Article
Multidisciplinary Sciences
Felix Wiggers, Samuel Wohl, Artem Dubovetskyi, Gabriel Rosenblum, Wenwei Zheng, Hagen Hofmann
Summary: Intrinsically disordered proteins form dynamic complexes with their ligands, with motions hidden in classical binding kinetics. By directly measuring dynamics in a highly mobile, high-affinity complex, researchers found that the energy landscape of the complex is rugged with small barriers reconciling specificity, high affinity, and extreme disorder. Single-molecule experiments and molecular simulations provide high resolution in space and time for resolving these motions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Ulrich Sternberg, Raiker Witter
Summary: In this study, molecular dynamics simulations with orientational tensorial constraints (MDOC) were used to investigate the flexibility of strychnine. The results revealed the population of ring conformers and validated the related nuclear magnetic resonance parameters. This provides new insights into the structure and properties of strychnine.
Article
Chemistry, Multidisciplinary
Gang Huang, Aderik Voorspoels, Roderick Corstiaan Abraham Versloot, Nieck Jordy van der Heide, Enrico Carlon, Kherim Willems, Giovanni Maglia
Summary: Real-time identification of protein biomarkers is essential for the development of point-of-care and portable devices. Researchers have used a biological nanopore, PlyAB, to successfully detect different variants of haemoglobin with high accuracy. The study revealed that haemoglobin occupies two energy minima within the nanopore and its dynamics are influenced by thermal fluctuations, protein charge, and external bias. This method also proved the feasibility of direct discrimination and quantification of haemoglobin from blood using nanopores.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Brataraj Ghosh, Neelanjana Sengupta
Summary: This study reveals the impact of glucose as a molecular crowder on the solvent environment around protein surfaces in folded and intrinsically disordered states, showing differences in structural responses between the two states and the influence of glucose-induced crowding on hydration layers.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
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, Physical
Surya Pratap S. Deopa, Shivprasad Patil
Summary: The advent of atomic force microscopy and optical tweezers introduced single molecule force spectroscopy, which measures the response of a single protein or macromolecule to external mechanical perturbations. Controlled forces are applied to measure unfolding force distribution and unfolding time distribution. Efforts were made to measure the elastic and viscous response of a single protein domain through sinusoidal forces, and a new promising method reported the viscoelasticity of a folded protein and its implications for protein dynamics and structural flexibility.
Article
Chemistry, Multidisciplinary
Gyeong Hee Ryu, Gang Seob Jung, Hyoju Park, Ren-Jie Chang, Jamie H. Warner
Summary: This study investigates the impact of triangular nanovoids in 2D materials on material properties, revealing the atomistic mechanics of folding in WS2 monolayers with statistical preferences under geometric conditions. It is found that loading directions and interlayer friction interact with WS2 lattice's crack preference, influencing the deformation and fracture pattern of the material.
Article
Chemistry, Physical
Khatereh Azizi, Alessandro Laio, Ali Hassanali
Summary: Through advanced data analysis techniques, researchers characterized the shape of voids surrounding model polymers in water. The voids were found to be rough even when the polymer is folded, with branches extending over 1 nm away. When the voids surround particles with a radius similar to 1 nm, they start to resemble the quasispherical shape predicted by dewetting theory, providing insights into vapor-like interfaces underlying dewetting transitions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Unmesh D. Chowdhury, B. L. Bhargava
Summary: The study examines the conformational and dynamical changes of Aβ monomers in coordination with Zn2+ ions using all-atom molecular dynamics simulations. The presence of Zn2+ ions leads to differential intra-peptide interactions and shifts in hydrogen bonding, resulting in structural and dynamical variations in Aβ monomers. The transition from an alpha-helix dominated structure to an unfolded coil structure highlights the impact of Zn2+ ions on Aβ monomers under fibrillation-like conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Materials Science, Multidisciplinary
Shaoyu Zhao, Yingyan Zhang, Jie Yang, Sritawat Kitipornchai
Summary: A folded graphene reinforced copper nanocomposite has been developed, overcoming the conflict between toughness and strength. The mechanical properties of the nanocomposite can be effectively tuned by pre-strain, opening up possibilities for developing tough and strong metal nanocomposites.
