1
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Li Y, Zhang H, Fu Y, Zhou Z, Yu W, Zhou J, Li J, Du G, Liu S. Enhancing Acid Resistance of Aspergillus niger Pectin Lyase through Surface Charge Design for Improved Application in Juice Clarification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11652-11662. [PMID: 38738910 DOI: 10.1021/acs.jafc.4c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Pectin lyases (PNLs) can enhance juice clarity and flavor by degrading pectin in highly esterified fruits, but their inadequate acid resistance leads to rapid activity loss in juice. This study aimed to improve the acid resistance of Aspergillus niger PNL pelA through surface charge design. A modification platform was established by fusing pelA with a protein tag and expressing the fusion enzyme in Escherichia coli. Four single-point mutants were identified to increase the surface charge using computational tools. Moreover, the combined mutant M6 (S514D/S538E) exhibited 99.8% residual activity at pH 3.0. The M6 gene was then integrated into the A. niger genome using a multigene integration system to obtain the recombinant PNL AM6. Notably, AM6 improved the light transmittance of orange juice to 45.3%, which was 8.39 times higher than that of pelA. In conclusion, AM6 demonstrated the best-reported acid resistance, making it a promising candidate for industrial juice clarification.
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Affiliation(s)
- Yangyang Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Haiyun Zhang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yishan Fu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Zhitong Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Wenwen Yu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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2
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Kim DN, McNaughton AD, Kumar N. Leveraging Artificial Intelligence to Expedite Antibody Design and Enhance Antibody-Antigen Interactions. Bioengineering (Basel) 2024; 11:185. [PMID: 38391671 PMCID: PMC10886287 DOI: 10.3390/bioengineering11020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
This perspective sheds light on the transformative impact of recent computational advancements in the field of protein therapeutics, with a particular focus on the design and development of antibodies. Cutting-edge computational methods have revolutionized our understanding of protein-protein interactions (PPIs), enhancing the efficacy of protein therapeutics in preclinical and clinical settings. Central to these advancements is the application of machine learning and deep learning, which offers unprecedented insights into the intricate mechanisms of PPIs and facilitates precise control over protein functions. Despite these advancements, the complex structural nuances of antibodies pose ongoing challenges in their design and optimization. Our review provides a comprehensive exploration of the latest deep learning approaches, including language models and diffusion techniques, and their role in surmounting these challenges. We also present a critical analysis of these methods, offering insights to drive further progress in this rapidly evolving field. The paper includes practical recommendations for the application of these computational techniques, supplemented with independent benchmark studies. These studies focus on key performance metrics such as accuracy and the ease of program execution, providing a valuable resource for researchers engaged in antibody design and development. Through this detailed perspective, we aim to contribute to the advancement of antibody design, equipping researchers with the tools and knowledge to navigate the complexities of this field.
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Affiliation(s)
- Doo Nam Kim
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Andrew D McNaughton
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
| | - Neeraj Kumar
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99352, USA
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3
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Lang L, Böhler H, Wagler H, Beck T. Assembly Requirements for the Construction of Large-Scale Binary Protein Structures. Biomacromolecules 2024; 25:177-187. [PMID: 38059469 DOI: 10.1021/acs.biomac.3c00891] [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: 12/08/2023]
Abstract
The precise assembly of multiple biomacromolecules into well-defined structures and materials is of great importance for various biomedical and nanobiotechnological applications. In this study, we investigate the assembly requirements for two-component materials using charged protein nanocages as building blocks. To achieve this, we designed several variants of ferritin nanocages to determine the surface characteristics necessary for the formation of large-scale binary three-dimensional (3D) assemblies. These nanocage variants were employed in protein crystallization experiments and macromolecular crystallography analyses, complemented by computational methods. Through the screening of nanocage variant combinations at various ionic strengths, we identified three essential features for successful assembly: (1) the presence of a favored crystal contact region, (2) the presence of a charged patch not involved in crystal contacts, and (3) sufficient distinctiveness between the nanocages. Surprisingly, the absence of noncrystal contact mediating patches had a detrimental effect on the assemblies, highlighting their unexpected importance. Intriguingly, we observed the formation of not only binary structures but also both negatively and positively charged unitary structures under previously exclusively binary conditions. Overall, our findings will inform future design strategies by providing some design rules, showcasing the utility of supercharging symmetric building blocks in facilitating the assembly of biomacromolecules into large-scale binary 3D assemblies.
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Affiliation(s)
- Laurin Lang
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Hendrik Böhler
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Henrike Wagler
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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4
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Kumar N, Towers D, Myers S, Galvin C, Kireev D, Ellington AD, Akinwande D. Graphene Field Effect Biosensor for Concurrent and Specific Detection of SARS-CoV-2 and Influenza. ACS NANO 2023; 17:18629-18640. [PMID: 37703454 DOI: 10.1021/acsnano.3c07707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The SARS-CoV-2 pandemic has highlighted the need for devices capable of carrying out rapid differential detection of viruses that may manifest similar physiological symptoms yet demand tailored treatment plans. Seasonal influenza may be exacerbated by COVID-19 infections, increasing the burden on healthcare systems. In this work, we demonstrate a technology based on liquid-gated graphene field-effect transistors (GFETs), for rapid and ultraprecise sensing and differentiation of influenza and SARS-CoV-2 surface protein. Most distinctively, the device consists of 4 onboard GFETs arranged in a quadruple architecture, where each quarter is functionalized individually (with either antibodies or chemically passivated control) but measured jointly. The sensor platform was tested against a range of concentrations of viral surface proteins from both viruses with the lowest tested and detected concentration at ∼50 ag/mL, or 88 zM for COVID-19 and 227 zM for Flu, which is 5-fold lower than the values reported previously on a similar platform. Unlike the classic real-time polymerase chain reaction test, which has a turnaround time of a few hours, the graphene technology presents an ultrafast response time of ∼10 s even in complex and clinically relevant media such as saliva. Thus, we have developed a multianalyte, highly sensitive, and fault-tolerant technology for rapid diagnostic of contemporary, emerging, and future pandemics.
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Affiliation(s)
- Neelotpala Kumar
- Microelectronics Research Center, The University of Texas at Austin, Austin, Texas 78758, United States
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dalton Towers
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Samantha Myers
- College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Cooper Galvin
- College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Dmitry Kireev
- Microelectronics Research Center, The University of Texas at Austin, Austin, Texas 78758, United States
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Biomedical Engineering, University of Massachusetts Amherst, Massachusetts 01003, United States
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Deji Akinwande
- Microelectronics Research Center, The University of Texas at Austin, Austin, Texas 78758, United States
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Kettisen K, Nyblom M, Smeds E, Fago A, Bülow L. Structural and oxidative investigation of a recombinant high-yielding fetal hemoglobin mutant. Front Mol Biosci 2023; 10:1133985. [PMID: 37006610 PMCID: PMC10060959 DOI: 10.3389/fmolb.2023.1133985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Human fetal hemoglobin (HbF) is an attractive starting protein for developing an effective agent for oxygen therapeutics applications. This requires that HbF can be produced in heterologous systems at high levels and in a homogeneous form. The introduction of negative charges on the surface of the α-chain in HbF can enhance the recombinant production yield of a functional protein in Escherichia coli. In this study, we characterized the structural, biophysical, and biological properties of an HbF mutant carrying four additional negative charges on each α-chain (rHbFα4). The 3D structure of the rHbFα4 mutant was solved with X-ray crystallography at 1.6 Å resolution. Apart from enabling a higher yield in recombinant protein production in E. coli, we observed that the normal DNA cleavage activity of the HbF was significantly lowered, with a four-time reduced rate constant for the rHbFα4 mutant. The oxygen-binding properties of the rHbFα4 mutant were identical to the wild-type protein. No significant difference between the wild-type and rHbFα4 was observed for the investigated oxidation rates (autoxidation and H2O2-mediated ferryl formation). However, the ferryl reduction reaction indicated some differences, which appear to be related to the reaction rates linked to the α-chain.
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Affiliation(s)
- Karin Kettisen
- Pure and Applied Biochemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Maria Nyblom
- Lund Protein Production Platform, Department of Biology, Lund University, Lund, Sweden
| | - Emanuel Smeds
- Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
- Anesthesiology and Intensive Care, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Angela Fago
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Leif Bülow
- Pure and Applied Biochemistry, Department of Chemistry, Lund University, Lund, Sweden
- *Correspondence: Leif Bülow,
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6
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Böhler H, Rütten M, Lang L, Beck T. Crystalline Biohybrid Materials Based on Protein Cages. Methods Mol Biol 2023; 2671:361-386. [PMID: 37308656 DOI: 10.1007/978-1-0716-3222-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Highly ordered superstructures of nanomaterials can be synthesized using protein cages as templates for the assembly of inorganic nanoparticles. Here, we describe in detail the creation of these biohybrid materials. The approach involves computational redesign of ferritin cages, followed by recombinant protein production and purification of the new variants. Metal oxide nanoparticles are synthesized inside the surface-charged variants. The composites are assembled using protein crystallization to yield highly ordered superlattices, which are characterized, for example, with small angle X-ray scattering. This protocol provides a detailed and comprehensive account on our newly established strategy for the synthesis of crystalline biohybrid materials.
