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Gagné F, Gauthier M, André C. Plastic Analysis with a Plasmonic Nano-Gold Sensor Coated with Plastic-Binding Peptides. J Xenobiot 2024; 14:690-700. [PMID: 38921649 PMCID: PMC11204973 DOI: 10.3390/jox14020040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Contamination with plastics of small dimensions (<1 µm) represents a health concern for many terrestrial and aquatic organisms. This study examined the use of plastic-binding peptides as a coating probe to detect various types of plastic using a plasmon nano-gold sensor. Plastic-binding peptides were selected for polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), and polystyrene (PS) based on the reported literature. Using nAu with each of these peptides to test the target plastics revealed high signal, at 525/630 nm, suggesting that the target plastic limited HCl-induced nAu aggregation. Testing with other plastics revealed some lack of specificity but the signal was always lower than that of the target plastic. This suggests that these peptides, although reacting mainly with their target plastic, show partial reactivity with the other target plastics. By using a multiple regression model, the relative levels of a given plastic could be corrected by the presence of other plastics. This approach was tested in freshwater mussels caged for 3 months at sites suspected to release plastic materials: in rainfall overflow discharges, downstream a largely populated city, and in a municipal effluent dispersion plume. The data revealed that the digestive glands of the mussels contained higher levels of PP, PE, and PET plastic particles at the rainfall overflow and downstream city sites compared to the treated municipal effluent site. This corroborated earlier findings that wastewater treatment could remove nanoparticles, at least in part. A quick and inexpensive screening test for plastic nanoparticles in biological samples with plasmonic nAu-peptides is proposed.
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Affiliation(s)
- Francois Gagné
- Environment and Climate Change Canada, Aquatic Contaminants Research Division, 105 McGill, Montréal, QC H2Y 2E7, Canada; (M.G.); (C.A.)
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Deng Y, Liu J, Lu Y, Fan X, Yang Y, Xu Y, Qin X, Nian R, Liu W. Novel Polystyrene-Binding Nanobody for Enhancing Immunoassays: Insights into Affinity, Immobilization, and Application Potential. Anal Chem 2024; 96:1597-1605. [PMID: 38235613 DOI: 10.1021/acs.analchem.3c04375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Nanobodies, which represent the next generation of antibodies due to their unique properties, face a significant limitation in their poor physical adsorption on solid supports. In this study, we successfully discovered polystyrene binding nanobodies from a synthetic nanobody library. Notably, bivalent nanobody B2 exhibited high affinity for polystyrene (0.7 nM for ELISA saturation binding analysis and 15.6 nM for isothermal titration calorimetry), displaying a pH-dependent behavior. Remarkably, hydrophobic and electrostatic interactions contribute minimally to the binding process. Molecular modeling provided insights into the interaction between B2 and polystyrene, revealing that the Trp51 residue within the CDR2 loop formed an aromatic H-bond with polystyrene at a distance of 2.74 Å, thus explaining the observed reduction in B2 affinity caused by Trp51 mutations. To explore B2's potential in protein immobilization, we constructed a bispecific nanobody by fusing B2 to an anticarcinoembryonic antigen nanobody 11C12, which cannot be immobilized on polystyrene through passive adsorption. Remarkably, the fusion construct achieved effective immobilization on polystyrene within 5 min by passing the need for periplasmic protein purification despite its low expression level. Moreover, the fusion construct demonstrated excellent linearity in the chemiluminescent enzyme immunoassay. For the first time, this study reports a simplified and seamless platform for the oriented immobilization of nanobody. Importantly, the entire process eliminated the need for protein purification, enabling efficient and rapid immobilization of fusion proteins directly from crude cell extracts, even when the expression level was low. Our developed process dramatically reduced the processing time from 2.5 days to just 5 min.
