Article
Biochemical Research Methods
Jing Liang, Huibin Zhang, Yee Ling Tan, Huimin Zhao, Ee Lui Ang
Summary: Bacteriophages are a promising alternative to antibiotics in combating antimicrobial resistance. This study presents a strategy for generating large libraries of phage variants, allowing for engineering of phage specificity and improved qualities. The findings demonstrate the potential of directed evolution in enhancing phage therapy for therapeutic applications.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Linnea Charlotta Hjelm, Hanna Lindberg, Stefan Stahl, John Lofblom
Summary: Affibody molecules are small affinity proteins with excellent properties. A new type of protein scaffold based on a dimeric form of affibodies has been developed, which has a distinct secondary structure content and mode of binding. The scaffold forms a tunnel-like cavity upon binding, encapsulating the target peptide. Selections from a high-complexity phage-displayed library using this scaffold resulted in the identification of high-affinity binders that effectively inhibit amyloid aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jared S. S. Morse, Yan J. J. Sheng, Joshua Trae Hampton, Lauralee D. D. Sylvain, Sukant Das, Yugendar R. Alugubelli, Peng-Hsun Chase Chen, Kai S. S. Yang, Shiqing Xu, Carol A. A. Fierke, Wenshe Ray Liu
Summary: Phage-assisted, active site-directed ligand evolution (PADLE) is a technique that uses a noncanonical amino acid as an anchor to direct phage-displayed peptides to a target for enhanced ligand identification. By using PADLE, researchers successfully identified potent HDAC8 inhibitors GH8HA01 and its analogue Ac-GH8HA01 Delta 1 Delta 7 with high selectivity against HDAC8.
Article
Biochemistry & Molecular Biology
Karl W. Barber, Ellen Shrock, Stephen J. Elledge
Summary: CRISPR-inspired systems have been developed for genome editing and nucleic acid detection. The CRISPR-based peptide display technology introduced in this study allows for customized, high-throughput in vitro protein interaction studies by self-assembling bespoke peptide libraries on a DNA microarray surface for rapid, multiplexed binding assays. This platform shows promise for viral epitope mapping and multiplexed diagnostics.
Article
Biochemical Research Methods
Wen-Ching Lin, Hao-Cheng Tang, Han Ying Wang, Chia-Yi Kao, You-Chiun Chang, Athena Hsu Li, Shi-Bing Yang, Kurt Yun Mou
Summary: This study introduces a unique mutagenesis method called the reverse Kunkel method, which combines the advantages of user-defined mutagenesis and random mutagenesis. By coupling with phage display and yeast display selections, the method successfully generates improved antibodies with enhanced affinity and immunostaining performance.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Valerio G. Giacobelli, Kosuke Fujishima, Martin Lepsik, Vyacheslav Tretyachenko, Tereza Kadava, Mikhail Makarov, Lucie Bednarova, Petr Novak, Klara Hlouchova
Summary: RNA-peptide/protein interactions are crucial to life and have been studied in the context of early evolution. This study focused on an RNA-binding variant of the ribosomal uL11 C-terminal domain, selected from a library of prebiotically plausible amino acid sequences. The study found that the selected variant binds RNA with a similar overall affinity, utilizing ion bridging interactions for stabilization in the absence of aromatic/basic residues. These findings provide insights into how early protein-RNA interactions may have evolved.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Chemistry, Organic
Beatriz de Pina Mariz, Sara Carvalho, Iris L. Batalha, Ana Sofia Pina
Summary: Enzymes are protein catalysts widely used in natural and industrial processes, with the global enzymes market projected to reach $10.5 billion in 2024. The development of artificial enzymes, created through computational design and directed evolution, aims to expand catalytic power and create novel catalysts with promising activity. The combination of these technologies is opening new opportunities in pharmaceutical, chemical, biofuels, and food industries, contributing to a more sustainable development.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Jakub Chrustowicz, Dawafuti Sherpa, Joan Teyra, Mun Siong Loke, Grzegorz M. Popowicz, Jerome Basquin, Michael Sattler, J. Rajan Prabu, Sachdev S. Sidhu, Brenda A. Schulman