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Affiliation(s)
- Hendrik Böhler
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Hamburg, Germany
| | - Michael Rütten
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Hamburg, Germany
| | - Laurin Lang
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
| | - Tobias Beck
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Hamburg, Germany.
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany.
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7
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Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
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Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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8
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Lai HM, Tang Y, Lau ZYH, Campbell RAA, Yau JCN, Chan CCY, Chan DCW, Wong TY, Wong HKT, Yan LYC, Wu WKK, Wong SH, Kwok KW, Wing YK, Lam HHN, Ng HK, Mrsic-Flogel TD, Mok VCT, Chan JYK, Ko H. Antibody stabilization for thermally accelerated deep immunostaining. Nat Methods 2022; 19:1137-1146. [PMID: 36050489 PMCID: PMC9467915 DOI: 10.1038/s41592-022-01569-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/27/2022] [Indexed: 01/02/2023]
Abstract
Antibodies have diverse applications due to their high reaction specificities but are sensitive to denaturation when a higher working temperature is required. We have developed a simple, highly scalable and generalizable chemical approach for stabilizing off-the-shelf antibodies against thermal and chemical denaturation. We demonstrate that the stabilized antibodies (termed SPEARs) can withstand up to 4 weeks of continuous heating at 55 °C and harsh denaturants, and apply our method to 33 tested antibodies. SPEARs enable flexible applications of thermocycling and denaturants to dynamically modulate their binding kinetics, reaction equilibrium, macromolecular diffusivity and aggregation propensity. In particular, we show that SPEARs permit the use of a thermally facilitated three-dimensional immunolabeling strategy (termed ThICK staining), achieving whole mouse brain immunolabeling within 72 h, as well as nearly fourfold deeper penetration with threefold less antibodies in human brain tissue. With faster deep-tissue immunolabeling and broad compatibility with tissue processing and clearing methods without the need for any specialized equipment, we anticipate the wide applicability of ThICK staining with SPEARs for deep immunostaining. Thermostable antibodies called SPEARs enable rapid immunostaining with improved tissue penetration.
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Affiliation(s)
- Hei Ming Lai
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Margaret K. L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Yumi Tang
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zachary Y H Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Robert A A Campbell
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, UK
| | - Juno C N Yau
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Caleb C Y Chan
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Danny C W Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Margaret K. L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Harriet K T Wong
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Leo Y C Yan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong.,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sunny H Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, Hong Kong.,Lee Kong Chian School of Medicine, Nanyang Technological University, Nanyang Avenue, Singapore
| | - Ka-Wai Kwok
- Department of Mechanical Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yun-Kwok Wing
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong.,Margaret K. L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Henry H N Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Thomas D Mrsic-Flogel
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, UK
| | - Vincent C T Mok
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong.,Margaret K. L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jason Y K Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ho Ko
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Margaret K. L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Shatin, Hong Kong. .,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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9
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Shang Y, Li L, Zhang T, Luo Q, Yu Q, Zeng Z, Li L, Jia M, Tang G, Fan S, Lu Q, Zhang W, Xue Y, Wang H, Liu W, Wang H, Zhang R, Ding C, Shao H, Wen G. Quantitative regulation of the thermal stability of enveloped virus vaccines by surface charge engineering to prevent the self-aggregation of attachment glycoproteins. PLoS Pathog 2022; 18:e1010564. [PMID: 35679257 PMCID: PMC9182686 DOI: 10.1371/journal.ppat.1010564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/01/2022] [Indexed: 11/18/2022] Open
Abstract
The development of thermostable vaccines can relieve the bottleneck of existing vaccines caused by thermal instability and subsequent poor efficacy, which is one of the predominant reasons for the millions of deaths caused by vaccine-preventable diseases. Research into the mechanism of viral thermostability may provide strategies for developing thermostable vaccines. Using Newcastle disease virus (NDV) as model, we identified the negative surface charge of attachment glycoprotein as a novel determinant of viral thermostability. It prevented the temperature-induced aggregation of glycoprotein and subsequent detachment from virion surface. Then structural stability of virion surface was improved and virus could bind to and infect cells efficiently after heat-treatment. Employing the approach of surface charge engineering, thermal stability of NDV and influenza A virus (IAV) vaccines was successfully improved. The increase in the level of vaccine thermal stability was determined by the value-added in the negative surface charge of the attachment glycoprotein. The engineered live and inactivated vaccines could be used efficiently after storage at 37°C for at least 10 and 60 days, respectively. Thus, our results revealed a novel surface-charge-mediated link between HN protein and NDV thermostability, which could be used to design thermal stable NDV and IAV vaccines rationally.
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Affiliation(s)
- Yu Shang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Li Li
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Tengfei Zhang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Qingping Luo
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Qingzhong Yu
- US National Poultry Research Center, Agricultural Research Services, United States Department of Agriculture, Athens, Georgia, United States of America
| | - Zhe Zeng
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Lintao Li
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Miaomiao Jia
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Guoyi Tang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Sanlin Fan
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Qin Lu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Wenting Zhang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Yuhan Xue
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Hongling Wang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Wei Liu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Hongcai Wang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Rongrong Zhang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huabin Shao
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Wuhan, China
| | - Guoyuan Wen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan, China
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Wuhan, China
- * E-mail:
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10
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Paik I, Bhadra S, Ellington AD. Charge Engineering Improves the Performance of Bst DNA Polymerase Fusions. ACS Synth Biol 2022; 11:1488-1496. [PMID: 35320674 DOI: 10.1021/acssynbio.1c00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The charge states of proteins can greatly influence their stabilities and interactions with substrates, and the addition of multiple charges (supercharging) has been shown to be a successful approach for engineering protein stability and function. The addition of a fast-folding fusion domain to the Bacillus stearothermophilus DNA polymerase improved its functionality in isothermal amplification assays, and further charge engineering of this domain has increased both protein stability and diagnostics performance. When combined with mutations that stabilize the core of the protein, the charge-engineered fusion domain leads to the ability to carry out loop-mediated isothermal amplification (LAMP) at temperatures up to 74° C or in the presence of high concentrations of urea, with detection times under 10 min. Adding both positive and negative charges to the fusion domain led to changes in the relative reverse transcriptase and DNA polymerase activities of the polymerase. Overall, the development of a modular fusion domain whose charged surface can be modified at will should prove to be of use in the engineering of other polymerases and, in general, may prove useful for protein stabilization.
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Affiliation(s)
- Inyup Paik
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sanchita Bhadra
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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11
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Guo R, Sinha NJ, Misra R, Tang Y, Langenstein M, Kim K, Fagan JA, Kloxin CJ, Jensen G, Pochan DJ, Saven JG. Computational Design of Homotetrameric Peptide Bundle Variants Spanning a Wide Range of Charge States. Biomacromolecules 2022; 23:1652-1661. [PMID: 35312288 DOI: 10.1021/acs.biomac.1c01539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the ability to design their sequences and structures, peptides can be engineered to realize a wide variety of functionalities and structures. Herein, computational design was used to identify a set of 17 peptides having a wide range of putative charge states but the same tetrameric coiled-coil bundle structure. Calculations were performed to identify suitable locations for ionizable residues (D, E, K, and R) at the bundle's exterior sites, while interior hydrophobic interactions were retained. The designed bundle structures spanned putative charge states of -32 to +32 in units of electron charge. The peptides were experimentally investigated using spectroscopic and scattering techniques. Thermal stabilities of the bundles were investigated using circular dichroism. Molecular dynamics simulations assessed structural fluctuations within the bundles. The cylindrical peptide bundles, 4 nm long by 2 nm in diameter, were covalently linked to form rigid, micron-scale polymers and characterized using transmission electron microscopy. The designed suite of sequences provides a set of readily realized nanometer-scale structures of tunable charge that can also be polymerized to yield rigid-rod polyelectrolytes.
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Affiliation(s)
- Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Rajkumar Misra
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Yao Tang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Kyunghee Kim
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffrey A Fagan
- Materials Science and Engineering Division, National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Grethe Jensen
- NIST Center for Neutron Research (NCNR), National Institute of Standards & Technology (NIST), Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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ElGamacy M. Accelerating therapeutic protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:85-118. [PMID: 35534117 DOI: 10.1016/bs.apcsb.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein structures provide for defined microenvironments that can support complex pharmacological functions, otherwise unachievable by small molecules. The advent of therapeutic proteins has thus greatly broadened the range of manageable disorders. Leveraging the knowledge and recent advances in de novo protein design methods has the prospect of revolutionizing how protein drugs are discovered and developed. This review lays out the main challenges facing therapeutic proteins discovery and development, and how present and future advancements of protein design can accelerate the protein drug pipelines.
