Article
Chemistry, Multidisciplinary
Jiahui Wu, Nina Svensen, Wenjiao Song, Hyaeyeong Kim, Sulei Zhang, Xing Li, Samie R. Jaffrey
Summary: DNA and RNA can self-assemble into various structures, and there are methods available to achieve RNA self-assembly in cells. The use of dimeric aptamers allows the creation of RNA and RNA-protein assemblies in cells. These studies provide an approach for inducing RNA self-assembly, demonstrate that proteins can be recruited to RNA assemblies to genetically encode intracellular RNA-protein assemblies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Applied
Mi Zhang, Liuping Fan, Yuanfa Liu, Jinwei Li
Summary: The objective of this study was to effectively migrate gallic acid (GA) to the oil-water interface and inhibit lipid oxidation in water-in-oil (W/O) emulsions. The conjugate of GA and a natural emulsifier (pea protein isolate, PPI) showed superior binding efficiency and stability. The conjugate exhibited enhanced functional properties, including antioxidant and interfacial properties. It also improved the physical stability and oxidative stability of the W/O emulsion. These findings have important implications for interface engineering and improving the oxidative stability of W/O emulsions.
FOOD HYDROCOLLOIDS
(2023)
Article
Biochemistry & Molecular Biology
Andrew J. Lee, Masayuki Endo, Jamie K. Hobbs, A. Giles Davies, Christoph Walti
Summary: The study used DNA nanostructure-augmented high-speed AFM to directly observe the RecA-orchestrated alignment of homologous DNA strands, revealing transient sampling of micro-homology by RecA during the search for sequence alignment. These transient interactions are early steps in the search for sequence homology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Arumay Pal, Pinak Chakrabarti, Sucharita Dey
Summary: This article introduces a web tool called ProDFace, which characterizes the binding region of a protein-DNA complex. The tool uses multiple parameters, including amino acid propensity, hydrogen bond donor capacity, sequence conservation, and geometry to predict and analyze protein-DNA binding sites.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Glen. E. E. Kellogg, Anna Marabotti, Francesca Spyrakis, Andrea Mozzarelli
Summary: The aim of computational biochemists, medicinal chemists, and structural biologists has been to develop tools that can decode the interaction between molecules, resulting in a variety of complex biomolecular assemblies. The software application HINT, based on LogP scores, has been successful in mimicking the interactions among various biomolecules and providing insights into their energetics. The extensive collaboration between Abraham, Kellogg, and the University of Parma has played a crucial role in testing HINT for different biomolecular interactions.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Biochemical Research Methods
Lingqi Qiu, Michael D. Psimos, R. Graham Cooks
Summary: This study reports the accelerated oxidation of aromatic sulfones in microdroplets, which shows a high reaction rate and regioselectivity. Experimental data suggest that the water radical cation derived from traces of water in the solvent acts as the oxidant.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Juliette Martin, Elisa Frezza
Summary: Protein-protein interactions are essential for protein functions, and understanding the 3D structures of protein-protein complexes provides valuable information for their functions. Molecular dynamics simulations revealed rearrangements of interfaces and highlighted the role of water molecules in estimating interaction strength.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Deepika Kagra, Raman Jangra, Purshotam Sharma
Summary: A nonredundant dataset of around 300 high-resolution X-ray structures of RNA:protein complexes was analyzed for hydrogen bonds, identifying 17100 contacts that were classified based on various criteria. Comparison with DNA:protein complexes revealed differences in hydrogen bonding due to the absence of 2'-OH group in DNA. The search for stable base:amino acid pairs yielded 37 unique pairs that may act as well-defined RNA:protein interaction motifs.
Article
Environmental Sciences
Jeison Manuel Arroyave, Marcelo Avena, Wenfeng Tan, Mingxia Wang
Summary: This article investigates the adsorption-desorption kinetics of phosphate on goethite using ATR-FTIR spectroscopy, providing new insights and experimental methods for understanding the behavior of pollutants with phosphonic or phosphinic moieties in the environment.