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Affiliation(s)
- Yang Deng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
- University of Chinese Academy of Sciences, No 19(A), Yuquan Road, Beijing 100049, China
| | - Jinyan Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Yaoping Lu
- WEGO Holding Co., Ltd., No. 18, Xingshan Road, Torch Hi-tech Science Park, Weihai 264210, China
| | - Xiying Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Yuansheng Yang
- Agency for Science, Technology and Research (A*STAR), Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Yaozheng Xu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang 110004, China
- Liaoning Clinical Research Center for Laboratory Medicine, No. 36, Sanhao Street, Shenyang 110004, China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang 110004, China
- Liaoning Clinical Research Center for Laboratory Medicine, No. 36, Sanhao Street, Shenyang 110004, China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
| | - Wenshuai Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189, Songling Road, Qingdao 266101, China
- Shandong Energy Institute, No. 189, Songling Road, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, No. 189, Songling Road, Qingdao 266101, China
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Yamada Y, Anderson CF, Schneider JP. De Novo Design of a Versatile Peptide-Based Coating to Impart Targeted Functionality at the Surface of Native Polystyrene. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37276244 DOI: 10.1021/acsami.3c02606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Peptide sequence periodicity is a simple design tool that can be used to generate functional peptide-based surface coatings. De novo-designed peptide N3-PEG-VK16 is characterized by a hydrophobic periodicity of two that avidly binds to native polystyrene priming its surface for subsequent targeted functionalization via chemical ligation. The peptidic portion of N3-PEG-VK16 is responsible for surface binding, converting polystyrene's hydrophobic surface into a wettable and electrostatically charged environment that facilitates cell attachment. Native polystyrene surfaces are coated by simple peptide adsorption from an aqueous buffered solution, and the resulting primed surface is easily functionalized by cycloaddition chemistry. Herein, we show that ligating a vitronectin-derived peptide to primed polystyrene surfaces enables adhesion, expansion, long-term culture, and phenotype maintenance of human induced pluripotent stem cells. To demonstrate scope, we also show that additional functional ligands can be used, for example, nerve growth factor protein, to control neurite outgrowth.
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Affiliation(s)
- Yuji Yamada
- Department of Clinical Biochemistry, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Caleb F Anderson
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Joel P Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
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4
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Tang Y, Hardy TJ, Yoon JY. Receptor-based detection of microplastics and nanoplastics: Current and future. Biosens Bioelectron 2023; 234:115361. [PMID: 37148803 DOI: 10.1016/j.bios.2023.115361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
Plastic pollution is an emerging environmental concern, gaining significant attention worldwide. They are classified into microplastics (MP; defined from 1 μm to 5 mm) and smaller nanoplastics (NP; <1 μm). NPs may pose higher ecological risks than MPs. Various microscopic and spectroscopic techniques have been used to detect MPs, and the same methods have occasionally been used for NPs. However, they are not based on receptors, which provide high specificity in most biosensing applications. Receptor-based micro/nanoplastics (MNP) detection can provide high specificity, distinguishing MNPs from the environmental samples and, more importantly, identifying the plastic types. It can also offer a low limit of detection (LOD) required for environmental screening. Such receptors are expected to detect NPs specifically at the molecular level. This review categorizes the receptors into cells, proteins, peptides, fluorescent dyes, polymers, and micro/nanostructures. Detection techniques used with these receptors are also summarized and categorized. There is plenty of room for future research to test for broader classes of environmental samples and many plastic types, to lower the LOD, and to apply the current techniques for NPs. Portable and handheld MNP detection should also be demonstrated for field use since the current demonstrations primarily utilized laboratory instruments. Detection on microfluidic platforms will also be crucial in miniaturizing and automating the assay and, eventually, collecting an extensive database to support machine learning-based classification of MNP types.
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Affiliation(s)
- Yisha Tang
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, United States
| | - Trinity J Hardy
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, United States
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, United States.
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5
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Biomedical applications of solid-binding peptides and proteins. Mater Today Bio 2023; 19:100580. [PMID: 36846310 PMCID: PMC9950531 DOI: 10.1016/j.mtbio.2023.100580] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.