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Affiliation(s)
- Mohammad ElGamacy
- University Hospital Tübingen, Division of Translational Oncology, Tübingen, Germany; Max Planck Institute for Biology, Tübingen, Germany.
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13
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Thumuluri V, Martiny HM, Almagro Armenteros JJ, Salomon J, Nielsen H, Johansen AR. NetSolP: predicting protein solubility in Escherichia coli using language models. Bioinformatics 2022; 38:941-946. [PMID: 35088833 DOI: 10.1093/bioinformatics/btab801] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/13/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Solubility and expression levels of proteins can be a limiting factor for large-scale studies and industrial production. By determining the solubility and expression directly from the protein sequence, the success rate of wet-lab experiments can be increased. RESULTS In this study, we focus on predicting the solubility and usability for purification of proteins expressed in Escherichia coli directly from the sequence. Our model NetSolP is based on deep learning protein language models called transformers and we show that it achieves state-of-the-art performance and improves extrapolation across datasets. As we find current methods are built on biased datasets, we curate existing datasets by using strict sequence-identity partitioning and ensure that there is minimal bias in the sequences. AVAILABILITY AND IMPLEMENTATION The predictor and data are available at https://services.healthtech.dtu.dk/service.php?NetSolP and the open-sourced code is available at https://github.com/tvinet/NetSolP-1.0. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Hannah-Marie Martiny
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby 2800, Denmark
| | - Jose J Almagro Armenteros
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Henrik Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Alexander Rosenberg Johansen
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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14
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Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2313:57-113. [PMID: 34478132 DOI: 10.1007/978-1-0716-1450-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.
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15
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Wang X, Du J, Zhao B, Wang H, Rao S, Du G, Zhou J, Chen J, Liu S. Significantly Improving the Thermostability and Catalytic Efficiency of Streptomyces mobaraenesis Transglutaminase through Combined Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15268-15278. [PMID: 34874715 DOI: 10.1021/acs.jafc.1c05256] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Streptomyces mobaraenesis transglutaminase has been widely used in food processing. We here significantly improved the catalytic properties of S2P-S23V-Y24N-S199A-K294L (TGm1), a highly stabilized variant of the transglutaminase. First, a virtual proline scan was performed based on folding free energy changes to obtain TGm1 variants with enhanced thermostability. Second, the residues within 15 Å of Cys64 in the enzyme-substrate complex of TGm1 were subjected to virtual saturation mutagenesis to generate the variants with reduced binding free energy and increased activity. After combining the favorable mutations, we obtained the variant FRAPD-TGm1-E28T-A265P-A287P (FRAPD-TGm2), exhibiting 66.9 min of half-life at 60 °C (t1/2(60 °C)), 67.8 °C of melting temperature (Tm), and 71.8 U/mg of specific activity, which are 2-fold, 2.6 °C, and 43.8% higher than those of FRAPD-TGm1, respectively. At last, to increase the surface negative net charge of FRAPD-TGm2, we introduced the mutations N96E-S144E-N163D-R183E-R208E-K325E, yielding FRAPD-TGm3. The latter's t1/2(60 °C), Tm, and specific activity were 122.9 min, 68.6 °C, and 83.7 U/mg, which are 83.8%, 0.8 °C, and 16.6% higher than the former, respectively. FRAPD-TGm3 is thus a robust candidate for transglutaminase application.
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Affiliation(s)
- Xinglong Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jianhui Du
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Beichen Zhao
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Haiyan Wang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 214122, China
| | - Guocheng Du
- College of Food Science and Engineering, Yangzhou University, Yangzhou, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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16
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Bulos JA, Guo R, Wang Z, DeLessio MA, Saven JG, Dmochowski IJ. Design of a Superpositively Charged Enzyme: Human Carbonic Anhydrase II Variant with Ferritin Encapsulation and Immobilization. Biochemistry 2021; 60:3596-3609. [PMID: 34757723 DOI: 10.1021/acs.biochem.1c00515] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Supercharged proteins exhibit high solubility and other desirable properties, but no engineered superpositively charged enzymes have previously been made. Superpositively charged variants of proteins such as green fluorescent protein have been efficiently encapsulated within Archaeoglobus fulgidus thermophilic ferritin (AfFtn). Encapsulation by supramolecular ferritin can yield systems with a variety of sequestered cargo. To advance applications in enzymology and green chemistry, we sought a general method for supercharging an enzyme that retains activity and is compatible with AfFtn encapsulation. The zinc metalloenzyme human carbonic anhydrase II (hCAII) is an attractive encapsulation target based on its hydrolytic activity and physiologic conversion of carbon dioxide to bicarbonate. A computationally designed variant of hCAII contains positively charged residues substituted at 19 sites on the protein's surface, resulting in a shift of the putative net charge from -1 to +21. This designed hCAII(+21) exhibits encapsulation within AfFtn without the need for fusion partners or additional reagents. The hCAII(+21) variant retains esterase activity comparable to the wild type and spontaneously templates the assembly of AfFtn 24mers around itself. The AfFtn-hCAII(+21) host-guest complex exhibits both greater activity and thermal stability when compared to hCAII(+21). Upon immobilization on a solid support, AfFtn-hCAII(+21) retains enzymatic activity and exhibits an enhancement of activity at elevated temperatures.
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Affiliation(s)
- Joshua A Bulos
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rui Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhiheng Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Maegan A DeLessio
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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17
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ATP and Tri-Polyphosphate (TPP) Suppress Protein Aggregate Growth by a Supercharging Mechanism. Biomedicines 2021; 9:biomedicines9111646. [PMID: 34829875 PMCID: PMC8616003 DOI: 10.3390/biomedicines9111646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
A common strategy to increase aggregation resistance is through rational mutagenesis to supercharge proteins, which leads to high colloidal stability, but often has the undesirable effect of lowering conformational stability. We show this trade-off can be overcome by using small multivalent polyphosphate ions, adenosine triphosphate (ATP) and tripolyphosphate (TPP) as excipients. These ions are equally effective at suppressing aggregation of ovalbumin and bovine serum albumin (BSA) upon thermal stress as monitored by dynamic and static light scattering. Monomer loss kinetic studies, combined with measurements of native state protein–protein interactions and ζ-potentials, indicate the ions reduce aggregate growth by increasing the protein colloidal stability through binding and overcharging the protein. Out of three additional proteins studied, ribonuclease A (RNaseA), α-chymotrypsinogen (α-Cgn), and lysozyme, we only observed a reduction in aggregate growth for RNaseA, although overcharging by the poly-phosphate ions still occurs for lysozyme and α-Cgn. Because the salts do not alter protein conformational stability, using them as excipients could be a promising strategy for stabilizing biopharmaceuticals once the protein structural factors that determine whether multivalent ion binding will increase colloidal stability are better elucidated. Our findings also have biological implications. Recently, it has been proposed that ATP also plays an important role in maintaining intracellular biological condensates and preventing protein aggregation in densely packed cellular environments. We expect electrostatic interactions are a significant factor in determining the stabilizing ability of ATP towards maintaining proteins in non-dispersed states in vivo.
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18
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Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences. Sci Rep 2021; 11:21362. [PMID: 34725391 PMCID: PMC8560851 DOI: 10.1038/s41598-021-00669-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/05/2021] [Indexed: 01/01/2023] Open
Abstract
The design of superior biologic therapeutics, including antibodies and engineered proteins, involves optimizing their specific ability to bind to disease-related molecular targets. Previously, we developed and applied the Assisted Design of Antibody and Protein Therapeutics (ADAPT) platform for virtual affinity maturation of antibodies (Vivcharuk et al. in PLoS One 12(7):e0181490, 10.1371/journal.pone.0181490, 2017). However, ADAPT is limited to point mutations of hot-spot residues in existing CDR loops. In this study, we explore the possibility of wholesale replacement of the entire H3 loop with no restriction to maintain the parental loop length. This complements other currently published studies that sample replacements for the CDR loops L1, L2, L3, H1 and H2. Given the immense sequence space theoretically available to H3, we focused on the virtual grafting of over 5000 human germline-derived H3 sequences from the IGMT/LIGM database increasing the diversity of the sequence space when compared to using crystalized H3 loop sequences. H3 loop conformations are generated and scored to identify optimized H3 sequences. Experimental testing of high-ranking H3 sequences grafted into the framework of the bH1 antibody against human VEGF-A led to the discovery of multiple hits, some of which had similar or better affinities relative to the parental antibody. In over 75% of the tested designs, the re-designed H3 loop contributed favorably to overall binding affinity. The hits also demonstrated good developability attributes such as high thermal stability and no aggregation. Crystal structures of select re-designed H3 variants were solved and indicated that although some deviations from predicted structures were seen in the more solvent accessible regions of the H3 loop, they did not significantly affect predicted affinity scores.