Article
Biochemistry & Molecular Biology
Yaqin Yang, Haobo Jin, Yongguo Jin, Guofeng Jin, Long Sheng
Summary: This study investigated the impact of varied pH treatments on the structural, emulsification, and interfacial adsorption properties of egg yolk. The solubility of egg yolk proteins decreased and then increased in response to pH changes, with a minimum value (41.95 %) observed at pH 5.0. The alkaline condition (pH 9.0) significantly impacted the secondary/tertiary structure of egg yolk, with the yolk solution displaying the lowest surface tension value (15.98 mN/m). Emulsion stability was found to be optimal when egg yolk was used as the stabilizer at pH 9.0, which corresponded to the more flexible diastolic structure, smaller emulsion droplets, increased viscoelasticity, and enhanced resistance to creaming.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Shanshan Yang, Xiao Zhao, Yi-Hsien Lu, Edward S. Barnard, Peidong Yang, Artem Baskin, John W. Lawson, David Prendergast, Miquel Salmeron
Summary: The structure of interfacial water near suspended graphene electrodes in contact with Na2SO4, NH4Cl, and (NH)(2)SO4 solutions has been investigated using confocal Raman spectroscopy, sum frequency vibrational spectroscopy, and Kelvin probe force microscopy. The results showed that SO42- anions preferentially accumulate near the interface at an open circuit potential, creating an electrical field that orients water molecules below the interface. Positive voltages further increased the degree of water molecule orientation and the strength of the electrical double layer, while negative voltages only affected the intensity and frequency of certain water peaks.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Rongfu Zhang, Timothy A. Cross, Xinhua Peng, Riqiang Fu
Summary: Understanding the dynamics and structure of water is crucial in biological systems. Directly probing the interfacial water in hydrated phospholipids is challenging, but a novel solid-state NMR technique was developed to successfully observe two distinct water species in the headgroup region of hydrated lipid bilayers. These findings provide an opportunity to study water dynamics on a millisecond or slower timescale in biomacromolecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Zilong Guo, Haiyan Hong, Hao Sun, Xiaofeng Zhang, Chen-Xu Wu, Bing Li, Yi Cao, Hu Chen
Summary: Single molecule force spectroscopy is a powerful tool for studying protein folding dynamics and other mechanobiological processes, but high force precision does not guarantee high force accuracy. The challenge in magnetic tweezers lies in accurately determining applied forces due to calibration uncertainties.
Article
Agriculture, Multidisciplinary
Lei Zhou, Ruyu Zhang, Jian Zhang, Yantao Yin, Lanlan Wei, Lujuan Xing, Wangang Zhang
Summary: This study compared the effects of ultrasound treatment on myofibrillar protein (MP) with and without the presence of soybean oil. The results showed that ultrasound treatment effectively reduced emulsion droplet size, increased zeta potential, and increased protein oxidation and disulfide bond formation in the MP-soybean oil system. The ultrasound treatment also resulted in a higher level of myosin and actin content at the soybean oil interface and accelerated the separation of myosin light chain from myosin in the MP-soybean oil system.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Multidisciplinary Sciences
Igor Orlov, Stephane Roche, Sandrine Brasiles, Natalya Lukoyanova, Marie-Christine Vaney, Paulo Tavares, Elena Orlova
Summary: The authors report the atomic structure and assembly mechanism of the phage SPP1 portal DNA gatekeeper, as well as identify evolutionary breakpoints between different tailed bacteriophages morphotypes and herpesviruses.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jaydeep Belapure, Marija Sorokina, Panagiotis L. Kastritis
Summary: Understanding protein-protein interactions is essential for understanding the function of molecular systems. We developed a Monte Carlo method-based algorithm, IRAA, to calculate the buried surface area (BSA) of a given complex. By applying IRAA to the ACE2 and SARS-CoV-2 Spike protein complex, we found a broader distribution of BSA compared to using only bound structures, suggesting important implications for biomolecular recognition.
Article
Biochemistry & Molecular Biology
Yong Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant G. Honavar
Summary: Protein-protein interactions are crucial for biological function, and understanding their three-dimensional structures is essential. Computational docking is a useful alternative to experimental approaches for determining these structures, but the scoring problem still needs improvement. MetaScore is a machine-learning-based approach that uses protein-protein interfacial features to score docked conformations. It consistently outperforms traditional scoring functions and an ensemble method combining MetaScore with traditional functions achieves even better performance. Machine learning and ensemble methods can improve the accuracy of scoring protein-protein interactions.
