Article
Multidisciplinary Sciences
J. S. Park, J. D. Almer, K. C. James, L. J. Natanson, S. R. Stock
Summary: Members of subclass Elasmobranchii possess bioapatite mineralization in their cartilage skeletons, which has similar crystallography to bone but exhibits some differences. The mineral phase in shark centra has larger nanocrystallite sizes and is associated with less microstrain compared to bone.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Biochemistry & Molecular Biology
Alexander W. Mauney, Uma M. Muthurajan, Karolin Luger, Lois Pollack
Summary: Nucleosomes in eukaryotic cells are organized into higher order structures for genome compaction, and understanding their organization is crucial in studying DNA storage efficiency. Arrays of linked nucleosomes serve as models for understanding how DNA and protein properties affect their arrangement, while important questions remain regarding the effects of histone proteins and other chromatin-associated protein partners on nucleosome spacing.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Polymer Science
Apisit Banpean, Hideaki Takagi, Nobutaka Shimizu, Noriyuki Igarashi, Shinichi Sakurai
Summary: The study focused on the confined crystallization of PEG in PLLA spherulite in a PLLA/PEG blend specimen using SAXS/WAXS measurements. The results showed suppression of PEG lamellae growth in the thickness direction due to space confinement by preformed PLLA lamellae, while also observing more regular stacking in the blend specimen.
Review
Chemistry, Analytical
Seema Thakral, Kyungtae Kim
Summary: Small-angle scattering (SAS) is a versatile analytical technique that provides detailed structural information at the nanometer scale. It has diverse applications in pharmaceutical material characterization, including identification of liquid-crystalline mesophase of drugs, study of excipient microstructure influence, and optimization of solid dispersions and protein-based therapeutics formulations.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Physical
Kun Qian, Randall E. Winans, Tao Li
Summary: Understanding the nanostructures of liquid electrolytes is crucial for enhancing electrochemical energy storage capacities, but the solvation structures and molecular dynamics in electrolytes are difficult to probe. Small-angle X-ray scattering (SAXS) offers unique insights into molecular clusters and ion pairs in electrolytes, with excellent time-resolution for studying molecular dynamics. This review focuses on the microscopic understanding of liquid electrolytes by SAXS and highlights the unique capabilities of X-ray scattering for nanostructure characterization.
ADVANCED ENERGY MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Hiroshi Imamura, Shinya Honda
Summary: Antibody aggregation and acid denaturation followed by neutralization of pH contribute to the high cost of therapeutic monoclonal antibody production. Understanding the structural details of acid-denatured antibodies is crucial for antibody engineering. Research has shown that acid-denatured monoclonal antibodies become smaller globules at pH 2 compared to their native structure at pH 7. Small-angle X-ray scattering data indicate conformational changes that can lead to aggregation. The distortion of the Fc region and longer inter-domain correlations are found to initiate acid denaturation and aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Enyi Chi, Haiying Huang, Fajun Zhang, Tianbai He
Summary: Crystalline block copolymers have been utilized to create plate-like colloidal systems with controlled size and shape. The structure in solution and the face-to-face spacing were characterized using small- and ultrasmall-angle X-ray scattering techniques, revealing the importance of lateral attraction between polar crystalline blocks for the formation of the nematic phase.
Article
Chemistry, Applied
Thomas Konegger, Christina Drechsel, Herwig Peterlik
Summary: In this study, in-situ small angle X-ray scattering (SAXS) was used to monitor the structural evolution of polymer-derived ceramic materials during the pyrolytic conversion process, focusing on the emergence, transformation, and collapse of transient microporosity. Results showed that the in-situ experiments were in good agreement with conventionally obtained ex-situ data, indicating the significant potential of this method for gaining fundamental insights into the conversion of polymer-derived ceramics.
MICROPOROUS AND MESOPOROUS MATERIALS
(2021)
Article
Polymer Science
Sascha A. Wilhelm, Michail Maricanov, Volker Brandt, Frank Katzenberg, Joerg C. Tiller
Summary: Amphiphilic polymer conetworks (APCNs) combine two incompatible properties within one material by featuring two interconnected independently swelling nanophases. Two novel APCN families have been synthesized using hydrophilic and hydrophobic polymers, respectively, and have demonstrated the ability to swell in orthogonal solvents without changing their nanostructure.
