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Pierzynowska K, Morcinek-Orłowska J, Gaffke L, Jaroszewicz W, Skowron PM, Węgrzyn G. Applications of the phage display technology in molecular biology, biotechnology and medicine. Crit Rev Microbiol 2024; 50:450-490. [PMID: 37270791 DOI: 10.1080/1040841x.2023.2219741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 10/17/2022] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The phage display technology is based on the presentation of peptide sequences on the surface of virions of bacteriophages. Its development led to creation of sophisticated systems based on the possibility of the presentation of a huge variability of peptides, attached to one of proteins of bacteriophage capsids. The use of such systems allowed for achieving enormous advantages in the processes of selection of bioactive molecules. In fact, the phage display technology has been employed in numerous fields of biotechnology, as diverse as immunological and biomedical applications (in both diagnostics and therapy), the formation of novel materials, and many others. In this paper, contrary to many other review articles which were focussed on either specific display systems or the use of phage display in selected fields, we present a comprehensive overview of various possibilities of applications of this technology. We discuss an usefulness of the phage display technology in various fields of science, medicine and the broad sense of biotechnology. This overview indicates the spread and importance of applications of microbial systems (exemplified by the phage display technology), pointing to the possibility of developing such sophisticated tools when advanced molecular methods are used in microbiological studies, accompanied with understanding of details of structures and functions of microbial entities (bacteriophages in this case).
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Weronika Jaroszewicz
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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2
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Industry news update covering May 2021. Ther Deliv 2021. [DOI: 10.4155/tde-2021-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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3
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Glasgow BJ. Tear Lipocalin and Lipocalin-Interacting Membrane Receptor. Front Physiol 2021; 12:684211. [PMID: 34489718 PMCID: PMC8417070 DOI: 10.3389/fphys.2021.684211] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/13/2021] [Indexed: 11/24/2022] Open
Abstract
Tear lipocalin is a primate protein that was recognized as a lipocalin from the homology of the primary sequence. The protein is most concentrated in tears and produced by lacrimal glands. Tear lipocalin is also produced in the tongue, pituitary, prostate, and the tracheobronchial tree. Tear lipocalin has been assigned a multitude of functions. The functions of tear lipocalin are inexorably linked to structural characteristics that are often shared by the lipocalin family. These characteristics result in the binding and or transport of a wide range of small hydrophobic molecules. The cavity of tear lipocalin is formed by eight strands (A-H) that are arranged in a β-barrel and are joined by loops between the β-strands. Recently, studies of the solution structure of tear lipocalin have unveiled new structural features such as cation-π interactions, which are extant throughout the lipocalin family. Lipocalin has many unique features that affect ligand specificity. These include a capacious and a flexible cavity with mobile and short overhanging loops. Specific features that confer promiscuity for ligand binding in tear lipocalin will be analyzed. The functions of tear lipocalin include the following: antimicrobial activities, scavenger of toxic and tear disruptive compounds, endonuclease activity, and inhibition of cysteine proteases. In addition, tear lipocalin binds and may modulate lipids in the tears. Such actions support roles as an acceptor for phospholipid transfer protein, heteropolymer formation to alter viscosity, and tear surface interactions. The promiscuous lipid-binding properties of tear lipocalin have created opportunities for its use as a drug carrier. Mutant analogs have been created to bind other molecules such as vascular endothelial growth factor for medicinal use. Tear lipocalin has been touted as a useful biomarker for several diseases including breast cancer, chronic obstructive pulmonary disease, diabetic retinopathy, and keratoconus. The functional possibilities of tear lipocalin dramatically expanded when a putative receptor, lipocalin-interacting membrane receptor was identified. However, opposing studies claim that lipocalin-interacting membrane receptor is not specific for lipocalin. A recent study even suggests a different function for the membrane protein. This controversy will be reviewed in light of gene expression data, which suggest that tear lipocalin has a different tissue distribution than the putative receptor. But the data show lipocalin-interacting membrane receptor is expressed on ocular surface epithelium and that a receptor function here would be rational.