Article
Biochemistry & Molecular Biology
Yue Zhou, Jawhar H. Syed, Dmitry A. Semchonok, Edward Wright, Fotis L. Kyrilis, Farzad Hamdi, Panagiotis L. Kastritis, Barry D. Bruce, Todd B. Reynolds
Summary: Phosphatidylserine (PS) synthase encoded by the CHO1 gene is a potential drug target for antifungals against systemic candidiasis. This study investigated methods to solubilize and purify Cho1 protein, which has a transmembrane nature. The results showed that digitonin or DDM were the most effective detergents for solubilization, and protein purification was achieved through affinity chromatography and TEV protease treatment. The purified Cho1 protein exhibited optimal enzyme activity under specific conditions of temperature, pH, and manganese and detergent concentrations, which is important for substrate determination and drug screening.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Sotiria Demisli, Eleni Galani, Maria Goulielmaki, Fotios L. Kyrilis, Tanja Llic, Farzad Hamdi, Milkica Crevar, Panagiotis L. Kastritis, Vasiliki Pletsa, Frederic Nallet, Snezana Savic, Aristotelis Xenakis, Vassiliki Papadimitriou
Summary: This study verifies that lipophilic cannabidiol can be dissolved in oil-in-water nanoemulsions and impregnated into chitosan hydrogels to facilitate its release. The effects of carrier structure on the release and toxicity of the systems were compared through structural and biological studies.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Martin Stroet, Bertrand Caron, Martin S. S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen M. M. Visscher, Josef Holownia, Callum Macfarlane, Brian J. J. Bennion, Svetlana Gelpi-Dominguez, Felice C. C. Lightstone, Tijs van der Storm, Daan P. P. Geerke, Alan E. E. Mark, Gunnar W. W. Klau
Summary: OFraMP is an online tool that assigns atomic interaction parameters to large molecules by matching sub-fragments within the target molecule to equivalent sub-fragments within the ATB database. It uses a novel hierarchical matching procedure and allows users to manually alter interaction parameters and automate the submission of missing substructures to the ATB. The utility of OFraMP is demonstrated using the anti-cancer agent paclitaxel and a dendrimer used in organic semiconductor devices.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2023)
Article
Plant Sciences
Tanja Zahn, Zihao Zhu, Niklas Ritoff, Jonathan Krapf, Astrid Junker, Thomas Altmann, Thomas Schmutzer, Christian Tueting, Panagiotis L. Kastritis, Steve Babben, Marcel Quint, Klaus Pillen, Andreas Maurer
Summary: Novel exotic ELF3 alleles have been discovered and shown to be associated with agronomic traits in barley. These findings suggest a central role for ELF3 in barley adaptation.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Toni Traeger, Panagiotis L. Kastritis
Summary: Integration of experimental and computational methods is crucial for understanding PPIs in their cellular context. Rappsilber and colleagues identified bacterial PPIs using a combination of whole-cell crosslinking, co-fractionation mass spectrometry, data mining, and AI-based structure prediction. This innovative approach reveals in-cell PPI architecture lost upon cell lysis, making it useful for genetically intractable organisms.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Siri C. van Keulen, Alexandre M. J. J. Bonvin
Summary: The increase in protein sequences and structures has allowed for the use of bioinformatics approaches to predict residue-residue interactions. Multiple sequence alignments are commonly used in contact predictions but often produce false positives, which can affect the accuracy of biomolecular complex structure predictions. A tool called DisVis, originally developed for mass spectrometry data, is investigated for its potential to improve the precision of co-evolution predicted contacts. Results show that integrating DisVis with docking software HADDOCK can enhance the quality of docking predictions for low precision contact data.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Christian Tueting, Lisa Schmidt, Ioannis Skalidis, Andrea Sinz, Panagiotis L. Kastritis
Summary: In this study, protein communities and inter-protein interactions were identified in a yeast native cell extract using proteomics analysis and cryogenic electron microscopy. By combining AI-guided protein structure prediction, a density was successfully assigned to the yeast fatty acid synthase complex.