Article
Medicine, Research & Experimental
Yiwen Li, Jianqiao Zhang, Panqi Song, Xiaran Miao, Guangfeng Liu, Chunming Yang, Xiaohui Wei, Na Li, Fenggang Bian
Summary: This study used SAXS to investigate the structure of PEGylated liposomal doxorubicin (PLD) and compared the suitability of different models. The results showed that spherical-shell and flat-slab models with Gaussian electron density distribution were able to effectively reveal the structural features of the liposomal membrane, while models with uniform electron density distribution performed poorly. This study highlights the applicability of SAXS in liposomal drugs.
MOLECULAR PHARMACEUTICS
(2023)
Article
Biochemistry & Molecular Biology
Daria Wojciechowska, Michal Taube, Karolina Rucinska, Joanna Maksim, Maciej Kozak
Summary: This study characterized the oligomeric states of human cystatin C in different pH conditions, revealing the ability to form tetramers at low pH and dissociate into dimers at neutral pH.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Bichitra Borah, Gobin Raj Acharya, Diana Grajeda, Matthew S. Emerson, Matthew A. Harris, Am Milinda Abeykoon, Joshua Sangoro, Gary A. Baker, Andrew J. Nieuwkoop, Claudio J. Margulis
Summary: This article reports on the structural-dynamic pathway from liquid to glass in ionic liquids containing a specific cation. Experimental and computational evidence suggests that the transition from liquid to glass occurs in separate stages.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Materials Science, Multidisciplinary
Jana Smilauerova, Petr Harcuba, Jitka Straska, Josef Strasky, Milos Janecek, Jiri Pospisil, Jan Ilavsky, Vaclav Holy
Summary: The shapes and orientations of lamellae in single crystals of metastable beta-Ti alloy were investigated using synchrotron small-angle x-ray scattering. The results provide information on the kinetics of the beta-alpha transformation and the thermodynamic equilibrium of the final alpha-beta composite.
MATERIALS CHARACTERIZATION
(2023)
Article
Chemistry, Physical
Kohei Yamanoi, Satoshi Shibuta, Atsushi Shiro, Masao Noumi, Melvin John F. Empizo, Marilou Cadatal-Raduban, Nobuhiko Sarukura, Keiko Nishikawa, Takeshi Morita
Summary: Fluoropolymers have diverse applications in various industries. Neat fluoropolymers and fluorinated copolymers were synthesized using suspension polymerization method, with an increase in structural disorder observed at a slower rate with higher VdF content in the copolymer. The copolymer with the highest VdF content showed similar crystallinity before and after the stimulus, indicating good thermal stability and microvoid tolerance.
JOURNAL OF SUPERCRITICAL FLUIDS
(2022)
Article
Chemistry, Multidisciplinary
Shuji Fujisawa, Yuichi Takasaki, Tsuguyuki Saito
Summary: We investigated the structure of polymer-grafted nanocellulose in the colloidal dispersion system through small-angle X-ray scattering measurement and all-atom molecular dynamics simulation. Our results showed the formation of a polymer brush layer on the nanocellulose surface in solvents, explaining its excellent colloidal stability. We also found that the presence of the polymer brush layer suppressed the twisting of the nanocellulose core.
