Editorial Material
Biochemistry & Molecular Biology
Albertus Viljoen, Yves F. Dufrene
Summary: In this study, Ritzmann et al. use single-molecule force spectroscopy to investigate the mechanical properties of a molecular component, BamA, and how it is affected by an antibiotic. The findings shed light on the impact of antibiotics on Gram-negative outer membrane proteins.
Article
Chemistry, Multidisciplinary
Xingyue Li, Andrew L. Sabol, Patrick J. Salveson, James S. Nowick
Summary: Researchers have developed a new beta-turn template, (delta)MeOrn, which can induce a beta-hairpin conformation in peptides. This template demonstrates superior folding compared to (delta)Orn and is comparable to d-Pro-Gly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Polymer Science
Harry W. Gibson, Mason A. Rouser, Daniel Schoonover
Summary: A new method for synthesizing bottlebrush copolymers is introduced using crown ether-containing polyester and viologen in styrene solution, which allows for control over the structure and composition of the resulting polymers.
Article
Biochemistry & Molecular Biology
Koichi Yamamoto, Satoru Nagatoishi, Ryo Matsunaga, Makoto Nakakido, Daisuke Kuroda, Kouhei Tsumoto
Summary: The beta-hairpin conformation is important for protein-protein interactions. In this study, the molecular recognition of the anti-HigB2 VHH antibody Nb8, which has a beta-hairpin CDR3, was investigated. The results revealed the key positions outside of CDR3 that maintain the structural stability and binding properties of Nb8. These findings will be useful for the design and optimization of single-domain antibodies.
Article
Biochemistry & Molecular Biology
Federico M. Ruiz, Francisco J. Medrano, Anna-Kristin Ludwig, Herbert Kaltner, Nadezhda V. Shilova, Nicolai V. Bovin, Hans-Joachim Gabius, Antonio Romero
Summary: This study presents the first crystallographic information on the N-terminal extension of rat galectin-5, revealing the structured organization around the central Trp77 of the carbohydrate recognition domain. The ligand-bound structure demonstrates a shift in the amino acid alignment, potentially acting as a molecular switch for new contacts in this region.
Article
Materials Science, Characterization & Testing
H. He, Q. Deng, C. X. Wang, J. Li, K. X. Weng, Y. G. Miao
Summary: A methodology was proposed to achieve large strains under intermediate strain rates, with an experimental system constructed based on it. The system includes a striker bar generating continuous stress wave loading and a long polymethylmethacrylate bar as the transmitted bar, allowing for nearly constant amplitude loading stress wave with infinite duration. The measurement capacity was confirmed through loading a thermoplastic polyurethane with maximum strains up to 12% and 65% under different strain rates.
Article
Biotechnology & Applied Microbiology
Hannah C. Hymel, Jeffery C. Anderson, Dong Liu, Ted J. Gauthier, Adam T. Melvin
Summary: Peptide-based PROTACs utilize UPS for proteasomal degradation of undruggable targets, but often suffer from low cell permeability and protease susceptibility. This study demonstrates that a beta-hairpin sequence can replace unstructured peptides sequences as a degron and CPP, facilitating the degradation of Tau protein and increasing the lifetime in cells.
BIOCHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Xue-Yi Sun, Yulong Zhong, Yao-Hua Li, Daniel P. Miller, Sagar Buttan, Xiang-Xiang Wu, Yukun Zhang, Quan Tang, Hong-Wei Tan, Jin Zhu, Rui Liu, Eva Zurek, Zhong-Lin Lu, Bing Gong
Summary: Five hybrid tetrapeptides consisting of a central dipeptide segment and flanked by aromatic gamma-amino acid residues fold into well-defined beta-hairpin conformations. The turn loop in this beta-hairpin motif can accommodate different alpha-amino acid sequences, and the presence of alpha-amino acid side chains enhances the stability of beta-hairpins, except for D-Pro-Gly.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Yajun Zhao, Jin Jung, Kyoko Nozaki
Summary: Polyethylene-poly(methyl acrylate) multiblock copolymers were synthesized using a catalyst system comprised of a cobalt complex and modified methylaluminoxane. The proposed polymerization mechanism involves the self-switching between OMRP and CIP mechanisms. The copolymer structures were confirmed through NMR, TGA/DSC, and SEC analyses.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Cory D. DuPai, Bryan W. Davies, Claus O. Wilke
Summary: The beta hairpin motif is a widely distributed protein structural motif known for its stability and adaptability to various functions. Research revealed that specific amino acid preferences within the structure, particularly in the turn region, depend on subtle dynamics associated with turn length and secondary structure. Broad design principles, such as including specific aspartic acid residues and considering desired secondary structure in selecting residues for the turn region, were established for generating libraries encoding proteins or peptides containing beta hairpin structures.
Article
Chemistry, Multidisciplinary
Yongliang Xia, Pengjun Yuan, Yanping Zhang, Yangyang Sun, Miao Hong
Summary: This study reports the efficient conversion of gamma-valerolactone and its derivatives into sustainable and degradable polythioesters through the establishment of the first isomerization-driven ring-opening polymerizations (IROPs) of corresponding thionolactone intermediates. The development of a new cationic initiator [Et3O](+)[B(C6F5)(4)](-) with high activity, exclusive selectivity, living nature, and broad scope of thionolactones is the key to this success. The study also reveals the complete inversion of configuration during IROP of enantiopure gamma-thionovalerolactone and the formation of a highly crystalline supramolecular stereocomplex.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Ling Mo, Jiang Chen, Chuanbin Cai, Yi Guo, Ling-Hui Zeng, Song Li, Jun Tan
Summary: Recent studies show that A beta oligomers are more important than amyloid plaques in the pathogenesis of Alzheimer's disease. The complexity of A beta makes it challenging to study its structural basis. This study evaluated the amphiphilic property and beta-hairpin structure of A beta monomer, and found that A beta oligomer can alter the activity of two enzymes. Modifications on the hydrophobic region and beta-turn structure of A beta monomer significantly change its impacts on enzyme activities, and these modifications also affect the bonding modes of A beta monomers or oligomers binding to HRP.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Chemistry, Analytical
Ru-Yi Zhang, Shi-Hua Luo, Xiao-Min Lin, Xiu-Mei Hu, Ye Zhang, Xiao-He Zhang, Chang-Meng Wu, Lei Zheng, Qian Wang
Summary: An electrochemical biosensor based on SP-CHA was designed for detection of exosomal miR-181, showing high sensitivity and stability. The method was successfully applied for differentiation of CHD patients from healthy controls.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Alberto Mills, Federico Gago
Summary: This study characterized the different DNA structures involved in the construction of a double-stranded DNA microcircle using model building and molecular dynamics simulations. The core of the nascent dsDNA microcircle was proposed to be a kissing loop involving six base pairs, and the final covalently closed dsDNA microcircle was characterized as possessing two well-defined U-turns.
Article
Chemistry, Multidisciplinary
Shinji Kishimoto, Ayumi Minami, Yoshimitsu Aoki, Yuya Matsubara, Shogo Watanabe, Kenji Watanabe
Summary: Pathogenic fungi of Aspergillus section Fumigati are capable of producing various secondary metabolites. This study reports the isolation of fumimycin and a new compound named lentofuranine from A. lentulus. These compounds were found to be assembled through a nonenzymatic condensation involving a polyketide intermediate from the terrein biosynthetic pathway and a highly reactive azlactone intermediate. The formation of an unusual carbon skeleton is attributed to the reactivity of azlactone.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Endocrinology & Metabolism
Hei Man Fan, Alice L. Mitchell, Elena Bellafante, Saraid McIlvride, Laura Primicheru, Mirko Giorgi, Ivano Eberini, Argyro Syngelaki, Anita Lovgren-Sandblom, Peter Jones, David McCance, Nithya Sukumar, Nishanthi Periyathambi, Yonas Weldeselassie, Katharine F. Hunt, Kypros H. Nicolaides, David Andersson, Stuart Bevan, Paul T. Seed, Gavin A. Bewick, James E. Bowe, Franca Fraternali, Ponnusamy Saravanan, Hanns-Ulrich Marschall, Catherine Williamson
Summary: This study evaluated the role of serum progesterone sulfates in the etiology of gestational diabetes mellitus (GDM). The results showed that concentrations of epiallopregnanolone sulfate (PM5S) were reduced in GDM and in women with higher fasting plasma glucose. PM5S increased glucose-stimulated insulin secretion (GSIS) and this effect was mediated by TRPM3. These findings highlight the importance of progesterone sulfates in the pathogenesis of GDM.