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Affiliation(s)
- Ben J. Glasgow
- Departments of Ophthalmology, Pathology and Laboratory Medicine, Jules Stein Eye Institute, University of California, Los Angeles, Los Angeles, CA, United States
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4
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Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci 2021; 30:1895-1903. [PMID: 34107549 DOI: 10.1002/pro.4142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022]
Abstract
Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rui Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, China
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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5
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Sécher T, Guilleminault L, Reckamp K, Amanam I, Plantier L, Heuzé-Vourc'h N. Therapeutic antibodies: A new era in the treatment of respiratory diseases? Pharmacol Ther 2018; 189:149-172. [PMID: 29730443 DOI: 10.1016/j.pharmthera.2018.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory diseases affect millions of people worldwide, and account for significant levels of disability and mortality. The treatment of lung cancer and asthma with therapeutic antibodies (Abs) is a breakthrough that opens up new paradigms for the management of respiratory diseases. Antibodies are becoming increasingly important in respiratory medicine; dozens of Abs have received marketing approval, and many more are currently in clinical development. Most of these Abs target asthma, lung cancer and respiratory infections, while very few target chronic obstructive pulmonary disease - one of the most common non-communicable causes of death - and idiopathic pulmonary fibrosis. Here, we review Abs approved for or in clinical development for the treatment of respiratory diseases. We notably highlight their molecular mechanisms, strengths, and likely future trends.
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Affiliation(s)
- T Sécher
- INSERM, Centre d'Etude des Pathologies Respiratoires, U1100, F-37032 Tours, France; Université François Rabelais de Tours, F-37032 Tours, France
| | - L Guilleminault
- Pôle des Voies respiratoires, Hôpital Larrey, CHU de Toulouse, F-31059 Toulouse, France; STROMALab, Université de Toulouse, CNRS ERL 5311, EFS, INP-ENVT, Inserm, UPS, F-31013 Toulouse, France
| | - K Reckamp
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - I Amanam
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - L Plantier
- INSERM, Centre d'Etude des Pathologies Respiratoires, U1100, F-37032 Tours, France; Université François Rabelais de Tours, F-37032 Tours, France; CHRU de Tours, Service de Pneumologie, F-37000 Tours, France
| | - N Heuzé-Vourc'h
- INSERM, Centre d'Etude des Pathologies Respiratoires, U1100, F-37032 Tours, France; Université François Rabelais de Tours, F-37032 Tours, France.
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6
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Affiliation(s)
- Madduri Srinivasarao
- Purdue Institute for Drug
Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Philip S. Low
- Purdue Institute for Drug
Discovery, Purdue University, West Lafayette, Indiana 47907, United States
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7
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Recent advances in the development of novel protein scaffolds based therapeutics. Int J Biol Macromol 2017; 102:630-641. [DOI: 10.1016/j.ijbiomac.2017.04.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022]
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8
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Shukla AA, Wolfe LS, Mostafa SS, Norman C. Evolving trends in mAb production processes. Bioeng Transl Med 2017; 2:58-69. [PMID: 29313024 PMCID: PMC5689530 DOI: 10.1002/btm2.10061] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 12/30/2022] Open
Abstract
Monoclonal antibodies (mAbs) have established themselves as the leading biopharmaceutical therapeutic modality. The establishment of robust manufacturing platforms are key for antibody drug discovery efforts to seamlessly translate into clinical and commercial successes. Several drivers are influencing the design of mAb manufacturing processes. The advent of biosimilars is driving a desire to achieve lower cost of goods and globalize biologics manufacturing. High titers are now routinely achieved for mAbs in mammalian cell culture. These drivers have resulted in significant evolution in process platform approaches. Additionally, several new trends in bioprocessing have arisen in keeping with these needs. These include the consideration of alternative expression systems, continuous biomanufacturing and non-chromatographic separation formats. This paper discusses these drivers in the context of the kinds of changes they are driving in mAb production processes.
