Article
Chemistry, Physical
Victoria Ariel Bjornestad, Xinmeng Li, Christophe Tribet, Reidar Lund, Michele Cascella
Summary: This study investigates the kinetics and mechanisms of growth and dissolution of micelles by using an isomerizable surfactant. The results show that micelle growth is mainly achieved through unimer exchange processes, while dissolution can occur through both fission and unimer expulsion. Fusion of micelles is unlikely to occur under the conditions studied.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Applied
Benjamin P. Westberry, Bradley W. Mansel, Timothy M. Ryan, Leif Lundin, M. A. K. Williams
Summary: The traditional notion that.-carrageenan exists in solution as a random coil has been challenged by new research, which shows that the solution-state structure of.-carrageenan retains the helical motifs present in the solid-state. Additionally, there is no evidence to suggest that single chains undergo any conformational transition upon the addition of ions.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemical Research Methods
Yizhi Qi, Christopher B. Fox
Summary: QS-21 is a potent vaccine adjuvant found in the bark of the Chilean soap bark tree Quillaja saponaria, but its purification has been challenging. A new two-step chromatographic process has been developed for efficiently purifying QS-21 from commercially available bark extract with high yield and purity, providing a simple method for obtaining highly pure QS-21 from saponin-enriched bark extract.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Medicinal
Henrique M. Cezar, Michele Cascella
Summary: Using small-angle scattering is common in investigating soft-matter systems, but more detailed information usually requires molecular simulations. This study introduces an extension in PLUMED for computing small-angle neutron scattering (SANS) and demonstrates its use in data processing and enhanced sampling, particularly in achieving agreement with experimental references using metainference.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Lisa Thomson, Daniel McDowall, Libby Marshall, Olivia Marshall, Henry Ng, W. Joseph A. Homer, Dipankar Ghosh, Wanli Liu, Adam M. Squires, Eirini Theodosiou, Paul D. Topham, Louise C. Serpell, Robert J. Poole, Annela Seddon, Dave J. Adams
Summary: This study demonstrates the treatment of a simple dipeptide building block as a polyelectrolyte and the use of polymer physics approaches to explain self-assembly, leading to the preparation of interesting materials.
Article
Biochemistry & Molecular Biology
D. S. Molodenskiy, D. Svergun, H. D. T. Mertens
Summary: Membrane proteins are important targets in biological and medical sciences, and small-angle X-ray scattering provides a rapid method for studying their structures and conformational changes. MPBuilder is a versatile tool that allows for generating and refining membrane protein systems in the popular PyMOL software.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Physical
Darya L. Gurina, Vladimir P. Barannikov, Marina S. Kurbatova
Summary: Molecular dynamics simulations were used to study the interaction between an anionic micelle and carno-sine and anserine in their three-pole cationic form. The formation of hydrogen bonds between the peptides and the micelle was confirmed, with H-bond lengths ranging from 0.184 to 0.198 nm. Specific binding sites were identified on both the peptides and the micelle. The differences in orientations of equally charged ions of carnosine and anserine relative to the micelle were discussed.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Dana Saad, Cristina Paissoni, Antonio Chaves-Sanjuan, Marco Nardini, Roberto Mantovani, Nerina Gnesutta, Carlo Camilloni
Summary: E2F1 as a master regulator of cell-cycle progression binds DNA as a heterodimer with DP partners, with an asymmetric contribution of dynamics in the complex. Tumor mutations in the flexible regions of the complex could affect protein function context-dependently, suggesting fundamental contributions of DP proteins in distinct aspects of E2F biology.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Polina P. P. Kobchikova, Sergey V. V. Efimov, Vladimir V. V. Klochkov
Summary: Peptides have different biological functions and their activity can be determined by membrane permeability. This study focuses on the interaction of cyclosporins with lipid bilayers using molecular dynamics simulations and NMR spectroscopy. Changes in NMR spectra were observed when cyclosporins were dissolved in water containing DPC micelles, indicating the influence of the micelle on the peptide. Simulation of the peptide-micelle interaction revealed important insights into the membrane permeability and biological action of cyclosporin.