Article
Chemistry, Physical
Angel Pineiro, James Pipkin, Vince Antle, Rebeca Garcia-Fandino
Summary: Modified cyclodextrins (CDs) are used as enabling excipients in pharmaceutical formulations to improve solubility and stability of drugs. The affinity between CDs and drugs should be balanced for optimal formulation. This study investigates the effect of substitutions on complexation using sulphobutylether-beta-cyclodextrin and remdesivir as a case study, providing insights for the optimization of formulations based on modified CDs.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Barbara Claro, Eva Gonzalez-Freire, Juan R. Granja, Rebeca Garcia-Fandino, Jana Gallova, Daniela Uhrikova, Aleksander Fedorov, Ana Coutinho, Margarida Bastos
Summary: Fluorescence spectroscopy is used to study the partition of second-generation D,L-alpha-cyclic peptides in lipid model membranes. The introduction of a hydrocarbon tail significantly improves the partition of the modified peptides to both membrane systems, with the length of the tail being a key factor for the extension of the partition process. Peptides with a tail promote fast membrane leakage compared to the parent peptide, which induces limited leakage.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Biochemistry & Molecular Biology
Fabian Suarez-Leston, Martin Calvelo, Gideon F. Tolufashe, Alicia Munoz, Uxia Veleiro, Cesar Porto, Margarida Bastos, Angel Pineiro, Rebeca Garcia-Fandino
Summary: Host defense peptides (HDPs) play a crucial role in the innate immune response and can target and disrupt the membranes of various pathogenic cells. By exploring the interaction between HDPs and membrane models using molecular dynamics (MD) simulations, valuable qualitative and quantitative information can be obtained. SuPepMem is an open-access database that provides MD simulations of different peptides interacting with membrane models, offering potential insights for designing therapeutic peptides.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Daniel Conde, Pablo F. Garrido, Martin Calvelo, Angel Pineiro, Rebeca Garcia-Fandino
Summary: This article investigates the behavior of self-assembled cyclic peptide nanotubes using molecular dynamics simulations and compares the performance of four different classical force fields in simulating these highly constrained peptides. Two methods to slow down the fastest degrees of freedom are also tested to improve simulation efficiency, and subtle differences are observed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Alexandre Blanco-Gonzalez, Angel Pineiro, Rebeca Garcia-Fandino
Summary: This article discusses the hierarchical structure of membrane models and defines different levels of structure. By analyzing lipid composition, interaction between layers, the existence and interaction of domains caused by lipid behavior, and the perturbation of lipid organization around macromolecules embedded in the membrane, primary, secondary, tertiary, and quaternary structures are defined respectively. Molecular Dynamics simulations are used to support this proposal.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Franck Bertorelle, K. David Wegner, Martina Peric Bakulic, Hussein Fakhouri, Clothilde Comby-Zerbino, Amin Sagar, Pau Bernado, Ute Resch-Genger, Vlasta Bonacic-Koutecky, Xavier Le Guevel, Rodolphe Antoine
Summary: Atomically precise gold nanoclusters with molecule-like properties and outstanding photoluminescence (PL) are highly attractive for selective biomolecule labeling in biological mechanism investigations. In this study, a simple method to incorporate a preformed Au-25 nanocluster into bovine serum albumin (BSA) protein was reported. The combination of small-angle X-ray scattering and molecular modeling successfully localized a single Au-25 within the protein to a cysteine residue on the gold nanocluster surface. Attaching Au-25 to BSA significantly modified the PL properties, resulting in enhancement and a redshift in the second near-infrared window. This research paves the way for the design of selective sensitive probes using a ligand-based strategy for optical detection of biomolecules in a cellular environment by live imaging.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Fabian Suarez-Leston, Pablo F. Garrido, Angel Pineiro
Summary: By performing molecular dynamics simulations on membranes based on cyclodextrin complexes, it was found that the structure, interactions, and permeability of the membranes to water and ions can be tuned by altering different factors. These findings provide new insights for the design of new functional capsules and applications based on cyclodextrin complexes.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Education & Educational Research
Santiago Delgado-Rodriguez, Silvia Carrascal Dominguez, Rebeca Garcia-Fandino
Summary: The main objective of this study is to design and validate an educational methodological model using augmented reality (AR) to enhance learning in secondary education science subjects. The research consisted of quantitative studies, including an exploratory study, a performance study divided into three cases, and an attitudinal study, as well as a qualitative study on teacher training. The findings provide empirical evidence for the effectiveness of the proposed model in explaining key concepts, improving motivation and acceptance of AR technology, and highlighting the need for teacher training in creating and using AR educational resources and digital evaluation systems.