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Affiliation(s)
| | - Leslie S. Wolfe
- Process Development & ManufacturingKBI Biopharma Inc.DurhamNC27704
| | - Sigma S. Mostafa
- Process Development & ManufacturingKBI Biopharma Inc.DurhamNC27704
| | - Carnley Norman
- Process Development & ManufacturingKBI Biopharma Inc.DurhamNC27704
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9
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Abstract
Gene therapy has been proposed as a means to combat cancer. However, systemic toxicity observed in preclinical trials suggested the importance of selectively targeted delivery and inducible gene expression in tumor tissues. Discovery of radiation-inducible promoter sequences provides one way to minimize inadvertent toxicity from gene therapy in normal tissues. Radiation is administered to selectively induce cytotoxic gene expression in the targeted tumor tissues. With promising results from phase II clinical trials using TNF-expressing adenovirus, it is possible to have radiation-guided gene therapy regimes once the tumor-targeted delivery has been achieved. Tumor endothelium is an attractive biological target for gene therapy, because it has the advantage of stability, accessibility, and bioavailability for therapeutic agents. Technological development of DNA microarray, proteomic profiling, and phage-displayed libraries accelerates the identification of tumor-specific endothelial biomarkers and discovery of its relevant affinity reagents for targeted delivery. The application of radiation-guided gene delivery, its amplification, as well as expression of gene therapy presents great opportunities to be employed as an alternative cancer treatment.
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Affiliation(s)
- Zhaozhong Han
- Department of Radiation Oncology, School of Medicine, Vanderbilt University, 1161 21st Ave. South, Nashville, TN 37232, USA
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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11
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Baloch AR, Baloch AW, Sutton BJ, Zhang X. Antibody mimetics: promising complementary agents to animal-sourced antibodies. Crit Rev Biotechnol 2014; 36:268-75. [PMID: 25264572 DOI: 10.3109/07388551.2014.958431] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite their wide use as therapeutic, diagnostic and detection agents, the limitations of polyclonal and monoclonal antibodies have inspired scientists to design the next generation biomedical agents, so-called antibody mimetics that offer many advantages over conventional antibodies. Antibody mimetics can be constructed by protein-directed evolution or fusion of complementarity-determining regions through intervening framework regions. Substantial progress in exploiting human, butterfly (Pieris brassicae) and bacterial systems to design and select mimetics using display technologies has been made in the past 10 years, and one of these mimetics [Kalbitor® (Dyax)] has made its way to market. Many challenges lie ahead to develop mimetics for various biomedical applications, especially those for which conventional antibodies are ineffective, and this review describes the current characteristics, construction and applications of antibody mimetics compared to animal-sourced antibodies. The possible limitations of mimetics and future perspectives are also discussed.
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Affiliation(s)
- Abdul Rasheed Baloch
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
| | - Abdul Wahid Baloch
- b Department of Plant Breeding and Genetics , Sindh Agriculture University , Tandojam , Pakistan , and
| | - Brian J Sutton
- c Randall Division of Cell and Molecular Biophysics, King's College London , London , UK
| | - Xiaoying Zhang
- a College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
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12
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Choi YS, Yoon S, Kim KL, Yoo J, Song P, Kim M, Shin YE, Yang WJ, Noh JE, Cho HS, Kim S, Chung J, Ryu SH. Computational design of binding proteins to EGFR domain II. PLoS One 2014; 9:e92513. [PMID: 24710267 PMCID: PMC3977815 DOI: 10.1371/journal.pone.0092513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/24/2014] [Indexed: 12/03/2022] Open
Abstract
We developed a process to produce novel interactions between two previously unrelated proteins. This process selects protein scaffolds and designs protein interfaces that bind to a surface patch of interest on a target protein. Scaffolds with shapes complementary to the target surface patch were screened using an exhaustive computational search of the human proteome and optimized by directed evolution using phage display. This method was applied to successfully design scaffolds that bind to epidermal growth factor receptor (EGFR) domain II, the interface of EGFR dimerization, with high reactivity toward the target surface patch of EGFR domain II. One potential application of these tailor-made protein interactions is the development of therapeutic agents against specific protein targets.