JOURNAL OF MATERIALS SCIENCE & TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bridget-K. Kawamala, Ravinder Abrol
Summary: In this study, the folding stability of helical structures in membrane proteins of different sizes was investigated using structural bioinformatics. The results suggest that the membrane-water interface may serve as a dominant holding vestibule during the release of membrane helices. This provides a new model for membrane protein folding and supports the critical role of the membrane-water interface observed in previous studies.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kirill Sergeevich Nikolsky, Liudmila Ivanovna Kulikova, Denis Vitalievich Petrovskiy, Vladimir Removich Rudnev, Tatiana Vladimirovna Butkova, Kristina Akhmedovna Malsagova, Arthur Tigranovich Kopylov, Anna Leonidovna Kaysheva
Summary: In this study, we investigated the autonomous stability of three-helix bundle and SH3-type barrels outside the protein environment. Through molecular experiments and comparative analysis, we demonstrated the potential for reducing computational time and improving performance without significant loss of information.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Jialin Liu, Ning Hu, Cheuk Lun Chow, Denvid Lau
Summary: A classical molecular dynamics simulation was conducted to study the unfolding behavior of self-folded boron nitride nanosheets (BNNSs) in cementitious composites. The study revealed that the unfolding of BNNSs occurs at the weaker interlayer interface, as compared to the BNNS-tobermorite interface under tensile and shear deformation. The presence of mechanical interlocking and hydrogen bonds between BNNSs and tobermorite contributes to a robust interfacial interaction. The atomistic scale reinforcement of self-folded BNNSs improves the ductility of cementitious composites.
APPLIED SURFACE SCIENCE
(2022)
Article
Chemistry, Applied
Xuan Feng, Fan Li, Mingming Ding, Ran Zhang, Tongfei Shi, Wei Jiang
Summary: The study using molecular dynamic simulation reveals the multi-chain conformational behavior of short curdlan, showing that the right-handed triple helix is the most stable conformation in aqueous solutions and is temperature sensitive. A critical value of 6 is found to connect the formation of triple helix with the chain length.
CARBOHYDRATE POLYMERS
(2021)
Article
Chemistry, Multidisciplinary
Mohammad Hassan Khatami, William Barber, Hendrick W. de Haan
Summary: Amylose chains form helix-like structures with imperfect H-bond patterns in water, despite the instability of perfectly H-bonded helices in pure water. Molecular dynamics simulations reveal short and long time helix-breaking mechanisms such as band-flips and kinks in the chain. Defining imperfect helices geometrically offers new insight into the secondary structure of single amylose chains.
Article
Chemistry, Multidisciplinary
Francesco Milanesi, Luca Unione, Ana Arda, Cristina Nativi, Jesus Jimenez-Barbero, Stefano Roelens, Oscar Francesconi
Summary: Glycomics research has revealed the essential role of carbohydrates in biological systems and the importance of chemical tools in studying glycan function. While biomimetic receptors can selectively bind to simple saccharides, this study demonstrates the unprecedented recognition of a complex glycopeptide by a biomimetic receptor. The receptor shows high affinity for the core disaccharide of the N-glycan and has the potential for versatile applications in glycoscience.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Marta G. Lete, Antonio Franconetti, Sara Bertuzzi, Sandra Delgado, Mikel Azkargorta, Felix Elortza, Oscar Millet, Gonzalo Jimenez-Oses, Ana Arda, Jesus Jimenez-Barbero
Summary: Fluorine (F-19) incorporation into lectins has allowed monitoring of carbohydrate binding through NMR spectroscopy. Galectin-3 (Gal3) and Galectin-8 (Gal8) with one and two carbohydrate recognition domains (CRDs), respectively, were chosen. The presence of fluorine did not significantly affect glycan binding affinity, and allowed differentiation of binding events at different sites within the same lectin.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Ana Pozo-Rodriguez, Juan A. A. Mendez-Liter, Rocio Garcia-Villalba, David Beltran, Eva Calvino, Andres G. Santana, Laura I. I. De Eugenio, Francisco Javier Canada, Alicia Prieto, Jorge Barriuso, Francisco A. A. Tomas-Barberan, Maria Jesus Martinez
Summary: Resveratrol was glycosylated by using rXynSOS-E236G glycosynthase, resulting in the production of 3-O-beta-D-xylobiosyl resveratrol as the major product. Response surface methodology was used to optimize the reaction, yielding 35% of 3-O-beta-D-xylobiosyl resveratrol. Xylobiosylation decreased the antioxidant capacity of resveratrol, but significantly improved its solubility for improved delivery and transit to the colon.