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Immunology
Veerle Somers, Deborah K. Dunn-Walters, Mirjam van der Burg, Judith Fraussen
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Immunology
Samuel Ken-En Gan, Jeremy P. Derrick, Franca Fraternali
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Qiongju Qiu, Giancarlo Abis, Florence Mattingly-Peck, Steven Lynham, Franca Fraternali, Maria R. Conte
Summary: Human soluble epoxide hydrolase (hsEH) is a crucial regulator of epoxy fatty acid metabolism. Inhibiting hsEH can ameliorate various pathological conditions. Previous research focused on finding drugs that directly inhibit the enzyme's activity, but the disappointing results of clinical trials have led to the exploration of alternative approaches. This study reveals that endogenous electrophilic lipids and nitro fatty acids can covalently bind to different sites of hsEH, providing insights for the design of new pharmacological agents.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Immunology
Alexander Stewart, Emma Sinclair, Joseph Chi-Fung Ng, Joselli Silva O'Hare, Audrey Page, Ilaria Serangeli, Christian Margreitter, Federica Orsenigo, Katherine Longman, Cecile Frampas, Catia Costa, Holly-May Lewis, Nora Kasar, Bryan Wu, David Kipling, Peter J. M. Openshaw, Christopher Chiu, J. Kenneth Baillie, Janet T. Scott, Malcolm G. Semple, Melanie J. Bailey, Franca Fraternali, Deborah K. Dunn-Walters
Summary: The heterogeneity of immunoglobulin gene reflects the diversity and focus of the immune response. Detailed analysis of samples from different viral infections reveals common responses and unique characteristics. The characteristics of COVID-19 patients vary with age.
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Alan Brown, Franca Fraternali
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maria-Armineh Tossounian, Maria Baczynska, William Dalton, Charlie Newell, Yilin Ma, Sayoni Das, Jonathan Alexis Semelak, Dario Ariel Estrin, Valeriy Filonenko, Madia Trujillo, Sew Yeu Peak-Chew, Mark Skehel, Franca Fraternali, Christine Orengo, Ivan Gout
Summary: Coenzyme A (CoA) plays a crucial role in metabolism and gene regulation. Recent studies have shown that CoA functions as an important antioxidant by forming a disulfide bond with proteins, called CoAlation. This study identified and classified CoAlated proteins from various organisms under stress conditions, and analyzed the stabilization interactions of CoA segments within the modified cysteines. The findings propose three modes of CoA binding to proteins and provide a comprehensive understanding of CoAlation proteins' functional distribution and CoA-protein stabilization interactions.