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19
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Arunmanee W, Duangkaew M, Taweecheep P, Aphicho K, Lerdvorasap P, Pitchayakorn J, Intasuk C, Jiraratmetacon R, Syamsidi A, Chanvorachote P, Chaotham C, Pornputtapong N. Resurfacing receptor binding domain of Colicin N to enhance its cytotoxic effect on human lung cancer cells. Comput Struct Biotechnol J 2021; 19:5225-5234. [PMID: 34630940 PMCID: PMC8479544 DOI: 10.1016/j.csbj.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022] Open
Abstract
Colicin N (ColN) is a bacteriocin secreted by Escherichia coli (E. coli) to kill other Gram-negative bacteria by forcefully generating ion channels in the inner membrane. In addition to its bactericidal activity, ColN have been reported to selectively induce apoptosis in human lung cancer cells via the suppression of integrin modulated survival pathway. However, ColN showed mild toxicity against human lung cancer cells which could be improved for further applications. The protein resurfacing strategy was chosen to engineer ColN by extensive mutagenesis at solvent-exposed residues on ColN. The highly accessible Asp and Glu on wildtype ColN (ColNWT) were replaced by Lys to create polycationic ColN (ColN+12). Previous studies have shown that increase of positive charges on proteins leads to the enhancement of mammalian cell penetration as well as increased interaction with negatively charged surface of cancer cells. Those solvent-exposed residues of ColN were identified by Rosetta and AvNAPSA (Average number of Neighboring Atoms Per Sidechain Atom) approaches. The findings revealed that the structural features and stability of ColN+12 determined by circular dichroism were similar to ColNWT. Furthermore, the toxicity of ColN+12 was cancer selective. Human lung cancer cells, H460 and H23, were sensitive to ColN but human dermal papilla cells were not. ColN+12 also showed more potent toxicity than ColNWT in cancer cells. This confirmed that polycationic resurfacing method has enabled us to improve the anticancer activity of ColN towards human lung cancer cells.
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Affiliation(s)
- Wanatchaporn Arunmanee
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Methawee Duangkaew
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchanok Taweecheep
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanokpol Aphicho
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panuwat Lerdvorasap
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jesada Pitchayakorn
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chayada Intasuk
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Runglada Jiraratmetacon
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Armini Syamsidi
- Department of Pharmacy, Faculty of Science, Tadulako University, Central Sulawesi 94118, Indonesia
| | - Pithi Chanvorachote
- Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chatchai Chaotham
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Cell-based Drug and Health Products Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Natapol Pornputtapong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Corresponding author.
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20
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Kopp MRG, Wolf Pérez AM, Zucca MV, Capasso Palmiero U, Friedrichsen B, Lorenzen N, Arosio P. An accelerated surface-mediated stress assay of antibody instability for developability studies. MAbs 2021; 12:1815995. [PMID: 32954930 PMCID: PMC7577746 DOI: 10.1080/19420862.2020.1815995] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
High physical stability is required for the development of monoclonal antibodies (mAbs) into successful therapeutic products. Developability assays are used to predict physical stability issues such as high viscosity and poor conformational stability, but protein aggregation remains a challenging property to predict. Among different types of stresses, air–water and solid–liquid interfaces are well known to potentially trigger protein instability and induce aggregation. Yet, in contrast to the increasing number of developability assays to evaluate bulk properties, there is still a lack of experimental methods to evaluate antibody stability against interfaces. Here, we investigate the potential of a hydrophobic nanoparticle surface-mediated stress assay to assess the stability of mAbs during the early stages of development. We evaluate this surface-mediated accelerated stability assay on a rationally designed library of 14 variants of a humanized IgG4, featuring a broad span of solubility values and other developability properties. The assay could identify variants characterized by high instability against agitation in the presence of air–water interfaces. Remarkably, for the set of investigated molecules, we observe strong correlations between the extent of aggregation induced by the surface-mediated stress assay and other developability properties of the molecules, such as aggregation upon storage at 45°C, self-association (evaluated by affinity-capture self-interaction nanoparticle spectroscopy) and nonspecific interactions (estimated by cross-interaction chromatography, stand-up monolayer chromatography (SMAC), SMAC*). This highly controlled surface-mediated stress assay has the potential to complement and increase the ability of the current set of screening techniques to assess protein aggregation and developability potential of mAbs during the early stages of drug development. Abbreviations:AC-SINS: Affinity-Capture Self-Interaction Nanoparticle Spectroscopy; AMS: Ammonium sulfate precipitation; ANS: 1-anilinonaphtalene-8-sulfonate; CIC: Cross-interaction chromatography; DLS: Dynamic light scattering; HIC: Hydrophobic interaction chromatography; HNSSA: Hydrophobic nanoparticles surface-stress assay; mAb: Monoclonal antibody; NP: Nanoparticle; SEC: Size exclusion chromatography; SMAC: Stand-up monolayer chromatography; WT: Wild type
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Affiliation(s)
- Marie R G Kopp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Adriana-Michelle Wolf Pérez
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark.,Aarhus University, iNANO , Aarhus C, Denmark
| | - Marta Virginia Zucca
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
| | | | - Nikolai Lorenzen
- Department of Biophysics, Biophysics and Injectable Formulation, Novo Nordisk , Måløv, Denmark
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Swiss Federal Institute of Technology , Zurich, Switzerland
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21
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Positive charge in the complementarity-determining regions of synthetic nanobody prevents aggregation. Biochem Biophys Res Commun 2021; 572:1-6. [PMID: 34332323 DOI: 10.1016/j.bbrc.2021.07.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 01/19/2023]
Abstract
In the past, specificity and affinity were the priority for synthetic antibody library. However, therapeutic antibodies need good stability for medical use. Through carefully adjust the chemical diversity in CDRs, one hopes to design a synthetic antibody library with good developability. Here we thoroughly analyzed 296 nanobody sequences and structures, constructed a fully-functional synthetic nanobody library, evaluated the relationship between aggregation and isoelectric point, and found that high-pI nanobodies were more resistant to aggregation than low-pIs. As we used the same framework for constructing the library, CDRs charge played a crucial role in mediating nanobody aggregation. We also analyzed the theoretical pI of 296 nanobodies from PDB, about 75% had basic pI, only 25% were acidic. Those results provided useful guidelines for designing next-generation synthetic nanobody libraries and for identifying potent and safe nanobody therapeutics.
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22
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Meric G, Naik S, Hunter AK, Robinson AS, Roberts CJ. Challenges for design of aggregation-resistant variants of granulocyte colony-stimulating factor. Biophys Chem 2021; 277:106630. [PMID: 34119805 DOI: 10.1016/j.bpc.2021.106630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/14/2021] [Accepted: 05/31/2021] [Indexed: 01/15/2023]
Abstract
Non-native protein aggregation is a long-standing issue in pharmaceutical biotechnology. A rational design approach was used in order to identify variants of recombinant human granulocyte colony-stimulating factor (rhG-CSF) with lower aggregation propensity at solution conditions that are typical of commercial formulation. The approach used aggregation-prone-region (APR) predictors to select single amino acid substitutions that were predicted to decrease intrinsic aggregation propensity (IAP). The results of static light scattering temperature-ramps and chemical unfolding experiments demonstrated that none of the selected variants exhibited improved aggregation resistance, and the apparent conformational stability of each variant was lower than that of WT. Aggregation studies under partly denaturing conditions suggested that the IAP of at least one variant remained unaltered. Overall, this study highlights a general challenge in designing aggregation resistance for proteins, due to the need to accurately predict both APRs and conformational stability.
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Affiliation(s)
- Gulsum Meric
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| | - Subhashchandra Naik
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
| | - Alan K Hunter
- Biopharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, MD 20878, United States.
| | - Anne S Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, United States.
| | - Christopher J Roberts
- Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States.