Article
Chemistry, Multidisciplinary
Atsushi Hirano, Tomoshi Kameda, Momoyo Wada, Takeshi Tanaka, Hiromichi Kataura
Summary: In this study, carbon nanobelts (CNBs) were successfully solubilized using aliphatic surfactant micelles through host-guest complexation. The solubility of CNB in non-aliphatic surfactant solutions was found to be poor. This finding provides important knowledge for the application of aliphatic compounds in solubilizing CNBs and their derivatives.
Article
Nanoscience & Nanotechnology
Lorenzo Veronico, Luigi Gentile
Summary: Release of contaminants poses a threat to human health and the environment, and self-assembled nanostructures of nonionic surfactants have shown high efficiency in removing these pollutants. This study evaluates the pollutant-removal efficiency of Brij L4 nonionic surfactant and its self-assembled structures. The interactions between Brij L4 micellar phase and lyotropic liquid crystals and ferrihydrite nanoparticles were investigated using small-angle X-ray scattering and rheology. The results provide effective strategies for formulating highly efficient pollutant-removal systems using nanotechnology.
ACS APPLIED NANO MATERIALS
(2023)
Article
Microbiology
Susan L. Baldwin, Valerie A. Reese, Sasha E. Larsen, Tiffany Pecor, Bryan P. Brown, Brian Granger, Brendan K. Podell, Christopher B. Fox, Steven G. Reed, Rhea N. Coler
Summary: This study aimed to test new lipid-based adjuvant formulations with ID93 in the context of a therapeutic vaccine, and compare it with drug treatment alone. The results showed that the combination of GLA-LSQ with ID93 provided enhanced protection compared to drug treatment alone.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Physical
Jhonatan Soto Puelles, Mahdi Ghorbani, Simon Crawford, M. Leigh Ackland, Fangfang Chen, Maria Forsyth, Anthony E. Somers
Summary: This study demonstrates through simulations and experiments that the molecular interactions between cetrimonium and 4-OH-cinnamate can improve the adsorption of cinnamate on mild steel and develop a protective mechanism against corrosive chloride diffusion. The fundamental understanding of this mechanism can contribute to the design of eco-friendly corrosion inhibitors.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Immunology
Karl J. J. Fisher, Robert Kinsey, Raodoh Mohamath, Tony Phan, Hong Liang, Mark T. T. Orr, William R. R. Lykins, Jeffrey A. A. Guderian, Julie Bakken, David Argilla, Gabi Ramer-Denisoff, Elise Larson, Yizhi Qi, Sandra Sivananthan, Karina Smolyar, Darrick Carter, Christopher J. J. Paddon, Christopher B. B. Fox
Summary: Synthetic biology has been used to produce supply-limited sesquiterpenoids, such as artemisinin and beta-farnesene. As the overfishing of deep-sea sharks has led to potential supply problems for squalene, a triterpenoid derived from shark liver oil, researchers have chemically generated squalene analogues from fermentation-derived beta-farnesene to serve as sustainable vaccine adjuvants. By evaluating the adjuvant activity of these analogues, they have identified compounds with enhanced, equivalent, or decreased activity compared to shark squalene emulsion, shedding light on the structural properties important for adjuvant activity.
Article
Chemistry, Physical
Kirian Tallo, Susana Vilchez, Ramon Pons, Olga Lopez
Summary: Research on colloidal dispersions has shown that gels can be formed from lipid vesicles with varying charge ratios, affecting their microstructure and rheological properties. A lipid gel with a charge ratio of 20:1 exhibited the highest resistance to deformation, while deviations from this ratio decreased its rigidity. Understanding how electrostatic balance influences gel properties can help tailor gel composition for specific applications.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Conrado Pedebos, Iain Peter Shand Smith, Alister Boags, Syma Khalid
Summary: This study used atomistic molecular dynamics simulations to investigate the behavior of the antibiotic polymyxin B1 in the crowded periplasm of Gram-negative bacteria. The simulations suggest that PMB1 may hitchhike within the periplasm by binding to lipoprotein carriers, forming interactions with various components and potentially interfering with the conformational dynamics of native proteins. These findings have important implications for understanding the mechanism of action of PMB1 and other antibiotics that rely on diffusion in crossing the periplasm.