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6
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Woo H, Kang SH, Kwon Y, Choi Y, Kim J, Ha DH, Tanaka M, Okochi M, Kim JS, Kim HK, Choi J. Sensitive and specific capture of polystyrene and polypropylene microplastics using engineered peptide biosensors. RSC Adv 2022; 12:7680-7688. [PMID: 35424716 PMCID: PMC8982333 DOI: 10.1039/d1ra08701k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/19/2022] [Indexed: 12/17/2022] Open
Abstract
Owing to increased environmental pollution, active research regarding microplastics circulating in the ocean has attracted significant interest in recent times. Microplastics accumulate in the bodies of living organisms and adversely affect them. In this study, a new method for the rapid detection of microplastics using peptides was proposed. Among the various types of plastics distributed in the ocean, polystyrene and polypropylene were selected. The binding affinity of the hydrophobic peptides suitable for each type of plastic was evaluated. The binding affinities of peptides were confirmed in unoxidized plastics and plasma-oxidized plastics in deionised or 3.5% saline water. Also, the detection of microplastics in small animals' intestine extracts were possible with the reported peptide biosensors. We expect plastic-binding peptides to be used in sensors to increase the detection efficiency of microplastics and potentially help separate microplastics from seawater.
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Affiliation(s)
- Hyunjeong Woo
- School of Integrative Engineering, Chung-Ang University Seoul 06974 Republic of Korea
| | - Seung Hyun Kang
- Department of Plastic and Reconstructive Surgery, Chung-Ang University Hospital Seoul 06973 Republic of Korea
| | - Yejin Kwon
- School of Integrative Engineering, Chung-Ang University Seoul 06974 Republic of Korea
| | - Yonghyun Choi
- School of Integrative Engineering, Chung-Ang University Seoul 06974 Republic of Korea
| | - Jiwon Kim
- School of Integrative Engineering, Chung-Ang University Seoul 06974 Republic of Korea
| | - Don-Hyung Ha
- School of Integrative Engineering, Chung-Ang University Seoul 06974 Republic of Korea
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology 2-12-1-S1-24, O-okayama, Meguro-ku Tokyo 152-8552 Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology 2-12-1-S1-24, O-okayama, Meguro-ku Tokyo 152-8552 Japan
| | - Jin Su Kim
- Division of RI Application, Korea Institute Radiological and Medical Sciences Seoul 01812 Republic of Korea
- Radiological and Medico-Oncological Sciences, University of Science and Technology (UST) Seoul 01812 Republic of Korea
| | - Han Koo Kim
- Department of Plastic and Reconstructive Surgery, Chung-Ang University Hospital Seoul 06973 Republic of Korea
| | - Jonghoon Choi
- School of Integrative Engineering, Chung-Ang University Seoul 06974 Republic of Korea
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7
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Engel H, Guischard F, Krause F, Nandy J, Kaas P, Höfflin N, Köhn M, Kilb N, Voigt K, Wolf S, Aslan T, Baezner F, Hahne S, Ruckes C, Weygant J, Zinina A, Akmeriç EB, Antwi EB, Dombrovskij D, Franke P, Lesch KL, Vesper N, Weis D, Gensch N, Di Ventura B, Öztürk MA. finDr: A web server for in silico D-peptide ligand identification. Synth Syst Biotechnol 2021; 6:402-413. [PMID: 34901479 PMCID: PMC8632724 DOI: 10.1016/j.synbio.2021.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/20/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
In the rapidly expanding field of peptide therapeutics, the short in vivo half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display. This technique is extremely powerful, but it requires the synthesis of the target in D-form, which is challenging for large proteins. Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. In a separate, heuristic approach to search the chemical space of 12-mer peptides, finDr executes a customizable evolutionary algorithm (EA) for the de novo identification or optimization of D-peptide ligands. As a proof of principle, we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3 (PSMα3), a toxin of methicillin-resistant Staphylococcus aureus (MRSA). We validate the predictions using in vitro binding assays, supporting the success of this approach. Compared to conventional methods, finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation. We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.
