Review
Biochemical Research Methods
Yi Wang, Kaili Zhang, Yanjie Zhao, Yifan Li, Weijun Su, Shuai Li
Summary: DNA-encoded peptide/protein libraries are widely used for protein evolutionary modification and peptide/antibody selection. Mammalian cells, with their post-translational modifications and natural conformation, provide a great platform for studying transmembrane proteins or disease-related proteins. However, the construction of large size DNA-encoded libraries in mammalian cells still faces technical challenges. This review summarizes the current progress and applications of DNA-encoded libraries in mammalian cells.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Kohei Umedera, Taiki Morita, Hiroyuki Nakamura
Summary: Asymmetric construction of densely functionalized three-dimensional aza-tetracyclic scaffolds was achieved through intramolecular Diels-Alder reaction of bicyclic precursors derived from l-tyrosine. Three substituents were systematically introduced into the developed scaffolds in various combinations, demonstrating their high utility in drug discovery.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Matthew G. Cyr, Henry D. Wilson, Anna-Lena Spierling, Jing Chang, Haiyong Peng, Peter Steinberger, Christoph Rader
Summary: This article introduces an unbiased approach to antibody discovery, which relies on generating monoclonal antibodies (mAbs) against native target cell surfaces via phage display. The authors demonstrated that this method efficiently identifies mAbs with the desired target cell reactivity and identified and validated three cell surface antigens in multiple myeloma. This study highlights the utility of optimized whole-cell phage display selection methods and their potential in target-unbiased antibody discovery workflows.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
David N. Philpott, Surath Gomis, Hansen Wang, Randy Atwal, Abdellali Kelil, Tanja Sack, Brandon Morningstar, Chris Burnie, Edward H. Sargent, Stephane Angers, Sachdev Sidhu, Shana O. Kelley
Summary: The rapid on-cell phage display platform presented in this study accelerates the development of high-performance human antibodies by mimicking the complex in vivo binding environment, improving screening efficiency and accuracy.
ACS CENTRAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Yuan Wang, Ruina Jin, Bingqing Shen, Na Li, He Zhou, Wei Wang, Yingjie Zhao, Mengshi Huang, Pan Fang, Shanshan Wang, Pascaline Mary, Ruikun Wang, Peixiang Ma, Ruonan Li, Yujie Tian, Youjia Cao, Fubin Li, Liang Schweizer, Hongkai Zhang
Summary: The lack of high-throughput approaches in isolating antibodies with functional readouts has hindered the advancement of next-generation cancer immunotherapeutics. The development of a highly efficient droplet-based microfluidic platform offers a solution for functional screening of millions of antibodies, potentially revolutionizing drug development in cancer immunotherapy.
Article
Biochemistry & Molecular Biology
Tian-Jiao Han, Fei Huan, Meng Liu, Meng-Si Li, Yang Yang, Gui-Xia Chen, Dong Lai, Min-Jie Cao, Guang-Ming Liu
Summary: SCP has been identified as a novel allergen in Crassostrea angulata, inducing basophil activation and showing significant allergenicity. The study successfully analyzed five linear epitopes and two conformational epitopes of SCP, as well as observed changes in its structural characteristics and IgE-binding capacity after Ca2+ depletion. These epitope data enhance the understanding of oyster allergens and could potentially lead to the development of hypoallergenic shellfish products.
Article
Biotechnology & Applied Microbiology
Carolin Mueller, Patrick J. Bakkes, Patrick Lenz, Vera Waffenschmidt, Laura M. Helleckes, Karl-Erich Jaeger, Wolfgang Wiechert, Andreas Knapp, Roland Freudl, Marco Oldiges
Summary: Automated workflows were developed for heterologous production of cutinase in Corynebacterium glutamicum. The best performing signal peptides for cutinase secretion were identified using enzymatic activity and split GFP assay.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhao Peng, Sheng Yao, Baolong Zhang, Kaiyao Huang, Cuihong Wan
Summary: This study investigates smORFs in green algae and provides a genome-wide and high-confident smORF database in the model green alga Chlamydomonas reinhardtii. A total of 2014 smORFs were identified, with some potentially involved in specific functions.
Article
Biochemistry & Molecular Biology
Yu Zeng, Michael Woolley, Karuppiah Chockalingam, Benjamin Thomas, Srishtee Arora, Magnus Hook, Zhilei Chen
Summary: We describe a novel method, click display, for in vitro protein display that does not rely on RNA integrity and can produce covalently linked protein-cDNA complexes from double-stranded input DNA within 2 hours. This method combines transcription, translation, and reverse transcription reactions to achieve stable linkage between proteins and encoding cDNA using a modified DNA linker generated through click chemistry. Biopanning with a click-displayed mock library revealed significant enrichment of target binders in just one round. A synthetic library of DARPins generated using click display and subjected to six rounds of panning yielded a panel of nanomolar binders, showcasing the power and convenience of this method even in RNase-rich environments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Takuto Furuhashi, Kensaku Sakamoto, Akira Wada
Summary: This study developed a ribosome display technique for selecting peptide epitopes bound to monoclonal antibodies. By using genetic code expansion and photo-cross-linking reactions, low-affinity peptide epitopes can be efficiently identified. The results of this study contribute to the advancement of diverse peptide-based research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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.
Review
Microbiology
Grace L. L. Allen, Ashley K. K. Grahn, Katerina Kourentzi, Richard C. C. Willson, Sean Waldrop, Jiantao Guo, Brian K. K. Kay
Summary: This article reviews how bioconjugation and the incorporation of ncAAs during translation have expanded the chemistry of peptides and proteins displayed by M13 virions for a variety of purposes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Tianyang You, Yuan Ding, He Chen, Guangyue Song, Lianrun Huang, Minghua Wang, Xiude Hua
Summary: Competitive and noncompetitive immunoassays for clothianidin based on phage-displayed peptides were developed to improve sensitivity and specificity. The noncompetitive method showed the best specificity and sensitivity for clothianidin, with no cross-reactivity with analogs. The results demonstrated good recoveries and consistency with high-performance liquid chromatography in the analysis of blind samples.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Haim Ashkenazy, Oren Avram, Arie Ryvkin, Anna Roitburd-Berman, Yael Weiss-Ottolenghi, Smadar Hada-Neeman, Jonathan M. Gershoni, Tal Pupko
Summary: This study describes Motifier, a computational pipeline that systematically generates discriminatory peptide motifs based on affinity-selected peptides identified by Deep-Panning. These motifs effectively characterize antibody binding activities and accurately classify complex antibody mixtures through machine-learning protocols.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
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)