Article
Nanoscience & Nanotechnology
Anna Blasi-Romero, Molly Angstrom, Antonio Franconetti, Taj Muhammad, Jesus Jimenez-Barbero, Ulf Goransson, Carlos Palo-Nieto, Natalia Ferraz
Summary: This study combines the wound-healing properties of KR-12 peptide with wood-derived cellulose nanofibrils (CNFs) to create bioactive materials for treating chronic wounds. Different coupling chemistries were used to covalently attach KR-12 derivatives onto CNFs, and the bioactivity of KR12-CNF conjugates was evaluated in terms of antibacterial activities and anti-inflammatory effects. The results showed that thiol-ene chemistry produced the most bioactive conjugates, attributed to favorable peptide conformation and accessibility. This study advances the development of CNF-based materials for chronic wound care and provides insights into the effect of conjugation chemistry on the bioactivity of host defense peptides.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Organic
Matteo A. . Tallarida, Fabrizio Olivito, Claudio D. Navo, Vincenzo Algieri, Antonio Jiritano, Paola Costanzo, Ana Poveda, Maria J. Moure, Jesus Jimenez-Barbero, Loredana Maiuolo, Gonzalo Jimenez-Oses, Antonio De Nino
Summary: The synthesis of polysubstituted spirocyclopropyl oxindoles using rare-earth metal (REM) salts, particularly Sc(OTf)3, was achieved with high diastereoselectivity (<= 94:6:0:0) in a multicomponent reaction. Density functional theory calculations on the model reaction confirmed the observed selectivity and demonstrated that the coordinating capabilities and oxophilicity of the metal played a crucial role in inducing the formation of one main diastereoisomer.
Article
Biochemistry & Molecular Biology
Hans-Christian Siebert, Thomas Eckert, Anirban Bhunia, Nele Klatte, Marzieh Mohri, Simone Siebert, Anna Kozarova, John W. Hudson, Ruiyan Zhang, Ning Zhang, Lan Li, Konstantinos Gousias, Dimitrios Kanakis, Mingdi Yan, Jesus Jimenez-Barbero, Tibor Kozar, Nikolay E. Nifantiev, Christian Vollmer, Timo Brandenburger, Detlef Kindgen-Milles, Thomas Haak, Athanasios K. Petridis
Summary: The global outbreak of SARS-CoV-2/COVID-19 has provided an opportunity and challenge to accumulate a large amount of biomedical data and test new concepts and strategies to combat the pandemic. This study correlated clinical biomedical data with structural biology and biophysical data to evaluate new diagnostic and therapeutic approaches against SARS-CoV-2. The methods used were effective in identifying potential peptide sequences and carbohydrate moieties to protect the blood-brain barrier and develop new therapeutic approaches against long-COVID symptoms.
Article
Chemistry, Multidisciplinary
Angeles Canales, Javier Sastre, Jose M. Orduna, Cindy M. Spruit, Javier Perez-Castells, Gema Dominguez, Kim M. Bouwman, Roosmarijn van der Woude, Francisco Javier Canada, Corwin M. Nycholat, James C. Paulson, Geert-Jan Boons, Jesus Jimenez-Barbero, Robert P. de Vries
Summary: Influenza virus infection remains a threat to human health due to the drifting of viral hemagglutinins, which evade infection and vaccine-induced antibody responses. Recent H3N2 and pandemic H1 viruses specifically recognize glycan structures containing at least three N-acetyllactosamine units. This study characterizes the glycan specificity of H1 variants, including the one responsible for the 2009 pandemic outbreak, and investigates the preference for tri-LacNAc motifs in human-type receptor-adapted viruses using glycan arrays, tissue binding analyses, and nuclear magnetic resonance experiments.
Article
Chemistry, Multidisciplinary
Giulio Fittolani, Theodore Tyrikos-Ergas, Ana Poveda, Yang Yu, Nishu Yadav, Peter H. Seeberger, Jesus Jimenez-Barbero, Martina Delbianco
Summary: This article introduces a synthetic glycan molecule that adopts a stable secondary structure not found in nature, called a glycan hairpin. The synthetic glycan is created by combining natural glycan motifs and utilizing unconventional hydrogen bonds and hydrophobic interactions. Nuclear magnetic resonance conformational analysis and long-range inter-residue nuclear Overhauser effects confirm the folded conformation of the synthetic glycan hairpin. The ability to control the 3D shape of glycans has the potential to provide more foldamer scaffolds with programmable properties and functions.