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Affiliation(s)
- Yoon Sup Choi
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- KT Institute of Convergence Technology, Seocho-gu, Seoul, Korea
| | - Soomin Yoon
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Kyung-Lock Kim
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jiho Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Parkyong Song
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Minsoo Kim
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Scripps Korea Antibody Institute, Chuncheon, Republic of Korea
| | - Young-Eun Shin
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Won Jun Yang
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Jung-eun Noh
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Hyun-soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sanguk Kim
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of IT Convergence Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
| | - Junho Chung
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
| | - Sung Ho Ryu
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
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Tiede C, Tang AAS, Deacon SE, Mandal U, Nettleship JE, Owen RL, George SE, Harrison DJ, Owens RJ, Tomlinson DC, McPherson MJ. Adhiron: a stable and versatile peptide display scaffold for molecular recognition applications. Protein Eng Des Sel 2014; 27:145-55. [PMID: 24668773 PMCID: PMC4000234 DOI: 10.1093/protein/gzu007] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We have designed a novel non-antibody scaffold protein, termed Adhiron, based on a phytocystatin consensus sequence. The Adhiron scaffold shows high thermal stability (Tm ca. 101°C), and is expressed well in Escherichia coli. We have determined the X-ray crystal structure of the Adhiron scaffold to 1.75 Å resolution revealing a compact cystatin-like fold. We have constructed a phage-display library in this scaffold by insertion of two variable peptide regions. The library is of high quality and complexity comprising 1.3 × 1010 clones. To demonstrate library efficacy, we screened against the yeast Small Ubiquitin-like Modifier (SUMO). In selected clones, variable region 1 often contained sequences homologous to the known SUMO interactive motif (V/I-X-V/I-V/I). Four Adhirons were further characterised and displayed low nanomolar affinities and high specificity for yeast SUMO with essentially no cross-reactivity to human SUMO protein isoforms. We have identified binders against >100 target molecules to date including as examples, a fibroblast growth factor (FGF1), platelet endothelial cell adhesion molecule (PECAM-1; CD31), the SH2 domain Grb2 and a 12-aa peptide. Adhirons are highly stable and well expressed allowing highly specific binding reagents to be selected for use in molecular recognition applications.
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Affiliation(s)
- Christian Tiede
- Biomedical Health Research Centre, BioScreening Technology Group, University of Leeds, Leeds LS2 9JT, UK
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14
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Pershad K, Kay BK. Generating thermal stable variants of protein domains through phage display. Methods 2012; 60:38-45. [PMID: 23276752 DOI: 10.1016/j.ymeth.2012.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022] Open
Abstract
Often in protein design research, one desires to generate thermally stable variants of a protein or domain. One route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. A library of protein domain variants can be generated by mutagenic PCR, expressed on the surface of bacteriophage M13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during subsequent affinity selection, whereas variants that still retain binding to their target are selected and enriched with each subsequent round of affinity selection. This approach takes advantage of the fact that bacteriophage M13 particles are heat stable and resistant to many proteases and protein denaturants. We present the application of this general approach to generating thermally stable variants of a eukaryotic peptide-binding domain. The benefits of producing such variants are that they typically express at high levels in Escherichia coli (30-60 mg/L shake flask) and remain soluble in solution at higher concentrations for longer periods of time than the wild-type form of the domain. The process of library generation and screening generally requires about one month of effort, and yields variants with >10 °C increase in thermal stability, as measured in a simple fluorescence-based thermal shift assay. It is anticipated that thermally stable variants will serve as excellent scaffolds for generating affinity reagents to a variety of targets of interest.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor St., 3240 SES-MC 066, Chicago, IL 60607-7060, USA