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23
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Kasahara K, Kuroda D, Tanabe A, Kawade R, Nagatoishi S, Tsumoto K. Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range. Biochem Biophys Res Commun 2021; 563:54-59. [PMID: 34058475 DOI: 10.1016/j.bbrc.2021.05.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 05/16/2021] [Indexed: 12/27/2022]
Abstract
Proteins function through interactions with other molecules. In protein engineering, scientists often engineer proteins by mutating their amino acid sequences on the protein surface to improve various physicochemical properties. "Supercharging" is a method to design proteins by mutating surface residues with charged amino acids. Previous studies demonstrated that supercharging mutations conferred better thermal resistance, solubility, and cell penetration to proteins. Likewise, antibodies recognize antigens through the antigen-binding site on the surface. The genetic and structural diversity of antibodies leads to high specificity and affinity toward antigens, enabling antibodies to be versatile tools in various applications. When assessing therapeutic antibodies, surface charge is an important factor to consider because the isoelectric point plays a role in protein clearance inside the body. In this study, we explored how supercharging mutations affect physicochemical properties of antibodies. Starting from a crystal structure of an antibody with the net charge of -4, we computationally designed a supercharged variant possessing the net charge of +10. The positive-supercharged antibody exhibited marginal improvement in thermal stability, but the secondary structure and the binding affinity to the antigen (net charge of +8) were preserved. We also used physicochemical measurements and molecular dynamics simulations to analyze the effects of supercharging mutations in sodium phosphate buffer with different pH and ion concentrations, which revealed preferential solvation of phosphate ions to the supercharged surface relative to the wild-type surface. These results suggest that supercharging would be a useful approach to preserving thermal stability of antibodies in a wide range of pH, which may enable further diversification of antibody repertoires beyond natural evolution.
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Affiliation(s)
- Keisuke Kasahara
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Raiji Kawade
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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24
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Schoeder CT, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, Bender BJ, Martina CE, Del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE, Meiler J, Moretti R. Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design. Biochemistry 2021; 60:825-846. [PMID: 33705117 PMCID: PMC7992133 DOI: 10.1021/acs.biochem.0c00912] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Structure-based antibody
and antigen design has advanced greatly
in recent years, due not only to the increasing availability of experimentally
determined structures but also to improved computational methods for
both prediction and design. Constant improvements in performance within
the Rosetta software suite for biomolecular modeling have given rise
to a greater breadth of structure prediction, including docking and
design application cases for antibody and antigen modeling. Here,
we present an overview of current protocols for antibody and antigen
modeling using Rosetta and exemplify those by detailed tutorials originally
developed for a Rosetta workshop at Vanderbilt University. These tutorials
cover antibody structure prediction, docking, and design and antigen
design strategies, including the addition of glycans in Rosetta. We
expect that these materials will allow novice users to apply Rosetta
in their own projects for modeling antibodies and antigens.
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Affiliation(s)
- Clara T Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Alexander M Sevy
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States
| | - Jessica A Finn
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Marion F Sauer
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States.,Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States
| | - Nina G Bozhanova
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Benjamin K Mueller
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Amandeep K Sangha
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jonathan H Sheehan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Institute for Drug Discovery, University Leipzig Medical School, 04103 Leipzig, Germany
| | - Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Shannon T Smith
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Hope Woods
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Brian J Bender
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Cristina E Martina
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Diego Del Alamo
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee 37232-0301, United States
| | - Pranav Kodali
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Alican Gulsevin
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0417, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States.,Institute for Drug Discovery, University Leipzig Medical School, 04103 Leipzig, Germany
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
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25
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Liu JL, Webb EM, Zabetakis D, Burke CW, Gardner CL, Glass PJ, Legler PM, Weger-Lucarelli J, Anderson GP, Goldman ER. Stabilization of a Broadly Neutralizing Anti-Chikungunya Virus Single Domain Antibody. Front Med (Lausanne) 2021; 8:626028. [PMID: 33585527 PMCID: PMC7876468 DOI: 10.3389/fmed.2021.626028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
A single domain antibody (clone CC3) previously found to neutralize a vaccine strain of the chikungunya virus (PRNT50 = 2. 5 ng/mL) was found to be broadly neutralizing. Clone CC3 is not only able to neutralize a wild-type (WT) strain of chikungunya virus (CHIKV), but also neutralizes WT strains of Mayaro virus (MAYV) and Ross River virus (RRV); both arthralgic, Old World alphaviruses. Interestingly, CC3 also demonstrated a degree of neutralizing activity against the New World alphavirus, Venezuelan equine encephalitis virus (VEEV); albeit both the vaccine strain, TC-83, and the parental, WT Trinidad donkey strain had PRNT50 values ~1,000-fold higher than that of CHIKV. However, no neutralization activity was observed with Western equine encephalitis virus (WEEV). Ten CC3 variants designed to possess a range of isoelectric points, both higher and lower, were constructed. This approach successfully identified several lower pI mutants which possessed improved thermal stabilities by as much as 10°C over the original CC3 (Tm = 62°C), and excellent refolding abilities while maintaining their capacity to bind and neutralize CHIKV.
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Affiliation(s)
- Jinny L Liu
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Emily M Webb
- Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Dan Zabetakis
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Crystal W Burke
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Christina L Gardner
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Pamela J Glass
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, United States
| | - Patricia M Legler
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | | | - George P Anderson
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
| | - Ellen R Goldman
- U.S. Naval Research Laboratory, Center for BioMolecular Science and Engineering, Washington, DC, United States
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26
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Local environment effects on charged mutations for developing aggregation-resistant monoclonal antibodies. Sci Rep 2020; 10:21191. [PMID: 33273506 PMCID: PMC7713239 DOI: 10.1038/s41598-020-78136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 11/11/2020] [Indexed: 11/10/2022] Open
Abstract
Protein aggregation is a major concern in biotherapeutic applications of monoclonal antibodies. Introducing charged mutations is among the promising strategies to improve aggregation resistance. However, the impact of such mutations on solubilizing activity depends largely on the inserting location, whose mechanism is still not well understood. Here, we address this issue from a solvation viewpoint, and this is done by analyzing how the change in solvation free energy upon charged mutation is composed of individual contributions from constituent residues. To this end, we perform molecular dynamics simulations for a number of antibody mutants and carry out the residue-wise decomposition of the solvation free energy. We find that, in addition to the previously identified “global” principle emphasizing the key role played by the protein total net charge, a local net charge within \documentclass[12pt]{minimal}
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\begin{document}$$\sim$$\end{document}∼15 Å from the mutation site exerts significant effects. For example, when the net charge of an antibody is positive, the global principle states that introducing a positively charged mutation will lead to more favorable solvation. Our finding further adds that an even more optimal mutation can be done at the site around which more positively charged residues and fewer negatively charged residues are present. Such a “local” design principle accounts for the location dependence of charged mutations, and will be useful in producing aggregation-resistant antibodies.
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27
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Surface charge-based rational design of aspartase modifies the optimal pH for efficient β-aminobutyric acid production. Int J Biol Macromol 2020; 164:4165-4172. [DOI: 10.1016/j.ijbiomac.2020.08.229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022]
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28
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Seyedhosseini Ghaheh H, Ganjalikhany MR, Yaghmaei P, Pourfarzam M, Mir Mohammad Sadeghi H. Investigation of Supercharging as A Strategy to Enhance the Solubility and Plasminogen Cleavage Activity of Reteplase. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2556. [PMID: 34056023 PMCID: PMC8148640 DOI: 10.30498/ijb.2020.2556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Reteplase, the recombinant form of tissue plasminogen activator, is a thrombolytic drug with outstanding characteristics, while demonstrating limited solubility and reduced plasminogen activation. Previously, we in silico designed a variant of Reteplase with positively supercharged surface, which showed promising stability, solubility and activity. This study was devoted to evaluation of the utility of supercharging technique for enhancing these characteristics in Reteplase. Objective To test the hypothesis that reinforced surface charge of a rationally-designed Reteplase variant will not compromise its stability, will increase its solubility, and will enhance its plasminogen cleavage activity. Materials and Methods Supercharged Reteplase coding sequence was cloned in pDest527 vector and expressed in E. coli BL21 (DE3). The expressed protein was extracted by cell disruption. Inclusion bodies were solubilized using guanidine hydrochloride, followed by dialysis for protein refolding. After confirmation with SDS-PAGE and western blotting, extracted proteins were assayed for solubility and tested for bioactivity. Results SDS-PAGE and western blot analysis confirmed the successful expression of Reteplase. Western blot experiments showed most of Reteplase expressed in the insoluble form. Plasminogen cleavage assay showed significantly higher activity of the supercharged variant than the wild type protein (P < 0.001). The stability of the supercharged variant was also comparable to the wild type. Conclusion Our findings, i.e. the contribution of the surface supercharging technique to retained stability, enhanced plasminogen cleavage activity, while inefficiently changed solubility of Reteplase, contain implications for future designs of soluble variants of this fibrinolytic protein drug.
