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
Biotechnology & Applied Microbiology
Sabrina Galinanes Reyes, Yutetsu Kuruma, Mai Fujimi, Masako Yamazaki, Sumie Eto, Shota Nishikawa, Satoshi Tamaki, Asaki Kobayashi, Ryo Mizuuchi, Lynn Rothschild, Mark Ditzler, Kosuke Fujishima
Summary: The refined PURE-based display method was developed for the preparation of mRNA and cDNA-peptide conjugates, showing efficient enrichment of FLAG epitope motifs, especially in mRNA display. The study demonstrated that gel purification steps improve conjugate formation efficiency and enhance the enrichment rate of specific epitope motifs. Overall, the research suggests the potential of the PURE system for exploring diverse polypeptide sequences and functional space in future studies.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Review
Chemistry, Multidisciplinary
Golnaz Kamalinia, Brian J. Grindel, Terry T. Takahashi, Steven W. Millward, Richard W. Roberts
Summary: mRNA display is a powerful platform for directed evolution of proteins and peptides, linking phenotype and genotype through puromycin. Iterative selection cycles lead to peptides with desired functional levels. This review discusses the development and broad application of mRNA display technology in selecting novel peptides and proteins.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Chemistry, Multidisciplinary
Romany J. McLure, Sheena E. Radford, David J. Brockwell
Summary: Directed evolution is a powerful tool for engineering new functions in biomolecules and gaining insights into protein behavior. It accelerates the process of natural evolution through multiple rounds of gene diversification and selection.
TRENDS IN CHEMISTRY
(2022)
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
Chemistry, Analytical
Asad Ali Siyal, Eric Sheng-Wen Chen, Hsin-Ju Chan, Reta Birhanu Kitata, Jhih-Ci Yang, Hsiung-Lin Tu, Yu-Ju Chen
Summary: The study presents a sample size-comparable library-based DIA approach, achieving higher protein group identification from small-size library compared to medium-size, large-size, and lung cancer resource spectral library. The approach shows good generality across different instruments and data analysis methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Sabrina E. Iskandar, Lilly F. Chiou, Tina M. Leisner, Devan J. Shell, Jacqueline L. Norris-Drouin, Cyrus Vaziri, Kenneth H. Pearce, Albert A. Bowers
Summary: This study reports a method to identify covalent cyclic peptide inhibitors in mRNA display. By combining co- and post-translational library diversification strategies, cyclic libraries with reactive dehydroalanines (Dhas) were created and used for selections against two model targets. The most potent hits showed low nanomolar inhibitory activities and disrupted known protein-protein interactions with their selected targets. Overall, this study establishes Dhas as electrophiles for covalent inhibition and demonstrates the synergy of separate library diversification methods in mRNA display for novel applications like covalent inhibitor discovery.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Brian J. Grindel, Brian J. Engel, Justin N. Ong, Anupallavi Srinivasamani, Xiaowen Liang, Niki M. Zacharias, Robert C. Bast, Michael A. Curran, Terry T. Takahashi, Richard W. Roberts, Steven W. Millward
Summary: This study describes the selection of a low nanomolar PD-L1-binding affibody using mRNA display, which showed significant tumor uptake in vivo.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Malin Jonsson, Julia Scheffel, Emma Larsson, Marit Moller, Gabriella Rossi, Magnus Lundqvist, Johan Rockberg, Mathias Uhlen, Hanna Tegel, Sara Kanje, Sophia Hober
Summary: This article presents a calcium-regulated affinity library (CaRA) that provides protein-binding domains with calcium-dependent behavior, which has important applications in protein purification and therapy.
Article
Biochemistry & Molecular Biology
Norman E. Davey, Leandro Simonetti, Ylva Ivarsson
Summary: Short linear motifs (SLiMs) are unique and ubiquitous protein interaction modules that play important regulatory roles and drive dynamic complex formation. Recent methodological advances have enabled high-throughput discovery of SLiM-mediated interactome in the human cell, filling a significant blind spot in current interactomics data. This article discusses the key methods used to explore the elusive SLiM-mediated interactome and its implications for the field.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
David M. Boragine, Wanzhi Huang, Lynn H. Su, Timothy Palzkill
Summary: Peptides that bind and disrupt protein-protein interaction interfaces can be identified through systematic peptide library construction, affinity selection, and deep sequencing.
Article
Multidisciplinary Sciences
Serena Vales, Jhanna Kryukova, Soumyanetra Chandra, Gintare Smagurauskaite, Megan Payne, Charlie J. Clark, Katrin Hafner, Philomena Mburu, Stepan Denisov, Graham Davies, Carlos Outeiral, Charlotte M. Deane, Garrett M. Morris, Shoumo Bhattacharya
Summary: In this study, short peptides with broad-spectrum anti-chemokine activity were identified from tick evasins using phage display screening. The researchers identified two conserved motifs within these peptides and characterized their functional importance. Computational modeling revealed the molecular interactions between the peptides and the receptor-binding regions of CC and CXC-chemokines. These findings suggest the potential of evasin-derived peptides as therapeutic agents for inflammatory diseases.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Yu Jung Kim, Min Ho Lee, Se-Ra Lee, Hyo-Young Chung, Kwangmin Kim, Tae Gyu Lee, Dae Young Kim
Summary: Phage display was used to develop human monoclonal antibodies (mAbs) that neutralize SARS-CoV-2. These antibodies showed desirable neutralizing activities and properties, making them potential candidates for antibody therapeutics for treating COVID-19, as well as for diagnostics and research tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
John Bowen, John Schneible, Kaitlyn Bacon, Collin Labar, Stefano Menegatti, Balaji M. Rao
Summary: This study describes the construction and screening of yeast display libraries of post-translationally modified peptides using bacterial transglutaminase. Two alternative routes were developed for enzymatic treatment of linear peptides before yeast surface display. The efficiency of peptide modification was evaluated by flow cytometry and cleavage assay, followed by screening of transglutaminase-treated peptides to isolate binders to specific protein targets. The identified cyclic peptide exhibited high binding selectivity and demonstrated the utility of enzyme-mediated cyclization in screening combinatorial libraries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Brooke D. Huisman, Zheng Dai, David K. Gifford, Michael E. Birnbaum, Satyajit Rath
Summary: T cells play a crucial role in adaptive immune response by recognizing peptide antigens presented on cell surfaces by MHC proteins. A yeast display-based platform has been developed to assess the binding of user-defined peptides in a high-throughput manner. The approach was used to evaluate the binding of SARS-CoV-2 and dengue virus peptides to human class II MHCs, revealing both consistent and experimentally validated computational false positives and false negatives. This approach can complement current datasets and predictions, providing insights into viral conservation and MHC binding.
