Article
Chemistry, Multidisciplinary
Johannes Strobl, Fanny Kozak, Meder Kamalov, Daniela Reichinger, Dennis Kurzbach, Christian F. W. Becker
Summary: The article discusses the limitations of mimicking biological materials and introduces a peptide library that enables the design of biomimetic materials. It explains that the formation of biomaterials is governed by self-assembling precursors, and these precursors can be manipulated to control the morphology of silica particles. The study uses residue-resolved real-time NMR spectroscopy and molecular dynamics simulations to understand the atomistic details of the templates.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Physical
Robin Koester, Michael Vogel
Summary: In this study, molecular dynamics simulations were conducted to investigate the confinement effects of ionic liquids between amorphous silica surfaces. The results showed a significant slowdown of ion dynamics near the surfaces. The analysis revealed a broad distribution of residence times for anions at adsorption sites, following Arrhenius laws. Additionally, the amorphous silica surfaces imposed static and disordered energy landscapes, hindering ion rearrangements.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Federica Lodesani, Maria Cristina Menziani, Shingo Urata, Alfonso Pedone
Summary: This study systematically investigates the effects of simulation conditions on crystallization in highly viscous systems and finds that bias factor and temperature are the most effective parameters. Moreover, temperature rescaling proves to be a reliable approach for recovering free energy surfaces at lower temperatures.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Review
Physiology
Antreas C. Kalli, Reinhart A. F. Reithmeier
Summary: Molecular dynamics simulations provide valuable insights into the structure and function of the red blood cell Band 3 anion exchanger. These simulations reveal specific lipid and protein interactions and have been used to reconstruct a model of the Wright blood group antigen complex of Band 3 and Glycophorin A. Current research is focused on describing the real-time trajectory of substrate binding and translocation.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Chemistry, Physical
Yubo Zhang, Marc Baaden
Summary: This study used molecular dynamics simulations to illustrate the substrate recognition process of the outer membrane enzyme OmpT of Escherichia coli in a hydrated lipid bilayer. Hydrogen bonds and salt bridges play a significant role in maintaining the integrity of the active site and substrate recognition by OmpT. Electrostatic interactions are crucial in all stages of substrate binding and docking at the active site. Computational alanine scanning confirmed the importance of multiple residues in the active site that form salt bridges. The substrate fluctuates along the axis of the beta-barrel and correlates with the oscillations of the binding cleft formed by specific residue pairs. Principal component analysis indicates a correlation between substrate and protein movements. Transient presence of putative catalytic water molecules near the active site suggests their involvement in the cleavage of the substrate's peptide bond.
Article
Chemistry, Multidisciplinary
Carlos A. Ramos-Guzman, Milorad Andjelkovic, Kirill Zinovjev, J. Javier Ruiz-Pernia, Inaki Tunon
Summary: In this study, the by-residue decomposition of noncovalent interactions and analysis of naturally occurring mutations were used to detect potential mutations in the 3CL protease of SARS-CoV-2 that confer resistance to nirmatrelvir. It was found that the E166V mutation reduces the binding affinity of the protease to nirmatrelvir and increases the activation free energy for the formation of the covalent enzyme-inhibitor complex, resulting in resistance to the treatment with this drug. The conclusions of this study can be useful for predicting the consequences of introducing nirmatrelvir in the virus fitness landscape and designing new inhibitors targeting possible resistance mechanisms.
Review
Food Science & Technology
Weria Pezeshkian, Julian C. Shillcock, John H. Ipsen
Summary: The investigation of bacterial toxin entry mechanism remains challenging, but computer simulations serve as robust complementary tools for exploring biological processes in detail. Recent developments in the study of toxin endocytosis have significantly advanced our understanding, with implications for nanoparticle design and protein phase separation at membrane surfaces. The discussed methods also show promise for future development in this field.