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Affiliation(s)
| | | | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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29
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Kang TH, Seong BL. Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms. Front Microbiol 2020; 11:1927. [PMID: 33101218 PMCID: PMC7546209 DOI: 10.3389/fmicb.2020.01927] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Solubility of recombinant proteins (i.e., the extent of soluble versus insoluble expression in heterogeneous hosts) is the first checkpoint criterion for determining recombinant protein quality. However, even soluble proteins often fail to represent functional activity because of the involvement of non-functional, misfolded, soluble aggregates, which compromise recombinant protein quality. Therefore, screening of solubility and folding competence is crucial for improving the quality of recombinant proteins, especially for therapeutic applications. The issue is often highlighted especially in bacterial recombinant hosts, since bacterial cytoplasm does not provide an optimal environment for the folding of target proteins of mammalian origin. Antibody fragments, such as single-chain variable fragment (scFv), single-chain antibody (scAb), and fragment antigen binding (Fab), have been utilized for numerous applications such as diagnostics, research reagents, or therapeutics. Antibody fragments can be efficiently expressed in microorganisms so that they offer several advantages for diagnostic applications such as low cost and high yield. However, scFv and scAb fragments have generally lower stability to thermal stress than full-length antibodies, necessitating a judicious combination of designer antibodies, and bacterial hosts harnessed with robust chaperone function. In this review, we discuss efforts on not only the production of antibodies or antibody fragments in microorganisms but also scFv stabilization via (i) directed evolution of variants with increased stability using display systems, (ii) stabilization of the interface between variable regions of heavy (VH) and light (VL) chains through the introduction of a non-native covalent bond between the two chains, (iii) rational engineering of VH-VL pair, based on the structure, and (iv) computational approaches. We also review recent advances in stability design, increase in avidity by multimerization, and maintaining the functional competence of chimeric proteins prompted by various types of chaperones.
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Affiliation(s)
- Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, South Korea
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30
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Kuroda D, Tsumoto K. Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design. J Pharm Sci 2020; 109:1631-1651. [DOI: 10.1016/j.xphs.2020.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/25/2019] [Accepted: 01/10/2020] [Indexed: 12/18/2022]
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31
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Ma C, Malessa A, Boersma AJ, Liu K, Herrmann A. Supercharged Proteins and Polypeptides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905309. [PMID: 31943419 DOI: 10.1002/adma.201905309] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Electrostatic interactions play a vital role in nature. Biomacromolecules such as proteins are orchestrated by electrostatics, among other intermolecular forces, to assemble and organize biochemistry. Natural proteins with a high net charge exist in a folded state or are unstructured and can be an inspiration for scientists to artificially supercharge other protein entities. Recent findings show that supercharging proteins allows for control of their properties such as temperature resistance and catalytic activity. One elegant method to transfer the favorable properties of supercharged proteins to other proteins is the fabrication of fusions. Genetically engineered, supercharged unstructured polypeptides (SUPs) are just one promising fusion tool. SUPs can also be complexed with artificial entities to yield thermotropic and lyotropic liquid crystals and liquids. These architectures represent novel bulk materials that are sensitive to external stimuli. Interestingly, SUPs undergo fluid-fluid phase separation to form coacervates. These coacervates can even be directly generated in living cells or can be combined with dissipative fiber assemblies that induce life-like features. Supercharged proteins and SUPs are developed into exciting classes of materials. Their synthesis, structures, and properties are summarized. Moreover, potential applications are highlighted and challenges are discussed.
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Affiliation(s)
- Chao Ma
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Anke Malessa
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Arnold J Boersma
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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32
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Cnudde T, Lakhrif Z, Bourgoin J, Boursin F, Horiot C, Henriquet C, di Tommaso A, Juste MO, Jiacomini IG, Dimier-Poisson I, Pugnière M, Mévélec MN, Aubrey N. Exploration and Modulation of Antibody Fragment Biophysical Properties by Replacing the Framework Region Sequences. Antibodies (Basel) 2020; 9:antib9020009. [PMID: 32326443 PMCID: PMC7344962 DOI: 10.3390/antib9020009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
In order to increase the successful development of recombinant antibodies and fragments, it seems fundamental to enhance their expression and/or biophysical properties, such as the thermal, chemical, and pH stabilities. In this study, we employed a method bases on replacing the antibody framework region sequences, in order to promote more particularly single-chain Fragment variable (scFv) product quality. We provide evidence that mutations of the VH- C-C′ loop might significantly improve the prokaryote production of well-folded and functional fragments with a production yield multiplied by 27 times. Additional mutations are accountable for an increase in the thermal (+19.6 °C) and chemical (+1.9 M) stabilities have also been identified. Furthermore, the hereby-produced fragments have shown to remain stable at a pH of 2.0, which avoids molecule functional and structural impairments during the purification process. Lastly, this study provides relevant information to the understanding of the relationship between the antibodies amino acid sequences and their respective biophysical properties.
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Affiliation(s)
- Thomas Cnudde
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Zineb Lakhrif
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Justine Bourgoin
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Fanny Boursin
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Catherine Horiot
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | - Corinne Henriquet
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer, 34090 Montpellier, France
| | - Anne di Tommaso
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
| | | | - Isabella Gizzi Jiacomini
- Laboratório de Imunoquímica, Departamento de Patologia Básica, Universidade Federal do Paraná, Curitiba 81530, PR, Brazil
| | | | - Martine Pugnière
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, Université Montpellier, ICM Institut Régional du Cancer, 34090 Montpellier, France
| | | | - Nicolas Aubrey
- INRAE, ISP, Université de Tours, F-37000 Tours, France; (T.C.); (Z.L.)
- Correspondence:
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33
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Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee CH, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, Zhang Y, Kuhlman B, Georgiou G, Ellington AD. Computer-based Engineering of Thermostabilized Antibody Fragments. AIChE J 2020; 66:e16864. [PMID: 32336757 PMCID: PMC7181397 DOI: 10.1002/aic.16864] [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] [Indexed: 01/07/2023]
Abstract
We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (Tm) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher Tm compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.
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Affiliation(s)
- Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | | | - Wenzong Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Nicholas M. Marshall
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Oana I. Lungu
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Aleksandr E. Miklos
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, APGEA, MD 21010
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seongbuk-gu, Seoul 02707, Republic of Korea
| | - Chang-Han Lee
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Bing Tan
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Randall A. Hughes
- US Army Research Laboratory, Austin, TX 78712,Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78712
| | - Sang Taek Jung
- Department of Biomedical Science, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Yan Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
| | - Andrew D. Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,Department of Chemistry, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
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Ebo JS, Guthertz N, Radford SE, Brockwell DJ. Using protein engineering to understand and modulate aggregation. Curr Opin Struct Biol 2020; 60:157-166. [PMID: 32087409 PMCID: PMC7132541 DOI: 10.1016/j.sbi.2020.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Protein aggregation occurs through a variety of mechanisms, initiated by the unfolded, non-native, or even the native state itself. Understanding the molecular mechanisms of protein aggregation is challenging, given the array of competing interactions that control solubility, stability, cooperativity and aggregation propensity. An array of methods have been developed to interrogate protein aggregation, spanning computational algorithms able to identify aggregation-prone regions, to deep mutational scanning to define the entire mutational landscape of a protein's sequence. Here, we review recent advances in this exciting and emerging field, focussing on protein engineering approaches that, together with improved computational methods, hold promise to predict and control protein aggregation linked to human disease, as well as facilitating the manufacture of protein-based therapeutics.
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Affiliation(s)
- Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicolas Guthertz
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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Baryakova TH, Ritter SC, Tresnak DT, Hackel BJ. Computationally Aided Discovery of LysEFm5 Variants with Improved Catalytic Activity and Stability. Appl Environ Microbiol 2020; 86:e02051-19. [PMID: 31811034 PMCID: PMC6997734 DOI: 10.1128/aem.02051-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/30/2019] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage-derived lysin proteins are potentially effective antimicrobials that would benefit from engineered improvements to their bioavailability and specific activity. Here, the catalytic domain of LysEFm5, a lysin with activity against vancomycin-resistant Enterococcus faecium (VRE), was subjected to site-saturation mutagenesis at positions whose selection was guided by sequence and structural information from homologous proteins. A second-order Potts model with parameters inferred from large sets of homologous sequence information was used to predict the average change in the statistical fitness for mutant libraries with diversity at pairs of sites within the secondary catalytic shell. Guided by the statistical fitness, nine double mutant saturation libraries were created and plated on agar containing autoclaved VRE to quickly identify and segregate catalytically active (halo-forming) and inactive (non-halo-forming) variants. High-throughput DNA sequencing of 873 unique variants showed that the statistical fitness was predictive of the retention or loss of catalytic activity (area under the curve [AUC], 0.840 to 0.894), with the inclusion of more diverse sequences in the starting multiple-sequence alignment improving the classification accuracy when pairwise amino acid couplings (epistasis) were considered. Of eight random halo-forming variants selected for more sensitive testing, one showed a 1.8 (±0.4)-fold improvement in specific activity and an 11.5 ± 0.8°C increase in melting temperature compared to those of the wild type. Our results demonstrate that a computationally informed approach employing homologous protein information coupled with a mid-throughput screening assay allows for the expedited discovery of lysin variants with improved properties.IMPORTANCE Broad-spectrum antibiotics can indiscriminately kill most bacteria, including commensal species that are a part of the normal human flora. This can potentially lead to the proliferation of drug-resistant bacteria upon elimination of competing species and to unwanted autoimmune effects in patients. Bacteriophage-derived lysin proteins are an alternative to conventional antibiotics that have coevolved alongside specific bacterial hosts. Lysins are capable of targeting conserved substrates in the bacterial cell wall essential for its viability. To engineer these proteins to exhibit improved therapeutically relevant properties, homology-guided statistical approaches can be used to identify compelling sites for mutation and to quantify the functional constraints acting on these sites to direct mutagenic library creation. The platform described herein couples this informed approach with a visual plate assay that can be used to simultaneously screen hundreds of mutants for catalytic activity, allowing for the streamlined identification of improved lysin variants.