JOURNAL OF NEW APPROACHES IN EDUCATIONAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nuria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that forms two different i-motif structures depending on pH and temperature. At neutral pH, the major structure is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated i-motif structure with C:C+ base pairs and G:T:G:T tetrads is observed. Molecular dynamics calculations showed that the conformational transition between the two structures is driven by the protonation state of key cytosines. This study reveals the pH-dependent plasticity and conformational switch of i-motif structures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Aleix Tarres-Sole, Federica Battistini, Joachim M. Gerhold, Olivier Pietrement, Belen Martinez-Garcia, Elena Ruiz-Lopez, Sebastien Lyonnais, Pau Bernado, Joaquim Roca, Modesto Orozco, Eric Le Cam, Juhan Sedman, Maria Sola
Summary: A new mechanism of mitochondrial DNA compaction was discovered, in which the Gcf1p protein in Candida albicans utilizes its multiple domains to connect co-aligned DNA segments without altering DNA topology.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Chemistry, Medicinal
Alexandre Blanco-Gonzalez, Alfonso Cabezon, Alejandro Seco-Gonzalez, Daniel Conde-Torres, Paula Antelo-Riveiro, Angel Pineiro, Rebeca Garcia-Fandino
Summary: Artificial intelligence (AI) has the potential to revolutionize the drug discovery process, offering improved efficiency, accuracy, and speed. However, successful application of AI relies on high-quality data availability, addressing ethical concerns, and recognizing AI limitations. This review examines the benefits, challenges, and drawbacks of AI in drug discovery, and proposes strategies to overcome obstacles. Data augmentation, explainable AI, AI integration with traditional methods, and potential advantages in pharmaceutical research are discussed.
Article
Biochemistry & Molecular Biology
Carlos A. Elena-Real, Annika Urbanek, Lionel Imbert, Anna Morato, Aurelie Fournet, Frederic Allemand, Nathalie Sibille, Jerome Boisbouvier, Pau Bernado
Summary: A strategy for efficiently assigning frequencies to individual nuclei in large biomolecular machines and repetitive proteins using in vitro protein expression is presented. The approach was demonstrated to be applicable for NMR assignment in four proteins by introducing isotopically labeled alanines. The labeling method enabled unambiguous assignments in large protein assemblies and revealed the correlation between helical stability and homorepeat length in Phox2B. Selectively introducing alanines with distinct labeling patterns proves to be a powerful tool for studying challenging biomolecular systems.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Medicinal
Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
Summary: The properties of DNA duplex have been accurately described using molecular dynamics simulations, but there lacks equivalent simulations for RNA duplex which is usually represented as a rigid rod. In this study, a massive simulation effort was conducted to derive the properties of RNA duplex and a simplified model for long RNA duplexes. Despite high chemical similarity, the local and global elastic properties of DNA and RNA duplexes are significantly different. Statement about the relative flexibility or stability of both polymers is meaningless and a detailed description depending on the sequence and deformation type should be used.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Israel Serrano-Chacon, Bartomeu Mir, Lorenzo Cupellini, Francesco Colizzi, Modesto Orozco, Nu'ria Escaja, Carlos Gonzalez
Summary: We studied a DNA oligonucleotide that can form two different i-motif structures, with their stability depending on pH and temperature. The structure at neutral pH is stabilized by C:C+ base pairs and G:C:G:C tetrads. At pH 5, a more elongated structure consisting of C:C+ base pairs and G:T:G:T tetrads is observed. The transition between these two structures is driven by the protonation state of key cytosines.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Juan Aranda, Milosz Wieczor, Montserrat Terrazas, Isabelle Brun-Heath, Modesto Orozco
Summary: We used molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to elucidate the replication mechanism of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Our findings showed that the viral RdRp is highly processive and has a higher catalytic rate of incorporation compared to human RNA Pol II. Furthermore, we observed that remdesivir, an antiviral nucleotide, is incorporated more slowly into the RNA than ATP, suggesting it is not a competitive inhibitor. Overall, this study provides a detailed understanding of the replication mechanism of RdRp.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)