Summary: The study identified the binding capacity of Gid4 and Gid10 substrate receptor subunits to a wide range of N-terminal residues, influenced by the downstream sequence context. Screening of phage displaying peptide libraries revealed novel consensus motifs with high affinity binding to Gid4 and Gid10, with structural data showing the complementary conformations with interacting peptides. The research demonstrates that degron identity, substrate domains containing targeted lysines, and the composition of E3 ligase higher-order assemblies collectively determine the efficiency of ubiquitylation and degradation.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lucas C. Wheeler, Michael J. Harms
Summary: The study suggests that ancestral proteins may have been less specific than modern proteins, but when interactions with random peptide targets are considered, the picture becomes more complex. It demonstrates that altered biological specificity does not necessarily indicate altered intrinsic specificity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Irum Rizvi, Malik Hisamuddin, Ajamaluddin Malik, Rizwan Hasan Khan
Summary: This study focused on host factors influencing the replication of Geminiviruses, identifying potential host proteins through phage display experiments and confirming the interaction of AtMCM3 with MYMIV Rep. The physiological relevance of AtMCM3 in MYMIV DNA replication was demonstrated, and yeast replication assay supported this interaction.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Microbiology
Ye Yang, Shuo Liu, Yufeng Luo, Bolun Wang, Junyi Wang, Juan Li, Jiaxin Li, Buqing Ye, Youchun Wang, Jianzhong Jeff Xi
Summary: We report a single-cell screening assay that allows rapid and high-throughput optimization of a human antibody displayed on a mammalian cell surface. Our approach can improve antibody affinity with an EC50 below 5 ng/mL within 2 weeks. This provides an effective strategy for fighting against evolving COVID variants.
Article
Biochemistry & Molecular Biology
Keisuke Fukunaga, Yohei Yokobayashi
Summary: In this study, a novel library-vs-library in vitro selection strategy was developed to select synthetic and orthogonal RNA-RBP pairs. The selected pairs exhibited picomolar affinity and >4000-fold selectivity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Food Science & Technology
Yuting Wu, Bing Liu, Zhiwei Liu, Pengjie Zhang, Xihui Mu, Zhaoyang Tong
Summary: In this study, a nonpathogenic model for COVID-19 research was constructed using phage display technology. The model successfully expressed the nucleocapsid protein of SARS-CoV-2 and showed potential as a standard for qPCR quantification and antibody affinity. Additionally, the model was used to develop a system for the classification and identification of samples using ATR-FTIR.
Review
Chemistry, Multidisciplinary
Yajie Wang, Pu Xue, Mingfeng Cao, Tianhao Yu, Stephan T. Lane, Huimin Zhao
Summary: Directed evolution aims to accelerate the natural evolution process of biological molecules and systems through gene diversification and library screening, serving as a powerful tool for engineering improved functions in proteins, metabolic pathways, and whole genomes. Common strategies include gene diversification, screening/selection methods, and continuous evolution, with applications in nucleic acids, proteins, pathways, genetic circuits, viruses, and cells. Challenges and future perspectives in directed evolution are also discussed.
Article
Biochemistry & Molecular Biology
Patrick N. Stoney, Akiko Yanagiya, Saori Nishijima, Tadashi Yamamoto
Summary: The CCR4-NOT deadenylase complex plays a crucial role in post-transcriptional regulation of gene expression in eukaryotes. CNOT7 and CNOT8, vertebrate homologs of the yeast CCR4-NOT catalytic subunit Caf1, exhibit distinct physiological functions and protein stability.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Balazs Mero, Laszlo Radnai, Gergo Gogl, Orsolya Toke, Ibolya Leveles, Kitti Koprivanacz, Balint Szeder, Metta Dulk, Gyoengyi Kudlik, Virag Vas, Anna Cserkaszky, Szabolcs Sipeki, Laszlo Nyitray, Beata G. Vertessy, Laszlo Buday