Article
Multidisciplinary Sciences
Marius Kausas, Diego Esposito, Katrin Rittinger, Franca Fraternali
Summary: The study uses a combination of small-angle X-ray scattering experiments and molecular dynamics simulations to explore the conformational dynamics of the RBR domain of HOIP, highlighting the importance of interdomain linker flexibility for protein flexibility.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Silvia Crescioli, Isabel Correa, Joseph Ng, Zena N. Willsmore, Roman Laddach, Alicia Chenoweth, Jitesh Chauhan, Ashley Di Meo, Alexander Stewart, Eleni Kalliolia, Elena Alberts, Rebecca Adams, Robert J. Harris, Silvia Mele, Giulia Pellizzari, Anna B. M. Black, Heather J. Bax, Anthony Cheung, Mano Nakamura, Ricarda M. Hoffmann, Manuela Terranova-Barberio, Niwa Ali, Ihor Batruch, Antoninus Soosaipillai, Ioannis Prassas, Antigona Ulndreaj, Miyo K. Chatanaka, Rosamund Nuamah, Shichina Kannambath, Pawan Dhami, Jenny L. C. Geh, Alastair D. MacKenzie Ross, Ciaran Healy, Anita Grigoriadis, David Kipling, Panagiotis Karagiannis, Deborah K. Dunn-Walters, Eleftherios P. Diamandis, Sophia Tsoka, James Spicer, Katie E. Lacy, Franca Fraternali, Sophia N. Karagiannis
Summary: B cells play an important role in the anti-tumor immune response in immunogenic tumors such as melanoma. Tumor-associated B cells undergo clonal expansion, class switch recombination, somatic hypermutation, and receptor revision. Tumor-associated B cells produce antibodies with higher levels of unproductive sequences and distinct complementarity determining region 3 properties. These findings suggest the presence of an active and aberrant autoimmune-like reaction in the tumor microenvironment.
NATURE COMMUNICATIONS
(2023)
Article
Dermatology
Niina K. Hassi, Timir Weston, Giulia Rinaldi, Joseph C. Ng, Asma Smahi, Sophie Twelves, Camilla Davan-Wetton, Dana Fakhreddine, Franca Fraternali, Francesca Capon
Summary: This study systematically investigated the effects of IL36RN sequence changes and identified the structural determinants of IL-36Ra activity. Experimental and machine learning methods were used to identify important amino acids for IL-36Ra stability and IL-36Ra/IL36R engagement. These findings have the potential to facilitate the design of new IL-36 inhibitors and aid in the interpretation of IL36RN variants in diagnostic settings.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jan Bohl, Mohammed Moudjou, Laetitia Herzog, Fabienne Reine, Fiona Sailer, Hannah Klute, Frederic Halgand, Guillaume Van der Rest, Yves Boulard, Vincent Beringue, Angelique Igel, Human Rezaei
Summary: Studies have shown that all mammalian prion assemblies exhibit the property of spontaneously generating two sets of discreet infectious tetrameric and dimeric species, which differ significantly in their specific infectivity. These oligomeric species are highly dynamic and evolve differently in the presence of chaotropic agents. The diversity in the quaternary structure of prion assemblies suggests that the structure of PrPSc can be divided into two independent folding domains.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Meeting Abstract
Dermatology
A. Onoufriadis, A. Cabezas, J. Ng, J. Canales, M. Costas, J. Ribeiro, J. Rodrigues, M. McAleer, L. Castelo-Soccio, M. Simpson, F. Fraternali, A. Irvine, J. Cameselle, J. McGrath
BRITISH JOURNAL OF DERMATOLOGY
(2022)
Meeting Abstract
Immunology
Jessica Mallaby, William Mwangi, Joseph Ng, Alex Stewart, Daniel Dorey Robinson, Uri Hershberg, Franca Fraternali, Venugopal Nair, Deborah Dunn Walters
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Article
Clinical Neurology
Davy Martin, Fabienne Reine, Laetitia Herzog, Angelique Igel-Egalon, Naima Aron, Christel Michel, Mohammed Moudjou, Guillaume Fichet, Isabelle Quadrio, Armand Perret-Liaudet, Olivier Andreoletti, Human Rezaei, Vincent Beringue
Summary: The study found that prions responsible for the most common form of sporadic Creutzfeldt-Jakob disease in humans can persist in the brain of transgenic mice for their entire life, potentially showing disease potency upon transmission to susceptible hosts. This highlights the ability of prions to persist and regain activity in non-replicative environments, raising concerns about the risk of indefinite prion persistence when utilizing therapeutic strategies aiming to lower PrP levels.
BRAIN COMMUNICATIONS
(2021)