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Affiliation(s)
- Tsvetelina H Baryakova
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Seth C Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Daniel T Tresnak
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
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Warszawski S, Borenstein Katz A, Lipsh R, Khmelnitsky L, Ben Nissan G, Javitt G, Dym O, Unger T, Knop O, Albeck S, Diskin R, Fass D, Sharon M, Fleishman SJ. Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. PLoS Comput Biol 2019; 15:e1007207. [PMID: 31442220 PMCID: PMC6728052 DOI: 10.1371/journal.pcbi.1007207] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 09/05/2019] [Accepted: 06/21/2019] [Indexed: 11/18/2022] Open
Abstract
Antibodies developed for research and clinical applications may exhibit suboptimal stability, expressibility, or affinity. Existing optimization strategies focus on surface mutations, whereas natural affinity maturation also introduces mutations in the antibody core, simultaneously improving stability and affinity. To systematically map the mutational tolerance of an antibody variable fragment (Fv), we performed yeast display and applied deep mutational scanning to an anti-lysozyme antibody and found that many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface, within the antibody core. Rosetta design combined enhancing mutations, yielding a variant with tenfold higher affinity and substantially improved stability. To make this approach broadly accessible, we developed AbLIFT, an automated web server that designs multipoint core mutations to improve contacts between specific Fv light and heavy chains (http://AbLIFT.weizmann.ac.il). We applied AbLIFT to two unrelated antibodies targeting the human antigens VEGF and QSOX1. Strikingly, the designs improved stability, affinity, and expression yields. The results provide proof-of-principle for bypassing laborious cycles of antibody engineering through automated computational affinity and stability design. Antibodies are highly important in research, biotechnology, and medical applications. Despite their great utility, however, many antibodies exhibit suboptimal stability and affinity, raising production costs and limiting their practical usefulness. To tackle this general limitation, we used deep mutational scanning to characterize the effects of mutations in an antibody variable fragment on its antigen-binding affinity. Surprisingly, many of the affinity-enhancing mutations clustered at the variable light-heavy chain interface. We, therefore, developed an automated method, called AbLIFT (http://AbLIFT.weizmann.ac.il) to optimize this interface through design. Two unrelated antibodies were tested and showed improvements in expression levels, stability, and antigen-binding affinity. Since AbLIFT requires testing of only a few dozen specific designs, it may dramatically accelerate the development of promising antibodies into useful research and clinical tools.
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Affiliation(s)
- Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rosalie Lipsh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lev Khmelnitsky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel Javitt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Orli Knop
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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37
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Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation. Cells 2019; 8:cells8080856. [PMID: 31398930 PMCID: PMC6721704 DOI: 10.3390/cells8080856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
The aggregation of proteins compromises cell fitness, either because it titrates functional proteins into non-productive inclusions or because it results in the formation of toxic assemblies. Accordingly, computational proteome-wide analyses suggest that prevention of aggregation upon misfolding plays a key role in sequence evolution. Most proteins spend their lifetimes in a folded state; therefore, it is conceivable that, in addition to sequences, protein structures would have also evolved to minimize the risk of aggregation in their natural environments. By exploiting the AGGRESCAN3D structure-based approach to predict the aggregation propensity of >600 Escherichia coli proteins, we show that the structural aggregation propensity of globular proteins is connected with their abundance, length, essentiality, subcellular location and quaternary structure. These data suggest that the avoidance of protein aggregation has contributed to shape the structural properties of proteins in bacterial cells.
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38
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Ghaheh HS, Ganjalikhany MR, Yaghmaei P, Pourfarzam M, Mir Mohammad Sadeghi H. Improving the solubility, activity, and stability of reteplase using in silico design of new variants. Res Pharm Sci 2019; 14:359-368. [PMID: 31516513 PMCID: PMC6714118 DOI: 10.4103/1735-5362.263560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Reteplase (recombinant plasminogen activator, r-PA) is a thrombolytic agent recombined from tissue-type plasminogen activator (t-PA), which has several prominent features such as strong thrombolytic ability and E. coli expressibility. Despite these outstanding features, it demonstrates reduced fibrin binding affinity, reduced stimulation of protease activity, and lower solubility, hence higher aggregation propensity, compared to t-PA. The present study was devoted to design r-PA variants with comparable structural stability, enhanced biological activity, and high solubility. For this purpose, computational molecular modeling techniques were utilized. The supercharging technique was applied for r-PA to designing new species of the protein. Based on the results from in silico evaluation of selected mutations in comparison to the wild-type r-PA, the designed supercharged mutant (S7 variant) exhibited augmented stability, decreased solvation energy, as well as enhanced binding affinity to fibrin. The data also implied increased plasminogen cleavage activity of the new variant. These findings have implications to therapies which involve removal of intravascular blood clots, including the treatment of acute myocardial infarction.
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Affiliation(s)
| | | | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, I.R. Iran
| | - Morteza Pourfarzam
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hamid Mir Mohammad Sadeghi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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39
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Austerberry JI, Thistlethwaite A, Fisher K, Golovanov AP, Pluen A, Esfandiary R, van der Walle CF, Warwicker J, Derrick JP, Curtis R. Arginine to Lysine Mutations Increase the Aggregation Stability of a Single-Chain Variable Fragment through Unfolded-State Interactions. Biochemistry 2019; 58:3413-3421. [DOI: 10.1021/acs.biochem.9b00367] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- James I. Austerberry
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Angela Thistlethwaite
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Karl Fisher
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Alexander P. Golovanov
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
- School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Alain Pluen
- Manchester Pharmacy School, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Reza Esfandiary
- Dosage Form Design & Development, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | | | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
- School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jeremy P. Derrick
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
- School of Chemical Engineering and Analytical Science, University of Manchester, Manchester M1 7DN, United Kingdom
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40
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Paladin L, Piovesan D, Tosatto SCE. SODA: prediction of protein solubility from disorder and aggregation propensity. Nucleic Acids Res 2019; 45:W236-W240. [PMID: 28505312 PMCID: PMC7059794 DOI: 10.1093/nar/gkx412] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2017] [Indexed: 01/08/2023] Open
Abstract
Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility. It has been trained and benchmarked on two different datasets. The comparison to other recently published methods shows that SODA has state-of-the-art performance and is particularly well suited to predict mutations decreasing solubility. The method is fast, returning results for single mutations in seconds. A usage example estimating the full repertoire of mutations for a human germline antibody highlights several solubility hotspots on the surface. The web server, complete with RESTful interface and extensive help, can be accessed from URL: http://protein.bio.unipd.it/soda.
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Affiliation(s)
- Lisanna Paladin
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35121 Padova, Italy.,CNR Institute of Neuroscience, Viale G. Colombo 3, 35121 Padova, Italy
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41
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Sakhnini LI, Greisen PJ, Wiberg C, Bozoky Z, Lund S, Wolf Perez AM, Karkov HS, Huus K, Hansen JJ, Bülow L, Lorenzen N, Dainiak MB, Pedersen AK. Improving the Developability of an Antigen Binding Fragment by Aspartate Substitutions. Biochemistry 2019; 58:2750-2759. [DOI: 10.1021/acs.biochem.9b00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laila I. Sakhnini
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
- Department of Pure and Applied Biochemistry, Lund University, 223 62 Lund, Sweden
| | - Per J. Greisen
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Charlotte Wiberg
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Zoltan Bozoky
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Søren Lund
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Hanne S. Karkov
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Kasper Huus
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | | | - Leif Bülow
- Department of Pure and Applied Biochemistry, Lund University, 223 62 Lund, Sweden
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Maria B. Dainiak
- Global Research Technologies, Novo Nordisk A/S, 2760 Måløv, Denmark
| | - Anja K. Pedersen
- Chemistry, Manufacturing and Control, Novo Nordisk A/S, 2820 Gentofte, Denmark
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Leem J, Deane CM. High-Throughput Antibody Structure Modeling and Design Using ABodyBuilder. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1851:367-380. [PMID: 30298409 DOI: 10.1007/978-1-4939-8736-8_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Antibodies are proteins of the adaptive immune system; they can be designed to bind almost any molecule, and are increasingly being used as biotherapeutics. Experimental antibody design is an expensive and time-consuming process, and computational antibody design methods can now be used to help develop new therapeutics and diagnostics. Within the design pipeline, accurate antibody structure modeling is essential, as it provides the basis for antibody-antigen docking, binding affinity prediction, and estimating thermal stability. Ideally, models should be rapidly generated, allowing the exploration of the breadth of antibody space. This allows methods to replicate the natural processes of antibody diversification (e.g., V(D)J recombination and somatic hypermutation), and cope with large volumes of data that are typical of next-generation sequencing datasets. Here we describe ABodyBuilder and PEARS, algorithms that build and mutate antibody model structures. These methods take ~30 s to generate a model antibody structure.