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Eszter Boros, Fanni Sebak, David Heja, David Szakacs, Katalin Zboray, Gitta Schlosser, Andras Micsonai, Jozsef Kardos, Andrea Bodor, Gabor Pal
JOURNAL OF MOLECULAR BIOLOGY
(2019)
Article
Infectious Diseases
Xiaoliang Ba, Lajos Kalmar, Nazreen F. Hadjirin, Heidrun Kerschner, Petra Apfalter, Fiona J. Morgan, Gavin K. Paterson, Samantha L. Girvan, Rui Zhou, Ewan M. Harrison, Mark A. Holmes
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2019)
Article
Biochemistry & Molecular Biology
Gergo Gogl, Beata Biri-Kovacs, Fabien Durbesson, Pau Jane, Yves Nomine, Camille Kostmann, Viktoria Bilics, Marton Simon, Attila Remenyi, Renaud Vincentelli, Gilles Trave, Laszlo Nyitray
JOURNAL OF MOLECULAR BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Beata Szabo, Tamas Horvath, Eva Schad, Nikoletta Murvai, Agnes Tantos, Lajos Kalmar, Lucia Beatriz Chemes, Kyou-Hoon Han, Peter Tompa
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Biochemistry & Molecular Biology
David Szakacs, Andrea Kocsis, Robert Szasz, Peter Gal, Gabor Pal
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Marton A. Simon, Peter Ecsedi, Gabor M. Kovacs, Adam L. Poti, Attila Remenyi, Jozsef Kardos, Gergo Gogl, Laszlo Nyitray
Article
Behavioral Sciences
Daniel Baksa, Xenia Gonda, Nora Eszlari, Peter Petschner, Veronika Acs, Lajos Kalmar, J. F. William Deakin, Gyorgy Bagdy, Gabriella Juhasz
FRONTIERS IN BEHAVIORAL NEUROSCIENCE
(2020)
Article
Genetics & Heredity
Christopher A. Jenkins, Lajos Kalmar, Kaspar Matiasek, Lorenzo Mari, Kaisa Kyostila, Hannes Lohi, Ellen C. Schofield, Cathryn S. Mellersh, Luisa De Risio, Sally L. Ricketts
Article
Biochemistry & Molecular Biology
Peter Ecsedi, Gergo Gogl, Henrietta Hof, Bence Kiss, Veronika Harmat, Laszlo Nyitray
Article
Chemistry, Analytical
Andrea Bodor, Jens D. Haller, Chafiaa Bouguechtouli, Francois-Xavier Theillet, Laszlo Nyitray, Burkhard Luy
ANALYTICAL CHEMISTRY
(2020)
Article
Genetics & Heredity
Lajos Kalmar, Srishti Gupta, Iain R. L. Kean, Xiaoliang Ba, Nazreen Hadjirin, Elizabeth M. Lay, Stefan P. W. de Vries, Michael Bateman, Harriet Bartlet, Juan Hernandez-Garcia, Alexander W. Tucker, Olivier Restif, Mark P. Stevens, James L. N. Wood, Duncan J. Maskell, Andrew J. Grant, Mark A. Holmes
Summary: Shotgun metagenomics is a powerful tool for identifying AMR genes in microbiomes but lacks the ability to link extrachromosomal DNA to bacterial chromosomes. We present HAM-ART, a comprehensive pipeline for generating metagenome-assembled genomes that includes both chromosomal and extrachromosomal AMR genes. The pipeline's performance was demonstrated in a study comparing pig faecal microbiomes from low- and high-antimicrobial use farms, revealing significant differences in AMR gene distribution.
Article
Biotechnology & Applied Microbiology
Dora Nagy-Fazekas, Pal Straner, Peter Ecsedi, Nora Taricska, Adina Borbely, Laszlo Nyitray, Andras Perczel
Summary: Antibodies are important proteins in the immune system, and camelid immunoglobulins (IgG), known as nanobodies, differ from human antibodies in terms of structure. By using ecotin as a fusion partner, a bacterial expression system is developed for easy and cost-effective production of nanobodies. The method can also be applied for the expression and purification of the receptor-binding domain of the SARS-CoV-2 S protein for interaction studies.
BIOENGINEERING-BASEL
(2023)
Article
Gastroenterology & Hepatology
Balint Zoltan Nemeth, Zoltan Attila Nagy, Bence Kiss, Gabriella Gellen, Gitta Schlosser, Alexandra Demcsak, Andrea Geisz, Eszter Hegyi, Miklos Sahin-Toth, Gabor Pal
Summary: Chymotrypsin-like protease (CTRL) plays a role in protecting the pancreas against pancreatitis and protein digestion in the human exocrine pancreas. The substrate specificity of CTRL is comparable to other chymotrypsins. However, CTRL may not have a significant role in preventing inappropriate trypsinogen activation and pancreatitis.
Article
Chemistry, Multidisciplinary
Attila Tokoli, Beata Mag, Eva Bartus, Edit Weber, Gerda Szakonyi, Marton A. Simon, Agnes Czibula, Eva Monostori, Laszlo Nyitray, Tamas A. Martinek