Article
Biochemistry & Molecular Biology
Norman Geist, Felix Nagel, Mihaela Delcea
Summary: In this study, modern replica-exchange molecular dynamics simulations were used to investigate the interaction between the ADAMTS13-MDTCS domains and the VWF-A2 domain. The findings provide comprehensive information on binding sites and interacting amino acids for each domain, revealing major binding modes. This study contributes to a better understanding of disease-related mutations and potential therapeutic improvements.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Pan Xu, Zhijie Shang, Meiling Yao, Zhenyu Ke, Xinxue Li, Pingde Liu
Summary: A novel TM-SiO2/PAM/PAA nanocomposite double network (DN) hydrogel with excellent mechanical performance was developed. By introducing nanoparticles and a DN structure, the hydrogel achieved higher fracture tensile stress and compressive stress, as well as a denser structure.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Valery Lutsyk, Pawel Wolski, Wojciech Plazinski
Summary: This article presents a coarse-grained force field dedicated to glucopyranose-based carbohydrates, compatible with the Martini force field. The new model successfully displays spontaneous formation of aggregates with experimentally identified features and accurately identifies binding pockets in carbohydrate-binding proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Fabio Pietrucci, Mauro Boero, Wanda Andreoni
Summary: Water pollution by heavy metals is a growing concern due to its severe environmental and health impacts. Natural materials, like spent coffee grains or fruit peels, are being explored as potential cheap alternatives for heavy metal removal. Molecular simulations show that hemicellulose may efficiently capture lead ions from water through spontaneous adsorption on specific functional groups.
Article
Biochemistry & Molecular Biology
Romina V. Sepulveda, Christopher Sbarbaro, Ma Cecilia Opazo, Yorley Duarte, Fernando Gonzalez-Nilo, Daniel Aguayo
Summary: This study investigated the self-assembly process of low-carbon short-chain fatty acids into vesicles at different temperatures and examined the insertion of a prebiotic-like peptide into primitive membranes. The findings from this research provide crucial insights into the interactions between molecules and primitive membranes, allowing us to better understand the nanometric compartments that were essential for triggering further reactions and the origin of life.
Article
Biochemistry & Molecular Biology
Shasha Liu, Hengming Zhang, Shiling Yuan
Summary: In this paper, molecular dynamics (MD) simulation was used to investigate the adsorption configuration of hydrophilic silica nanoparticles (SNPs) in an oil-water emulsion system and their effect on the coalescence of oil droplets. The simulation results showed that SNPs adsorbed on the surface of oil droplets and self-aggregated through hydrogen bonds. Additionally, hydrophilic asphaltene and resin molecules formed adsorption configurations with SNPs, changing the distribution of oil droplet components. SNPs extended the coalescence time of oil droplets and formed pi-pi stacking structures to enhance the connection between oil droplets. Furthermore, a sufficient amount of SNPs tightly wrapped around the oil droplet, hindering the contact and coalescence of components between oil droplets.
Article
Environmental Sciences
Mulan Chen, Faqin Dong, Hailong Li, Yulian Zhao, Shi Ou, Mingxue Liu, Wei Zhang
Summary: In this study, the interaction between high-siliceous/calcareous mineral granules and artificial membranes was investigated using giant and small unilamellar vesicles as model membranes. Nano calcium carbonate and nano silica were found to induce gelation by disrupting oppositely charged membranes, highlighting the role of electrostatic forces. The size of the mineral granules affects the electrostatic interactions and their damaging effects on the membranes.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jose Villalain
Summary: Bioactive furanocoumarins, a group of natural secondary metabolites common in higher plants, have been shown to have numerous biological properties. This study used molecular dynamics simulations to investigate the interaction between bergamottin (BGM), a furanocoumarin, and the biological membrane. The results suggest that BGM tends to locate in the middle of the hydrocarbon layer of the membrane, interacts with membrane lipids, and increases the fluidity of the membrane. These findings contribute to the understanding of the bioactive properties of BGM and its potential as a therapeutic molecule.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Massimo Delle Piane, Marta Corno
Summary: This study presents the first quantum mechanical investigation of the interactions between a model benzodiazepine drug, nitrazepam, and different models of amorphous silica surfaces. The results suggest that the adsorption of nitrazepam on amorphous silica is a highly exothermic process, accompanied by partial proton transfer from the surface to the drug, indicating a potential catalytic role of silica in the degradation reaction of benzodiazepines.