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15
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Scholz M, Lüking A. A protein-stabilizing technology for enhanced antibody stability and antibody-binding profiles in a microchip array. Biotechnol J 2012; 7:1002-7. [DOI: 10.1002/biot.201100494] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/14/2012] [Accepted: 03/13/2012] [Indexed: 11/09/2022]
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16
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Urvoas A, Guellouz A, Valerio-Lepiniec M, Graille M, Durand D, Desravines DC, van Tilbeurgh H, Desmadril M, Minard P. Design, Production and Molecular Structure of a New Family of Artificial Alpha-helicoidal Repeat Proteins (αRep) Based on Thermostable HEAT-like Repeats. J Mol Biol 2010; 404:307-27. [DOI: 10.1016/j.jmb.2010.09.048] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 09/15/2010] [Accepted: 09/21/2010] [Indexed: 01/07/2023]
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17
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Hoffmann T, Stadler LKJ, Busby M, Song Q, Buxton AT, Wagner SD, Davis JJ, Ko Ferrigno P. Structure-function studies of an engineered scaffold protein derived from stefin A. I: Development of the SQM variant. Protein Eng Des Sel 2010; 23:403-13. [PMID: 20179045 PMCID: PMC2851446 DOI: 10.1093/protein/gzq012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-antibody scaffold proteins are used for a range of applications, especially the assessment of protein-protein interactions within human cells. The search for a versatile, robust and biologically neutral scaffold previously led us to design STM (stefin A triple mutant), a scaffold derived from the intracellular protease inhibitor stefin A. Here, we describe five new STM-based scaffold proteins that contain modifications designed to further improve the versatility of our scaffold. In a step-by-step approach, we introduced restriction sites in the STM open reading frame that generated new peptide insertion sites in loop 1, loop 2 and the N-terminus of the scaffold protein. A second restriction site in 'loop 2' allows substitution of the native loop 2 sequence with alternative oligopeptides. None of the amino acid changes interfered significantly with the folding of the STM variants as assessed by circular dichroism spectroscopy. Of the five scaffold variants tested, one (stefin A quadruple mutant, SQM) was chosen as a versatile, stable scaffold. The insertion of epitope tags at varying positions showed that inserts into loop 1, attempted here for the first time, were generally well tolerated. However, N-terminal insertions of epitope tags in SQM had a detrimental effect on protein expression.
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Affiliation(s)
- Toni Hoffmann
- Section of Experimental Therapeutics, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett St, Leeds LS97TF, UK.
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Moosmeier MA, Bulkescher J, Reed J, Schnölzer M, Heid H, Hoppe-Seyler K, Hoppe-Seyler F. Transtactin: a universal transmembrane delivery system for Strep-tag II-fused cargos. J Cell Mol Med 2009; 14:1935-45. [PMID: 19602053 PMCID: PMC3823275 DOI: 10.1111/j.1582-4934.2009.00846.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The delivery of molecules into cells poses a critical problem that has to be solved for the development of diagnostic tools and therapeutic agents acting on intracellular targets. Cargos which by themselves cannot penetrate cellular membranes due to their biophysical properties can achieve cell membrane permeability by fusion to protein transduction domains (PTDs). Here, we engineered a universal delivery system based on PTD-fused Strep-Tactin, which we named Transtactin. Biochemical characterization of Transtactin variants bearing different PTDs indicated high thermal stabilities and robust secondary structures. Internalization studies demonstrated that Transtactins facilitated simple and safe transport of Strep-tag II-linked small molecules, peptides and multicomponent complexes, or biotinylated proteins into cultured human cells. Transtactin-introduced cargos were functionally active, as shown for horseradish peroxidase serving as a model protein. Our results demonstrate that Transtactin provides a universal and efficient delivery system for Strep-tag II-fused cargos.
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Affiliation(s)
- Markus A Moosmeier
- Molecular Therapy of Virus-Associated Cancers, German Cancer Research Center, Heidelberg, Germany.