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Key Words
- D-AA, dextrorotatory amino acid
- D-peptide
- EA, evolutionary algorithm
- Evolutionary algorithm
- L-AA, levorotatory amino acid
- MD, molecular dynamics
- MIEA, mirror-image evolutionary algorithm
- MIPD, mirror-image phage display
- MIVS, mirror-image virtual screening
- MRSA, methicillin-resistant Staphylococcus aureus
- Mirror-image phage display
- Molecular docking
- NCL, native chemical ligation
- PD-1, receptor programmed death 1
- PPI, protein-protein interaction
- PSMα3, phenol soluble modulin alpha 3
- Peptide design
- SPPS, solid phase peptide synthesis
- Web server
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Affiliation(s)
- Helena Engel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Felix Guischard
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Krause
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Janina Nandy
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Paulina Kaas
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nico Höfflin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Normann Kilb
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- AG Roth-Lab for MicroarrayCopying, ZBSA–Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Karsten Voigt
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3a, 79104, Freiburg, Germany
| | - Tahira Aslan
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Baezner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Salomé Hahne
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Carolin Ruckes
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Joshua Weygant
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Alisa Zinina
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Emir Bora Akmeriç
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Enoch B. Antwi
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Dennis Dombrovskij
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Philipp Franke
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Klara L. Lesch
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
- Internal Medicine IV, Department of Medicine, Medical Center, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - Niklas Vesper
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Daniel Weis
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nicole Gensch
- Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Corresponding author. Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Barbara Di Ventura
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Mehmet Ali Öztürk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
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8
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He B, Dzisoo AM, Derda R, Huang J. Development and Application of Computational Methods in Phage Display Technology. Curr Med Chem 2020; 26:7672-7693. [PMID: 29956612 DOI: 10.2174/0929867325666180629123117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/08/2018] [Accepted: 03/20/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. METHODS We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. RESULTS We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. CONCLUSION The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.
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Affiliation(s)
- Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China.,School of Medicine, Guizhou University, Guiyang 550025, China
| | - Anthony Mackitz Dzisoo
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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9
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He B, Chen H, Huang J. PhD7Faster 2.0: predicting clones propagating faster from the Ph.D.-7 phage display library by coupling PseAAC and tripeptide composition. PeerJ 2019; 7:e7131. [PMID: 31245183 PMCID: PMC6585900 DOI: 10.7717/peerj.7131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 05/15/2019] [Indexed: 01/08/2023] Open
Abstract
Selection from phage display libraries empowers isolation of high-affinity ligands for various targets. However, this method also identifies propagation-related target-unrelated peptides (PrTUPs). These false positive hits appear because of their amplification advantages. In this report, we present PhD7Faster 2.0 for predicting fast-propagating clones from the Ph.D.-7 phage display library, which was developed based on the support vector machine. Feature selection was performed against PseAAC and tripeptide composition using the incremental feature selection method. Ten-fold cross-validation results show that PhD7Faster 2.0 succeeds a decent performance with the accuracy of 81.84%, the Matthews correlation coefficient of 0.64 and the area under the ROC curve of 0.90. The permutation test with 1,000 shuffles resulted in p < 0.001. We implemented PhD7Faster 2.0 into a publicly accessible web tool (http://i.uestc.edu.cn/sarotup3/cgi-bin/PhD7Faster.pl) and constructed standalone graphical user interface and command-line versions for different systems. The standalone PhD7Faster 2.0 is able to detect PrTUPs within small datasets as well as large-scale datasets. This makes PhD7Faster 2.0 an enhanced and powerful tool for scanning and reporting faster-growing clones from the Ph.D.-7 phage display library.
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang, Guizhou, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang, Guizhou, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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10
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He B, Chen H, Li N, Huang J. SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data. Int J Biol Sci 2019; 15:1452-1459. [PMID: 31337975 PMCID: PMC6643146 DOI: 10.7150/ijbs.31957] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/09/2019] [Indexed: 01/13/2023] Open
Abstract
SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc.edu.cn/sarotup3.