Editorial Material
Chemistry, Multidisciplinary
Nicholas A. Kotov, Deji Akinwande, C. Jeffrey Brinker, Jillian M. Buriak, Warren C. W. Chan, Xiaodong Chen, Manish Chhowalla, William Chueh, Sharon C. Glotzer, Yury Gogotsi, Mark C. Hersam, Dean Ho, Tony Hu, Ali Javey, Cherie R. Kagan, Kazunori Kataoka, Il-Doo Kim, Shuit-Tong Lee, Young Hee Lee, Luis M. Liz-Marzan, Jill E. Millstone, Paul Mulvaney, Andre E. Nel, Peter Nordlander, Wolfgang J. Parak, Reginald M. Penner, Andrey L. Rogach, Mathieu Salanne, Raymond E. Schaak, Ajay K. Sood, Molly Stevens, Vladimir Tsukruk, Andrew T. S. Wee, Ilja Voets, Tanja Weil, Paul S. Weiss
Editorial Material
Chemistry, Multidisciplinary
Luis M. Liz-Marzan, Andre E. Nel, C. Jeffrey Brinker, Warren C. W. Chan, Chunying Chen, Xiaodong Chen, Dean Ho, Tony Hu, Kazunori Kataoka, Nicholas A. Kotov, Wolfgang J. Parak, Molly M. Stevens
Article
Biochemistry & Molecular Biology
Jana Rosenau, Isabell Louise Grothaus, Yikun Yang, Nilima Dinesh Kumar, Lucio Colombi Ciacchi, Sorge Kelm, Mario Waespy
Summary: This study reveals how N-glycans affect the enzymatic activity and structural stability of recombinant TS enzyme TconTS1 in Trypanosoma congolense. The removal of N-glycans decreases substrate affinity but has no impact on the conversion rate. Interactions between N-glycans and amino acids in the catalytic site may lead to conformational changes, enhancing substrate accessibility and enzyme-substrate complex stability.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Isabell Louise Grothaus, Giovanni Bussi, Lucio Colombi Ciacchi
Summary: Despite their biological relevance, structure-property relationships in N-glycans are currently not well understood. In this study, a novel enhanced-sampling scheme was developed to explore the highly multidimensional compositional and conformational phase spaces of N-glycans. The results reveal the effect of chemical substitutions on the conformational ensemble of selected glycans and assess the structure-prediction capabilities of commonly used force fields.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Kimberly S. Butler, C. Jeffrey Brinker, Hon Sing Leong
Summary: The avian embryo and chorioallantoic membrane (CAM) model provides a valuable in vivo preclinical platform for evaluating the behavior and performance of nanoparticles. It allows for the study of nanoparticle stability, distribution, and interactions at a cellular level, and can be used to accelerate the development of nanoparticle delivery and imaging agents.
Editorial Material
Chemistry, Multidisciplinary
Tony Hu, C. Jeffrey Brinker, Warren C. W. Chan, Chunying Chen, Xiaodong Chen, Dean Ho, Kazunori Kataoka, Nicholas A. Kotov, Luis M. Liz-Marzan, Andre E. Nel, Wolfgang J. Parak, Molly Stevens
Article
Chemistry, Physical
Tobias Wollborn, Monika Michaelis, Lucio Colombi Ciacchi, Udo Fritsching
Summary: This study provides evidence that beta-lactoglobulin proteins undergo conformational changes during membrane emulsification processes. The shear stress applied during oil droplet fragmentation causes the protein to transition into a more stable, partially unfolded interfacial state.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Review
Biotechnology & Applied Microbiology
Peng He, Guozheng Yang, Danzhu Zhu, Hao Kong, Yendry Regina Corrales-Urena, Lucio Colombi Ciacchi, Gang Wei
Summary: This review presents recent advances in the biomolecule-mimetic synthesis of functional nanomaterials for photothermal therapy (PTT) and photodynamic therapy (PDT) of cancers. It introduces different biomimetic synthesis methods and discusses the advantages of each method. The review also explores the synthesis of nanomaterials using biomolecules and discusses how to regulate the structure and functions of the obtained biomimetic nanomaterials. Additionally, potential applications of biomimetic nanomaterials for both PTT and PDT of cancers are demonstrated and discussed.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Editorial Material