Article
Biochemistry & Molecular Biology
Boris Schnider, Yacine M'Rad, Jalaa el Ahmadie, Alexandre G. de Brevern, Anne Imberty, Frederique Lisacek
Summary: The UniLectin portal is a website that centralizes curated and predicted data on lectins and provides support for the study of lectomes. The latest update includes new modules and details our knowledge of the human lectome, featuring 215 unevenly characterized lectins, with a focus on structural information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Jana Tomisch, Vincent Busse, Francesca Rosato, Olga N. Makshakova, Pavel Salavei, Anna-Sophia Kittel, Emilie Gillon, Levin Lataster, Anne Imberty, Ana Valeria Melendez, Winfried Roemer
Summary: The study demonstrates the selective targeting of Gb3-positive cancer cells using the StxB-scFv UCHT1 lectibody, which induces a killing effect of up to 80% on Gb3-overexpressing cancer cells in vitro. This highlights the potential of lectibodies and lectins in general for enhancing the efficacy of established cancer treatments through immunotherapeutic approaches.
Review
Chemistry, Multidisciplinary
Jon I. Quintana, Unai Atxabal, Luca Unione, Ana Arda, Jesus Jimenez-Barbero
Summary: Nuclear Magnetic Resonance (NMR) is widely used to study glycan-protein molecular recognition events, providing qualitative and quantitative information at different levels of resolution and complexity. However, the weak affinity of lectin-sugar interactions is overcome by multivalency in biological processes. The application of NMR methods to monitor multivalent lectin-glycan interactions is challenging due to the disappearance of NMR signals when large macromolecular complexes are formed.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Multidisciplinary
Antonio De Nicola, Costanza Montis, Greta Donati, Antonio Molinaro, Alba Silipo, Arianna Balestri, Debora Berti, Flaviana Di Lorenzo, You-Liang Zhu, Giuseppe Milano
Summary: By combining simulations and experiments, the complex supramolecular structures of lipopolysaccharides (LPS) and lipid A at low hydration levels were revealed, uncovering the presence of a nano-compartmentalized phase composed of liposomes of variable size and shape, which can be utilized in synthetic biological applications.
Article
Biochemistry & Molecular Biology
Katherine F. Warfel, Eugenie Laigre, Sarah E. Sobol, Emilie Gillon, Annabelle Varrot, Olivier Renaudet, Jerome Dejeu, Michael C. Jewett, Anne Imberty
Summary: Researchers have developed a new method for efficient expression of multivalent, disulfide bond-rich, rhamnose-binding lectins. This method allows for rapid expression and characterization without purification. The workflow enables determination of lectin substrate specificity and binding affinity. This method facilitates high-throughput expression, screening, and characterization of new and engineered multivalent lectins for synthetic glycobiology applications.
Article
Chemistry, Multidisciplinary
Carlo Pifferi, Leire Aguinagalde, Ane Ruiz-de-Angulo, Nagore Sacristan, Priscila Tonon Baschirotto, Ana Poveda, Jesus Jimenez-Barbero, Juan Anguita, Alberto Fernandez-Tejada
Summary: The overexpression of aberrantly glycosylated tumor-associated mucin-1 (TA-MUC1) in human cancers makes it a major target for the development of anticancer vaccines derived from synthetic MUC1-(glyco)peptide antigens. However, glycopeptide-based subunit vaccines are weakly immunogenic, requiring adjuvants and/or additional immunopotentiating approaches to generate optimal immune responses.
Article
Immunology
Leticia Martin-Cruz, Marcos Vinuela, Ioanna Kalograiaki, Alba Angelina, Paola Oquist-Phillips, Irene Real-Arevalo, Francisco Javier Canada, Jose Ignacio Tudela, Luis Molto, Jesus Moreno-Sierra, Jose Luis Subiza, Oscar Palomares
Summary: This study reveals novel molecular mechanisms by which heparan sulfate-related structures associated with tumor cells promote the generation of functional Tregs in cancer. Furthermore, the presence of a circulating human Ca10 counterpart (Ca10H) in cancer patients and its correlation with tumor size and metastasis suggests important clinical implications in cancer treatment.
CELLULAR & MOLECULAR IMMUNOLOGY
(2023)