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang 550025, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang 550025, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
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11
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Rübsam K, Davari MD, Jakob F, Schwaneberg U. KnowVolution of the Polymer-Binding Peptide LCI for Improved Polypropylene Binding. Polymers (Basel) 2018; 10:E423. [PMID: 30966458 PMCID: PMC6415234 DOI: 10.3390/polym10040423] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 12/02/2022] Open
Abstract
The functionalization of polymer surfaces by polymer-binding peptides offers tremendous opportunities for directed immobilization of enzymes, bioactive peptides, and antigens. The application of polymer-binding peptides as adhesion promoters requires reliable and stable binding under process conditions. Molecular modes of interactions between material surfaces, peptides, and solvent are often not understood to an extent that enables (semi-) rational design of polymer-binding peptides, hindering the full exploitation of their potential. Knowledge-gaining directed evolution (KnowVolution) is an efficient protein engineering strategy that facilitates tailoring protein properties to application demands through a combination of directed evolution and computational guided protein design. A single round of KnowVolution was performed to gain molecular insights into liquid chromatography peak I peptide, 47 aa (LCI)-binding to polypropylene (PP) in the presence of the competing surfactant Triton X-100. KnowVolution yielded a total of 8 key positions (D19, S27, Y29, D31, G35, I40, E42, and D45), which govern PP-binding in the presence of Triton X-100. The recombination of two of the identified amino acid substitutions (Y29R and G35R; variant KR-2) yielded a 5.4 ± 0.5-fold stronger PP-binding peptide compared to LCI WT in the presence of Triton X-100 (1 mM). The LCI variant KR-2 shows a maximum binding capacity of 8.8 ± 0.1 pmol/cm² on PP in the presence of Triton X-100 (up to 1 mM). The KnowVolution approach enables the development of polymer-binding peptides, which efficiently coat and functionalize PP surfaces and withstand surfactant concentrations that are commonly used, such as in household detergents.
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Affiliation(s)
- Kristin Rübsam
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.
| | - Felix Jakob
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany.
- DWI-Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, D-52074 Aachen, Germany.
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12
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He B, Jiang L, Duan Y, Chai G, Fang Y, Kang J, Yu M, Li N, Tang Z, Yao P, Wu P, Derda R, Huang J. Biopanning data bank 2018: hugging next generation phage display. Database (Oxford) 2018; 2018:4955852. [PMID: 29688378 PMCID: PMC7206649 DOI: 10.1093/database/bay032] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/07/2018] [Accepted: 03/07/2018] [Indexed: 12/12/2022]
Abstract
Database URL The BDB database is available at http://immunet.cn/bdb.
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Affiliation(s)
- Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Lixu Jiang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Yaocong Duan
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Guoshi Chai
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Yewei Fang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Juanjuan Kang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Min Yu
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Ning Li
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Zhongjie Tang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Pengcheng Yao
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Pengcheng Wu
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
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13
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Rübsam K, Weber L, Jakob F, Schwaneberg U. Directed evolution of polypropylene and polystyrene binding peptides. Biotechnol Bioeng 2017; 115:321-330. [DOI: 10.1002/bit.26481] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/12/2017] [Accepted: 10/15/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Kristin Rübsam
- RWTH Aachen University; Worringerweg 3; Aachen Germany
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
| | - Lina Weber
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
| | - Felix Jakob
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University; Worringerweg 3; Aachen Germany
- DWI - Leibniz-Institute for Interactive Materials; Forckenbeckstraße 50; Aachen Germany
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14
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Ghaffari Sharaf M, Cetinel S, Semenchenko V, Damji KF, Unsworth LD, Montemagno C. Peptides for targeting βB2-crystallin fibrils. Exp Eye Res 2017; 165:109-117. [PMID: 28986145 DOI: 10.1016/j.exer.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/20/2017] [Accepted: 10/01/2017] [Indexed: 01/24/2023]
Abstract
Crystallins are a major family of proteins located within the lens of the eye. Cataracts are thought to be due to the formation of insoluble fibrillar aggregates, which are largely composed of proteins from the crystallin family. Today the only cataract treatment that exists is surgery and this can be difficult to access for individuals in the developing world. Development of novel pharmacotherapeutic approaches for the treatment of cataract rests on the specific targeting of these structures. βB2-crystallin, a member of β-crystallin family, is a large component of the crystallin proteins within the lens, and as such was used to form model fibrils in vitro. Peptides were identified, using phage display techniques, that bound to these fibrils with high affinity. Fibrillation of recombinantly expressed human βB2-crystallin was performed in 10% (v/v) trifluoroethanol (TFE) solution (pH 2.0) at various temperatures, and its amyloid-like structure was confirmed using Thioflavin-T (ThT) assay, transmission electron microscopy (TEM), and X-ray fiber diffraction (XRFD) analysis. Affinity of identified phage-displayed peptides were analyzed using enzyme-linked immunosorbent assay (ELISA). Specific binding of a cyclic peptide (CKQFKDTTC) showed the highest affinity, which was confirmed using a competitive inhibition assay.