Chemistry, Multidisciplinary
Jillian M. Buriak, Deji Akinwande, Natalie Artzi, C. Jeffrey Brinker, Cynthia Burrows, Warren C. W. Chan, Chunying Chen, Xiaodong Chen, Manish Chhowalla, Lifeng Chi, William Chueh, Cathleen M. Crudden, Dino Di Carlo, Sharon C. Glotzer, Mark C. Hersam, Dean Ho, Tony Y. Hu, Jiaxing Huang, Ali Javey, Prashant V. Kamat, Il-Doo Kim, Nicholas A. Kotov, T. Randall Lee, Young Hee Lee, Yan Li, Luis M. Liz-Marzan, Paul Mulvaney, Prineha Narang, Peter Nordlander, Rahmi Oklu, Wolfgang J. Parak, Andrey L. Rogach, Mathieu Salanne, Paolo Samori, Raymond E. Schaak, Kirk S. Schanze, Tsuyoshi Sekitani, Sara Skrabalak, Ajay K. Sood, Ilja K. Voets, Shu Wang, Shutao Wang, Andrew T. S. Wee, Jinhua Ye
Article
Chemistry, Physical
Fanhui Kong, Qi Lei, Yi Ma, Peiying He, Guansheng Zheng, Yue Xu, Junda Huang, C. Jeffrey Brinker, Kaisheng Liu, Wei Zhu
Summary: By constructing a drug-loaded membrane fusion liposome, this study demonstrates a two-pronged strategy to trigger ferroptosis in cancer cells by delivering fatty acid hydroperoxide and blocking antioxidant systems.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Physical
Matteo Cioni, Daniela Polino, Daniele Rapetti, Luca Pesce, Massimo Delle Piane, Giovanni M. Pavan
Summary: Metals can undergo dynamic reconfigurations even below the melting temperature, which is important for understanding their surface properties. This study uses deep-potential molecular dynamics simulations to analyze the complex dynamics of different copper surfaces near the Huttig temperature. The use of high-dimensional structural descriptors and unsupervised machine learning allows the identification and tracking of atomic environments in these surfaces. The findings reveal the statistical identity of metal surfaces and their dynamic interconversions networks.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Antara Reja, Sumit Pal, Kishalay Mahato, Baishakhi Saha, Massimo Delle Piane, Giovanni M. Pavan, Dibyendu Das
Summary: Researchers reported a light-responsive reaction system where the binding sites for C-C bond manipulation were regulated by a photosensitive molecular cofactor. This system achieved a more efficient catalytic state under nonequilibrium conditions with the energy of the light source. Additionally, the binding of a molecular catalyst enhanced activity and facilitated the in situ generation of a light-sensitive cofactor.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Monika Michaelis, Lorenzo Cupellini, Carl Mensch, Carole C. Perry, Massimo Delle Piane, Lucio Colombi Ciacchi
Summary: The protein folding problem remains unsolved due to the limitations of current structure prediction methods in exploring the conformational ensemble of disordered peptides and proteins. A novel methodology is presented to predict spectroscopic fingerprints and tidy up the conformational ensembles of disordered peptides and regions. This finding has profound implications for the interpretation of experimental spectra and the development of improved structure prediction methods.
Article
Materials Science, Multidisciplinary
Alexander Avdoshin, Vladimir Naumov, Lucio Colombi Ciacchi, Stanislav Ignatov, Susan Koeppen
Summary: MicroRNA (miRNA) holds great potential as a new high-tech pharmacological agent and requires protective drug delivery carriers. Chitosan, with its useful properties such as mucoadhesion, ease of modification, low cost, and biocompatibility, is a promising material for these carriers. Molecular dynamics simulations of chitosan/miRNA complexes demonstrated that the protonation and acetylation degree of chitosan influenced the formation and adsorption properties of the complexes.
MATERIALS ADVANCES
(2023)