Article
Multidisciplinary Sciences
Alessio Di Ianni, Christian Tueting, Marc Kipping, Christian H. Ihling, Janett Koeppen, Claudio Iacobucci, Christian Arlt, Panagiotis L. Kastritis, Andrea Sinz
Summary: This study employed a combination of structural mass spectrometry (MS) and computational modeling to explore the structural and functional roles of p53's C-terminal region in full-length, wild-type human p53 tetramer and its importance for DNA binding. The results show no major conformational differences in p53 between DNA-bound and DNA-free states, but a significant compaction of p53's C-terminal region, supporting the proposed mechanism of unspecific DNA binding to the C-terminal region prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in this integrative approach are envisioned to serve as a general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs).
SCIENTIFIC REPORTS
(2023)
Article
Biology
Ioannis Skalidis, Fotis L. Kyrilis, Christian Tueting, Farzad Hamdi, Toni K. Traeger, Jaydeep Belapure, Gerd Hause, Marta Fratini, Francis J. O'Reilly, Ingo Heilmann, Juri Rappsilber, Panagiotis L. Kastritis
Summary: This study reveals the organization, 3D architecture, and molecular function of a thermophilic, eukaryotic, native OGDHc in its active state. The results demonstrate various structural adaptations of the OGDHc core and the presence of a flexible subunit connecting E2o and E3. This research provides a blueprint for structure-function studies of complex mixtures of medical and biotechnological value.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Felix van der Krift, Dick W. Zijlmans, Rhythm Shukla, Ali Javed, Panagiotis Koukos, Laura L. E. Schwarz, Elpetra P. M. Timmermans-Sprang, Peter E. M. Maas, Digvijay Gahtory, Maurits van den Nieuwboer, Jan A. Mol, Ger J. Strous, Alexandre M. J. J. Bonvin, Mario van der Stelt, Edwin J. A. Veldhuizen, Markus Weingarth, Michiel Vermeulen, Judith Klumperman, Madelon M. Maurice
Summary: Cancer cells rely heavily on the folate cycle for their metabolic needs, but chemotherapy drugs like methotrexate and 5-fluorouracil disrupt this cycle. However, therapy-induced resistance is a problem, and the lack of FPGS is associated with resistance to these drugs. The development of alternative antifolate drugs can selectively target FPGS-deficient cells during chemotherapy, taking advantage of their vulnerability.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Ahmed H. Hassan, Christian Ihling, Claudio Iacobucci, Panagiotis L. Kastritis, Andrea Sinz, Tobias Kruse
Summary: The trace element molybdenum (Mo) is biologically active within the cell when complexed with the nitrogenase-specific FeMo cofactor or the molybdenum cofactor (Moco). Moco consists of an organic part, molybdopterin (MPT), and an inorganic Mo-center. The molybdenum insertase (Mo-insertase) catalyzes the formation of the Mo-center, composed of two functional domains, G- and E-domains. In this study, a structural model of the eukaryotic Mo-insertase Cnx1 complex was generated, revealing an asymmetric hexameric complex that allows the active sites of the E- and G-domains to align for efficient catalysis.
Article
Biochemical Research Methods
Manon Reau, Nicolas Renaud, Li C. Xue, Alexandre M. J. J. Bonvin
Summary: DeepRank-GNN is a modular and customizable deep-learning framework that converts protein-protein interfaces into graphs for problem-specific interaction pattern learning. It demonstrates competitive performance in scoring docking poses and discriminating biological and crystal interfaces, with significant improvements in speed and storage requirement compared to DeepRank.
Article
Plant Sciences
Monika Opatikova, Dmitry A. Semchonok, David Kopecny, Petr Ilik, Pavel Pospisil, Iva Ilikova, Pavel Roudnicky, Sanja Cavar Zeljkovic, Petr Tarkowski, Fotis L. Kyrilis, Farzad Hamdi, Panagiotis L. Kastritis, Roman Kouril
Summary: This study presents the structure of photosystem II supercomplex from Picea abies determined by cryo-electron microscopy, revealing the presence of unique features such as the light-harvesting protein Lhcb8 and α-tocopherol molecule with potential physiological function.