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Affiliation(s)
- Mehdi Ghaffari Sharaf
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada; Ingenuity Lab, University of Alberta, Edmonton, AB, Canada
| | - Sibel Cetinel
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada; Ingenuity Lab, University of Alberta, Edmonton, AB, Canada
| | - Valentyna Semenchenko
- National Institute of Nanotechnology, National Research Council, Edmonton, AB, Canada
| | - Karim F Damji
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, AB, Canada
| | - Larry D Unsworth
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada; National Institute of Nanotechnology, National Research Council, Edmonton, AB, Canada.
| | - Carlo Montemagno
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada; National Institute of Nanotechnology, National Research Council, Edmonton, AB, Canada; Ingenuity Lab, University of Alberta, Edmonton, AB, Canada.
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15
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Zarei O, Benvenuti S, Ustun-Alkan F, Hamzeh-Mivehroud M, Dastmalchi S. Identification of a RON tyrosine kinase receptor binding peptide using phage display technique and computational modeling of its binding mode. J Mol Model 2017; 23:267. [DOI: 10.1007/s00894-017-3437-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
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16
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Discovery of a polystyrene binding peptide isolated from phage display library and its application in peptide immobilization. Sci Rep 2017; 7:2673. [PMID: 28572662 PMCID: PMC5453990 DOI: 10.1038/s41598-017-02891-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/10/2017] [Indexed: 12/05/2022] Open
Abstract
Phage peptide display is a powerful technique for discovery of various target-specific ligands. However, target-unrelated peptides can often be obtained and cause ambiguous results. Peptide PB-TUP has been isolated repeatedly in our laboratory on different targets and we conducted a research on PB-TUP phage to investigate their binding properties and rate of propagation. ELISA and phage recovery assay demonstrated that PB-TUP phage had a significant superior affinity to polystyrene solid surface compared with control phage clones. In this study, some incidental bindings are excluded like blocking agents and non-specific binding of secondary antibodies. Propagation rate assays of the selected phage clones showed that the growth rate of PB-TUP phage was not superior to the control phages. Furthermore, the binding of PB-TUB to polystyrene was concentration dependent and varied with solution pH. Molecular modeling revealed that stable structures of α-helix and β-turn may contribute to the binding of PB-TUP to polystyrene plate. The PB-TUP sequence was fused to the N-terminus of peptide P2 and the fusion peptide significantly increased the binding affinity to polystyrene. The fusion peptide also enhanced the cell adhesion ability of peptide P2 with human umbilical vein endothelial cell (HUVEC). The addition of the polystyrene binding peptide provided a convenient method for peptide immobilization.
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17
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Rübsam K, Stomps B, Böker A, Jakob F, Schwaneberg U. Anchor peptides: A green and versatile method for polypropylene functionalization. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.03.070] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Swaminathan S, Cui Y. A mild deposition of metallic materials on a plastic film enabled by phage display peptides. RSC Adv 2016. [DOI: 10.1039/c5ra25429a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We demonstrate for the first time a mild deposition of metallic materials on a plastic film, (poly)ethylene tetraphthalate (PET), enabled by phage displayed peptides.
