools. This study searched for conventional tertiary amines with low to medium basicity as initiators to control reaction rates and tailor industrial applications. Challenges arise from the stronger basicity of initiators, leading to an uncontrollable and short curing application period. This problem was put into quantitative data through kinetic and energetic studies for the first time. Furthermore, the base catalyst formulation of curing agents distinctively has a short pot life. More reactivity of terminal epoxy rings than internal ones was highlighted for the curing agents. It was revealed that the reactivity augments during the curing process while environmental polarity changes from higher to lower, which is one of the reasons that triggers an autocatalytic phenomenon. Electronegative atoms like fluorine on thiols significantly decrease the nucleophilicity of formed thiolate anion, enabling longer curing application.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108933"},"PeriodicalIF":2.7,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality.","authors":"Fabio J Cortés Rodríguez, Gianfranco Frattini, Sittha Phloi-Montri, Fernando Teixeira Pinto Meireles, Danaé A Terrien, Sergio Cruz-León, Matteo Dal Peraro, Eva Schier, Kresten Lindorff-Larsen, Taweetham Limpanuparb, Diego M Moreno, Luciano A Abriata","doi":"10.1016/j.jmgm.2024.108932","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108932","url":null,"abstract":"<p><p>MolecularWebXR is a new web-based platform for education, science communication and scientific peer discussion in chemistry and biology, based on modern web-based Virtual Reality (VR) and Augmented Reality (AR). With no installs as it is all web-served, MolecularWebXR enables multiple users to simultaneously explore, communicate and discuss concepts about chemistry and biology in immersive 3D environments, by manipulating and passing around objects with their bare hands and pointing at different elements with natural hand gestures. Users may either be present in the same physical space or distributed around the world, in the latter case talking naturally with each other thanks to built-in audio. While MolecularWebXR offers the most immersive experience on high-end AR/VR headsets, its WebXR core also supports participation on consumer devices such as smartphones (with optional cardboard goggles for enhanced immersion), computers, and tablets. MolecularWebXR includes preset VR rooms covering topics in general, inorganic, and organic chemistry, as well as biophysics, structural biology, and general biology. Users can also add new content via the PDB2AR tool. We demonstrate MolecularWebXR's versatility and ease of use across a wide age range (12-80) in fully virtual and mixed real-virtual sessions at science outreach events, undergraduate and graduate courses, scientific collaborations, and conference presentations. MolecularWebXR is available for free use without registration at https://molecularwebxr.org. A blog post version of this preprint with embedded videos is available at https://go.epfl.ch/molecularwebxr-blog-post.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108932"},"PeriodicalIF":2.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synergizing GA-XGBoost and QSAR modeling: Breaking down activity aliffs in HDAC1 inhibitors.","authors":"Rahul D Jawarkar, Suraj Mali, Prashant K Deshmukh, Rahul G Ingle, Sami A Al-Hussain, Aamal A Al-Mutairi, Magdi E A Zaki","doi":"10.1016/j.jmgm.2024.108915","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108915","url":null,"abstract":"<p><p>The work being presented now combines severe gradient boosting with Shapley values, a thriving merger within the field of explainable artificial intelligence. We also use a genetic algorithm to analyse the HDAC1 inhibitory activity of a broad pool of 1274 molecules experimentally reported for HDAC1 inhibition. We conduct this analysis to ascertain the HDAC1 inhibitory activity of these molecules. Based on a rigorous investigation of extreme gradient boosting, the proposed method suggests using a genetic algorithm to identify pharmacophoric features. The statistical acceptability of extreme gradient boosting analysis is robust, with parameters such as R²_tr = 0.8797, R²_L10 % = 0.8831, Q²_F1 = 0.9459, Q²_F2 = 0.9452, and Q²_F3 = 0.9474. This is the driving force behind the invention of nine Py-descriptor-containing genetic algorithms. Shapley additive explanations formed the basis for the interpretation, assigning a significant value to each variable in the model. This is followed by the use of counterfactual cases to analyse the impact of the discovered molecular descriptors on HDAC1 inhibition. An examination of the molecular descriptors, which include acc_N_3B, fsp2NringC8B, fsp3NC7B, and sp2N_sp3C_3B, demonstrates that these descriptors provide insight into the function that the nitrogen atom plays in influencing HDAC1's inhibitory activity. Furthermore, the investigation shed light on the significant role that the hybridized carbon atoms located in sp2 and sp3 play in HDAC1 inhibition. Thus, the QSAR results are in conformity with the reported findings. In addition, activity cliff analysis supports the QSAR findings. Thus, the genetic algorithm-extreme gradient-boosting GA-XGBoost model is easy to understand and makes decent predictions. Based on this, it indicates that \"explainable AI\" may prove to be beneficial in the future for the purpose of identifying and using structural features in the process of medication development.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108915"},"PeriodicalIF":2.