Article
Chemistry, Applied
Cilaine Veronica Teixeira, Yuri Alencar Marques, Marcia Carvalho de Abreu Fantini, Diomar da Rocha Santos Bittencourt, Cristiano Luis Pinto Oliveira
Summary: The study investigated the solubility behavior of Diol and Triol in different solvents and temperatures, revealing the formation of reversed micelles with increasing polymer concentrations. When the cloud point (CP) is reached, solvent nuclei are separated by large polymer domains, without phase separation. The design of novel polyether glycols with tailored solution behavior for efficient performance is facilitated by the elucidation of solubility mechanisms.
JOURNAL OF SURFACTANTS AND DETERGENTS
(2021)
Article
Biochemical Research Methods
Maria J. Gomara, Ramon Pons, Carolina Herrera, Paul Ziprin, Isabel Haro
Summary: A novel peptide amphiphile (PA) based on the E1P47 peptide sequence was designed and synthesized in this study to target lipid rafts of the cell membrane, demonstrating potential antiviral activity against HIV-1. The length of the polyethylene glycol spacer, the position of peptide conjugation, and the type of hydrophobic residue were found to affect the antiviral efficacy of the construct, with monoalkyl PAs showing the highest anti-HIV-1 activities in cellular and preclinical models.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Ederson Sales Moreira Pinto, Bruno Cesar Feltes, Conrado Pedebos, Marcio Dorn
Summary: Bioremediation is highlighted as a cost-effective and eco-friendly alternative to reverse the damage caused by oil pollution, but more efforts are needed to design enzymes for the process.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
News Item
Microbiology
Conrado Pedebos, Syma Khalid
Summary: This article discusses a few recent molecular simulation studies that have made substantial contributions to our understanding of the spike protein of SARS-CoV-2.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lorena Zuzic, Firdaus Samsudin, Aishwary T. Shivgan, Palur V. Raghuvamsi, Jan K. Marzinek, Alister Boags, Conrado Pedebos, Nikhil K. Tulsian, Jim Warwicker, Paul MacAry, Max Crispin, Syma Khalid, Ganesh S. Anand, Peter J. Bond
Summary: The COVID-19 pandemic has accelerated the development of vaccines and drugs. Researchers have used simulations and experiments to identify a potential druggable pocket in the SARS-CoV-2 spike glycoprotein and emphasized the importance of pocket dynamics. This pocket is associated with mutations found in concerning SARS-CoV-2 variants.
Article
Biochemistry & Molecular Biology
Cesar Gonzalez, Simone Balocco, Jaume Bosch, Juan Miguel de Haro, Maurizio Paolini, Antonio Filgueras, Carlos Alvarez, Ramon Pons
Summary: X-ray crystallography is an important method for understanding the biological function of proteins and other molecules. However, the production of crystals is often a bottleneck. To address this issue, researchers have proposed the use of whole pair distribution function and FPGA technology to reduce computation time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Melissa N. Webby, Abraham O. Oluwole, Conrado Pedebos, Patrick G. Inns, Anna Olerinyova, Dheeraj Prakaash, Nicholas G. Housden, Georgina Benn, Dawei Sun, Bart W. Hoogenboom, Philipp Kukura, Shabaz Mohammed, Carol V. Robinson, Syma Khalid, Colin Kleanthous
Summary: This study reveals that OMP-lipid-OMP complexes are the basic units of supramolecular OMP assembly, which extend across the entire cell surface and couple the multifunctionality, stability, and impermeability of the outer membrane.