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Affiliation(s)
| | - Yue Cui
- Department of Electrical Engineering and Computing Systems
- University of Cincinnati
- Cincinnati
- USA
- Department of Mechanical and Materials Engineering
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19
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He B, Chai G, Duan Y, Yan Z, Qiu L, Zhang H, Liu Z, He Q, Han K, Ru B, Guo FB, Ding H, Lin H, Wang X, Rao N, Zhou P, Huang J. BDB: biopanning data bank. Nucleic Acids Res 2015; 44:D1127-32. [PMID: 26503249 PMCID: PMC4702802 DOI: 10.1093/nar/gkv1100] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/10/2015] [Indexed: 12/19/2022] Open
Abstract
The BDB database (http://immunet.cn/bdb) is an update of the MimoDB database, which was previously described in the 2012 Nucleic Acids Research Database issue. The rebranded name BDB is short for Biopanning Data Bank, which aims to be a portal for biopanning results of the combinatorial peptide library. Last updated in July 2015, BDB contains 2904 sets of biopanning data collected from 1322 peer-reviewed papers. It contains 25,786 peptide sequences, 1704 targets, 492 known templates, 447 peptide libraries and 310 crystal structures of target-template or target-peptide complexes. All data stored in BDB were revisited, and information on peptide affinity, measurement method and procedures was added for 2298 peptides from 411 sets of biopanning data from 246 published papers. In addition, a more professional and user-friendly web interface was implemented, a more detailed help system was designed, and a new on-the-fly data visualization tool and a series of tools for data analysis were integrated. With these new data and tools made available, we expect that the BDB database would become a major resource for scholars using phage display, with improved utility for biopanning and related scientific communities.
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Affiliation(s)
- Bifang He
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guoshi Chai
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yaocong Duan
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zhiqiang Yan
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Liuyang Qiu
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Huixiong Zhang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zechun Liu
- School of Computer Science & Engineering, University of Electronic Science and Technology of China, No.2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu, Sichuan 611731, China
| | - Qiang He
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ke Han
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Beibei Ru
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Feng-Biao Guo
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Ding
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Xianlong Wang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Nini Rao
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Peng Zhou
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jian Huang
- Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China
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20
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Hakami AR, Ball JK, Tarr AW. Non-ionic detergents facilitate non-specific binding of M13 bacteriophage to polystyrene surfaces. J Virol Methods 2015; 221:1-8. [DOI: 10.1016/j.jviromet.2015.04.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 01/13/2023]
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Henry M, Debarbieux L. Tools from viruses: bacteriophage successes and beyond. Virology 2012; 434:151-61. [PMID: 23063405 DOI: 10.1016/j.virol.2012.09.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/14/2012] [Accepted: 09/20/2012] [Indexed: 01/21/2023]
Abstract
Viruses are ubiquitous and can infect any of the three existing cellular lineages (Archaea, Bacteria and Eukarya). Despite the persisting negative public perception of these entities, scientists learnt how to domesticate some of them. The study of molecular mechanisms essential to the completion of viral cycles has greatly contributed to deciphering fundamental processes in biology. Nowadays, viruses have entered the biotechnological era and numerous applications have already been developed. Viral-derived tools are used to manipulate genetic information, detect, diagnose, control and cure infectious diseases, or even design new structural assemblies. With the recent advances in the field of metagenomics, an overwhelming amount of information on novel viruses has become available. As current tools have been historically developed from a limited number of viruses, the potential of discoveries from new archaeal, bacterial and eukaryotic viruses may be limited only by our understanding of the multiple facets of viral cycles.
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Affiliation(s)
- Marine Henry
- Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, Department of Microbiology, F-75015 Paris, France
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22
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Swaminathan S, Cui Y. Recognition of poly(dimethylsiloxane) with phage displayed peptides. RSC Adv 2012. [DOI: 10.1039/c2ra22137c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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