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding the interaction mechanisms of active compounds extracted from Tabernaemontana penduliflora on the surface of magnetite (111) nanoparticles in aqueous medium by DFT and MD approaches.","authors":"Fredy Harcel Kamgang-Djioko, Christelle Ivane Azambou, Lucresse Kora Nguena Tiomo, Simeon Chukwudozie Nwanonenyi, Georges Kamgang Youbi, Chinyere Ada Madu, Emeka Emmanuel Oguzie","doi":"10.1016/j.jmgm.2024.108930","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108930","url":null,"abstract":"<p><p>Computational techniques have been used to analyze the molecules of 10-hydroxycoronahydine (HC) and voacangine hydroxyindolenine (VH) molecules with the aim of studying the effect of base and temperature on their interaction mechanisms during synthesis green magnetite nanoparticles. Density functional theory (DFT) descriptors such as: energy gap, overall reactivity descriptors, dipole moment and adsorption energy have all been explored in depth to understand the nature of the interaction. The DFT results showed that the molecules studied (HC and VH) are interactive and stable in an aqueous medium, due to the fact that these molecules have free electronic doublets on the nitrogen atom and the bond of the aromatic ring. It was observed that each molecule effectively increased the stabilization energy of magnetite nanoparticles through electron transfer. According to the Fukui function reactivity results, HC and VH compounds both have high oxidizing powers. Thus, showing that they are good agents for functionalizing magnetite nanoparticles. The adsorption energy and interaction force of HC and VH with the magnetite (111) nanoparticle surface were shown to increase with temperature and depend on the base used. The results of molecular dynamic (MD) simulation demonstrated that the adsorption of molecules on the adsorbate is chemical in nature and that chemical bonds predominate over electrostatic interactions. The molecular dynamics simulation parameters show that the adsorption of 10-hydroxycoronahydine and voacangine hydroxyindolenine molecules is chemisorption, exothermic and spontaneous.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108930"},"PeriodicalIF":2.7,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models.","authors":"Manjul Yadav, Shalmali Kharche, Shikha Prakash, Durba Sengupta","doi":"10.1016/j.jmgm.2024.108926","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108926","url":null,"abstract":"<p><p>Multi-scale models in which varying resolutions are considered in a single molecular dynamics simulation setup are gaining importance in integrative modeling. However, combining atomistic and coarse-grain resolutions, especially for coarse-grain force fields derived from top-down approaches, have not been well explored. In this study, we have implemented and tested a dual-resolution simulation approach to model globular proteins in atomistic detail (represented by the CHARMM36 model) with the surrounding solvent in Martini2 coarse-grain detail. The hybrid scheme considered is an extension of a model implemented earlier for mainly lipid and water molecules. We have considered a set of small globular proteins and have extensively compared to atomistic benchmark simulations as well as a host of experimental observables. We show that the protein structural dynamics sampled in the hybrid scheme is robust, and the intra-protein contact maps are reproduced, despite increased fluctuations of the loop regions. A good match is observed with experimental small angle X-ray scattering (SAXS) and NMR observables, such as chemical shifts and [Formula: see text] -coupling, with the best match obtained for the chemical shifts. However, deviations are observed in the water dynamics and protein-water interactions which we attribute to the limitation of solvent screening in the coarse-grain force field. The computational speed-up achieved is about 2-3 times compared to an all-atom system. Overall, the hybrid model is able to retain the main features of the underlying atomistic conformational landscape with a two-fold speed-up in computational cost.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108926"},"PeriodicalIF":2.7,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Absorption study of fat-soluble vitamins into dipalmitoylphosphatidylcholine (DPPC) bilayer by MD simulations.","authors":"Chanya Phromchaloem, Narissara Na Nakorn, Laksamee Muensritharam, Warabhorn Boonyarat","doi":"10.1016/j.jmgm.2024.108929","DOIUrl":"https://doi.org/10.1016/j.jmgm.2024.108929","url":null,"abstract":"<p><p>Retinol, α-tocopherol and phylloquinone (vitamins A, E, and K) are presented in high concentrations within the chloroplast and leaves of most plants. They are fat-soluble vitamins and absorb similarly to other dietary lipids. Because the molecular mechanism of retinol, α-tocopherol, and phylloquinone absorption is still unknown, this work aims to investigate the distribution of these vitamins at the water/membrane interface using molecular dynamics (MD) simulations. Structures and variations of the hydroxyl group in vitamins are the keys to the investigation of the absorption process. Binding orientations, favorable binding sites, interactions, and diffusion of vitamins were identified. All vitamins spontaneously penetrate the lipid bilayer. According to simulations, the formation of the hydrogen bonding interaction with the phosphate group of DPPC during absorption requires a hydroxyl group of retinol and tocopherol. Therefore, retinol has -OH group at the tail of the structure and shows the highest structural flexibility of retinol, broadest tilt angle toward the lipid membrane, and highest diffusion coefficient. Finally, retinol plugs its head group into the hydrocarbon core of the lipid bilayer. In the case of α-tocopherol, the hydroxyl at the head group produces α-tocopherol, which moves through one leaflet of the lipid membrane and is stabilized in the opposite leaflet. Interestingly, phylloquinone, a molecule without a hydroxyl group, stabilizes close to a phosphate group without hydrogen bond formation. The head group of phylloquinone penetrates at a precise tilting angle of 120°. High retention of phylloquinone inside gel-phase DPPC is suggested by its low diffusion coefficient. MD simulations reveal the characteristics of three fat-soluble vitamins during absorption through the phospholipid membrane. This information is useful as a guideline to improve the absorption of drugs along the membrane.</p>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"135 ","pages":"108929"},"PeriodicalIF":2.7,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}