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19
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Drevelle A, Urvoas A, Hamida-Rebaï MB, Van Vooren G, Nicaise M, Valerio-Lepiniec M, Desmadril M, Robert CH, Minard P. Disulfide Bond Substitution by Directed Evolution in an Engineered Binding Protein. Chembiochem 2009; 10:1349-59. [DOI: 10.1002/cbic.200800745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Grönwall C, Ståhl S. Engineered affinity proteins—Generation and applications. J Biotechnol 2009; 140:254-69. [DOI: 10.1016/j.jbiotec.2009.01.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 12/05/2008] [Accepted: 01/26/2009] [Indexed: 12/11/2022]
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21
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Vetter SW, Terentis AC, Osborne RL, Dawson JH, Goodin DB. Replacement of the axial histidine heme ligand with cysteine in nitrophorin 1: spectroscopic and crystallographic characterization. J Biol Inorg Chem 2009; 14:179-91. [PMID: 18923851 PMCID: PMC2635096 DOI: 10.1007/s00775-008-0436-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
To evaluate the potential of using heme-containing lipocalin nitrophorin 1 (NP1) as a template for protein engineering, we have replaced the native axial heme-coordinating histidine residue with glycine, alanine, and cysteine. We report here the characterization of the cysteine mutant H60C_NP1 by spectroscopic and crystallographic methods. The UV/vis, resonance Raman, and magnetic circular dichroism spectra suggest weak thiolate coordination of the ferric heme in the H60C_NP1 mutant. Reduction to the ferrous state resulted in loss of cysteine coordination, while addition of exogenous imidazole ligands gave coordination changes that varied with the ligand. Depending on the substitution of the imidazole, we could distinguish three heme coordination states: five-coordinate monoimidazole, six-coordinate bisimidazole, and six-coordinate imidazole/thiolate. Ligand binding affinities were measured and found to be generally 2-3 orders of magnitude lower for the H60C mutant relative to NP1. Two crystal structures of the H60C_NP1 in complex with imidazole and histamine were solved to 1.7- and 1.96-A resolution, respectively. Both structures show that the H60C mutation is well tolerated by the protein scaffold and suggest that heme-thiolate coordination in H60C_NP1 requires some movement of the heme within its binding cavity. This adjustment may be responsible for the ease with which the engineered heme-thiolate coordination can be displaced by exogenous ligands.
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Affiliation(s)
- Stefan W Vetter
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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22
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Zsila F, Matsunaga H, Bikádi Z, Haginaka J. Multiple ligand-binding properties of the lipocalin member chicken α1-acid glycoprotein studied by circular dichroism and electronic absorption spectroscopy: The essential role of the conserved tryptophan residue. Biochim Biophys Acta Gen Subj 2006; 1760:1248-73. [PMID: 16813999 DOI: 10.1016/j.bbagen.2006.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Revised: 04/19/2006] [Accepted: 04/25/2006] [Indexed: 11/28/2022]
Abstract
Multiple ligand-binding properties of the 30-kDa chicken alpha(1)-acid glycoprotein (cAGP), a member of the lipocalin protein family, were investigated for the first time by using circular dichroism (CD) and UV/Vis absorption spectroscopy methods. By measuring induced CD (ICD) spectra, high-affinity binding (K(a) approximately 10(5)-10(6) M(-1)) of several drugs, dyes and natural compounds to cAGP was demonstrated including antimalarial agents (quinacrine, primaquine), phenotiazines (chlorpromazine, methylene blue), propranolol, non-steroidal antiinflammatory drugs (ketoprofen, diclofenac), tamoxifen, diazepam, tacrine, dicoumarol, cationic dyes (auramine O, thioflavine T, ethidium bromide), benzo[a]pyrene, L-thyroxine, bile pigments (bilirubin, biliverdin), alkaloids (piperine, aristolochic acid), saturated and unsaturated fatty acids. Analysis of the extrinsic CD spectra with the study of the covalently modified protein and CD displacement experiments revealed that a single Trp26 residue of cAGP conserved in the whole lipocalin family is part of the binding site, and it is essentially involved in the ligand-binding process via pi-pi stacking interaction resulting in the appearance of strong induced CD bands due to the non-degenerate intermolecular exciton coupling between the pi-pi* transitions of the stacked indole ring-ligand chromophore. The finding that cAGP is able to accommodate a broad spectrum of ligands belonging to different chemical classes suggests that its core beta-barrel cavity is unusually wide containing overlapping sub-sites. Significance of these new data in understanding of the ligand-binding properties of other lipocalins, especially that of human AGP, and potential practical applications are briefly discussed. Overall, cAGP serves as a simple, ultimate model to extend our knowledge on ligand-binding properties of lipocalins and to study the role of tryptophan residues in molecular recognition processes.
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Affiliation(s)
- Ferenc Zsila
- Department of Molecular Pharmacology, Institute of Biomolecular Chemistry, Chemical Research Center, Budapest, P.O. Box 17, H-1525, Hungary.
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