Article
Thermodynamics
Cesar A. Godoy, Mercedes Valiente, Wilson Munoz, Pablo Bonilla, Ramon Pons, Gemma Montalvo
Summary: This study investigates the phase behaviors, microstructural and viscoelastic properties of ternary systems composed of lecithin, vegetal oils, and water with low water content. Understanding the microstructures and rheological properties of these phases can aid in the development of new biocompatible excipients. Phase determinations are made using a combination of optical microscopy, small-angle X-ray scattering, and rheology measurements. The saturation levels of the different fatty acid contents in biocompatible vegetal oils, such as olive oil and castor oil, are found to affect the phase behavior. The lamellar phase is preferred with biocompatible vegetal oils, while the cubic structure coexists with other liquid crystalline phases but does not appear in a monophasic region. Castor oil can form a pure inverse micellar region. Hexagonal liquid crystalline samples behave like solids, while lamellar liquid crystalline samples behave like a typical weak gel, with slight frequency dependence. High oil content favors a stiffer and more elastic lamellar structure at 37°C compared to 25°C, and an increase in temperature leads to a higher degree of structural ordering and a smaller lamellar phase region.
JOURNAL OF CHEMICAL AND ENGINEERING DATA
(2023)
Article
Pharmacology & Pharmacy
Maria De Luca, Carlo Ignazio Giovanni Tuberoso, Ramon Pons, Maria Teresa Garcia, Maria del Carmen Moran, Giulio Ferino, Antonio Vassallo, Giuseppe Martelli, Carla Caddeo
Summary: The study focuses on the use of phospholipid vesicles for the nanoformulation of plant extracts, aiming to overcome limitations in their topical application. The Prunus spinosa berries were used as a source of bioactive compounds, and two types of phospholipid vesicles were developed for improved applicability as topical formulations. Various characterization and safety tests were conducted to assess their properties and potential.
Article
Biochemistry & Molecular Biology
Maria De Luca, Carlo Ignazio Giovanni Tuberoso, Ramon Pons, Maria Teresa Garcia, Maria del Carmen Moran, Giuseppe Martelli, Antonio Vassallo, Carla Caddeo
Summary: Formulating plant extracts in phospholipid vesicles is a promising strategy to overcome challenges like poor solubility, instability, low skin permeation, and short retention time. In this study, a hydro-ethanolic extract was prepared from Ceratonia siliqua ripe pods, showing antioxidant properties due to the presence of active compounds. Liposomes were used to improve the extract's applicability, characterized by small size, negative charge, high entrapment efficiency, and biocompatibility. The extract demonstrated antioxidant activity by scavenging free radicals, reducing ferric ions, and protecting skin cells from oxidative damage.
Article
Pharmacology & Pharmacy
Zakaria Hafidi, Lourdes Perez, Mohammed El Achouri, Ramon Pons
Summary: Cationic surfactants based on phenylalanine and tryptophan were synthesized using renewable raw materials and a green synthetic procedure. The synthesis, acid-base equilibrium, aggregation properties, and antibacterial activity of these surfactants were investigated. The surfactants showed promising antibacterial efficacy and had a high affinity for DPPC bilayers, although their antibacterial activity was reduced when incorporated in vesicles.
Article
Food Science & Technology
Elena Tomassi, Daniela Lucchesi, Carla Caddeo, Donatella Valenti, Veronica Sancho, Ramon Pons, Laura Pucci
Summary: Research has shown that liposomes can effectively address the instability, low solubility, and poor absorption of compounds such as polyphenols, polyunsaturated fatty acids, vitamins, and alpha-lipoic acid in therapy. They provide protection from physiological degradation and offer a safe method of application to cells.
Article
Materials Science, Biomaterials
Kirian Tallo, Ramon Pons, Cesar Gonzalez, Olga Lopez
Summary: Colloidal gels made from lipid vesicles under highly diluted conditions have been described, which could be relevant for mimicking biological conditions. Mechanistic insights revealed that freezing and heating are crucial steps in gel formation, and techniques such as transmission electron microscopy, differential scanning calorimetry, and synchrotron small angle X-ray scattering allow for in-depth analysis.
JOURNAL OF MATERIALS CHEMISTRY B
(2021)