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Affiliation(s)
- Jinwoo Leem
- Department of Statistics, University of Oxford, Oxford, UK
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43
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Charoenwongpaiboon T, Klaewkla M, Chunsrivirot S, Wangpaiboon K, Pichyangkura R, Field RA, Prousoontorn MH. Rational re-design of Lactobacillus reuteri 121 inulosucrase for product chain length control. RSC Adv 2019; 9:14957-14965. [PMID: 35516339 PMCID: PMC9064246 DOI: 10.1039/c9ra02137j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/07/2019] [Indexed: 11/21/2022] Open
Abstract
Fructooligosaccharides (FOSs) are well-known prebiotics that are widely used in the food, beverage and pharmaceutical industries. Inulosucrase (E.C. 2.4.1.9) can potentially be used to synthesise FOSs from sucrose. In this study, inulosucrase from Lactobacillus reuteri 121 was engineered by site-directed mutagenesis to change the FOS chain length. Three variants (R483F, R483Y and R483W) were designed, and their binding free energies with 1,1,1-kestopentaose (GF4) were calculated with the Rosetta software. R483F and R483Y were predicted to bind with GF4 better than the wild type, suggesting that these engineered enzymes should be able to effectively extend GF4 by one residue and produce a greater quantity of GF5 than the wild type. MALDI-TOF MS analysis showed that R483F, R483Y and R483W variants could synthesise shorter chain FOSs with a degree of polymerization (DP) up to 11, 10, and 10, respectively, while wild type produced longer FOSs and in polymeric form. Although the decrease in catalytic activity and the increase of hydrolysis/transglycosylation activity ratio was observed, the variants could effectively synthesise FOSs with the yield up to 73% of substrate. Quantitative analysis demonstrated that these variants produced a larger quantity of GF5 than wild type, which was in good agreement with the predicted binding free energy results. Our findings demonstrate the success of using aromatic amino acid residues, at position D418, to block the oligosaccharide binding track of inulosucrase in controlling product chain length.
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Affiliation(s)
| | - Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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44
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Zahler CT, Shaw BF. What Are We Missing by Not Measuring the Net Charge of Proteins? Chemistry 2019; 25:7581-7590. [PMID: 30779227 DOI: 10.1002/chem.201900178] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pKa . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pKa values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔGz ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔGz contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.
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Affiliation(s)
- Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
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Protein engineering: the potential of remote mutations. Biochem Soc Trans 2019; 47:701-711. [PMID: 30902926 DOI: 10.1042/bst20180614] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 01/18/2019] [Accepted: 02/18/2019] [Indexed: 12/19/2022]
Abstract
Engineered proteins, especially enzymes, are now commonly used in many industries owing to their catalytic power, specific binding of ligands, and properties as materials and food additives. As the number of potential uses for engineered proteins has increased, the interest in engineering or designing proteins to have greater stability, activity and specificity has increased in turn. With any rational engineering or design pursuit, the success of these endeavours relies on our fundamental understanding of the systems themselves; in the case of proteins, their structure-dynamics-function relationships. Proteins are most commonly rationally engineered by targeting the residues that we understand to be functionally important, such as enzyme active sites or ligand-binding sites. This means that the majority of the protein, i.e. regions remote from the active- or ligand-binding site, is often ignored. However, there is a growing body of literature that reports on, and rationalises, the successful engineering of proteins at remote sites. This minireview will discuss the current state of the art in protein engineering, with a particular focus on engineering regions that are remote from active- or ligand-binding sites. As the use of protein technologies expands, exploiting the potential improvements made possible through modifying remote regions will become vital if we are to realise the full potential of protein engineering and design.
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Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations. Sci Rep 2019; 9:4482. [PMID: 30872635 PMCID: PMC6418251 DOI: 10.1038/s41598-019-40461-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/08/2019] [Indexed: 12/05/2022] Open
Abstract
Antibodies protect organisms from a huge variety of foreign antigens. Antibody diversity originates from both genetic and structural levels. Antigen recognition relies on complementarity between antigen-antibody interfaces. Recent methodological advances in structural biology and the accompanying rapid increase of the number of crystal structures of proteins have enabled atomic-level manipulation of protein structures to effect alterations in function. In this study, we explored the designability of electrostatic complementarity at an antigen-antibody interface on the basis of a crystal structure of the complex. We designed several variants with altered charged residues at the interface and characterized the designed variants by surface plasmon resonance, circular dichroism, differential scanning calorimetry, and molecular dynamics simulations. Both successes and failures of the structure-based design are discussed. The variants that compensate electrostatic interactions can restore the interface complementarity, enabling the cognate antigen-antibody binding. Retrospectively, we also show that these mutational effects could be predicted by the simulations. Our study demonstrates the importance of charged residues on the physical properties of this antigen-antibody interaction and suggests that computational approaches can facilitate design of antibodies that recognize a weakly immunogenic antigen.
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Simon AJ, Zhou Y, Ramasubramani V, Glaser J, Pothukuchy A, Gollihar J, Gerberich JC, Leggere JC, Morrow BR, Jung C, Glotzer SC, Taylor DW, Ellington AD. Supercharging enables organized assembly of synthetic biomolecules. Nat Chem 2019; 11:204-212. [DOI: 10.1038/s41557-018-0196-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 11/09/2022]
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Santos MLD, Quintilio W, Manieri TM, Tsuruta LR, Moro AM. Advances and challenges in therapeutic monoclonal antibodies drug development. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000001007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | - Ana Maria Moro
- Butantan Institute, Brazil; National Institute for Science and Technology, Brazil
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Thyer R, Shroff R, Klein DR, d'Oelsnitz S, Cotham VC, Byrom M, Brodbelt JS, Ellington AD. Custom selenoprotein production enabled by laboratory evolution of recoded bacterial strains. Nat Biotechnol 2018; 36:624-631. [PMID: 29863724 PMCID: PMC6035053 DOI: 10.1038/nbt.4154] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/23/2018] [Indexed: 02/06/2023]
Abstract
Incorporation of the rare amino acid selenocysteine to form diselenide bonds can improve stability and function of synthetic peptide therapeutics. However, application of this approach to recombinant proteins has been hampered by heterogeneous incorporation, low selenoprotein yields, and poor fitness of bacterial producer strains. We report the evolution of recoded Escherichia coli strains with improved fitness that are superior hosts for recombinant selenoprotein production. We apply an engineered β-lactamase containing an essential diselenide bond to enforce selenocysteine dependence during continuous evolution of recoded E. coli strains. Evolved strains maintain an expanded genetic code indefinitely. We engineer a fluorescent reporter to quantify selenocysteine incorporation in vivo and show complete decoding of UAG codons as selenocysteine. Replacement of native, labile disulfide bonds in antibody fragments with diselenide bonds vastly improves resistance to reducing conditions. Highly seleno-competent bacterial strains enable industrial-scale selenoprotein expression and unique diselenide architecture, advancing our ability to customize the selenoproteome.
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Affiliation(s)
- Ross Thyer
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Dustin R Klein
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Simon d'Oelsnitz
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - Victoria C Cotham
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | | | - Andrew D Ellington
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
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50
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Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ. An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:189. [PMID: 30002729 PMCID: PMC6036693 DOI: 10.1186/s13068-018-1178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/18/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host. RESULTS In this study, we use computational protein design to engineer the Zymomonas mobilis PDC to resist thermal denaturation at the growth temperature of a thermophilic host. We generate thirteen PDC variants using the Rosetta protein design software. We measure thermal stability of the wild-type PDC and PDC variants using circular dichroism. We then measure and compare enzyme endurance for wild-type PDC with the PDC variants at an elevated temperature of 60 °C (thermal endurance) using differential interference contrast imaging. CONCLUSIONS We find that increases in melting temperature (Tm) do not directly correlate with increases in thermal endurance at 60 °C. We also do not find evidence that any individual mutation or design approach is the major contributor to the most thermostable PDC variant. Rather, remarkable cooperativity among sixteen thermostabilizing mutations is key to rationally designing a PDC with significantly enhanced thermal endurance. These results suggest a generalizable iterative computational protein design approach to improve thermal stability and endurance of target enzymes.
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Affiliation(s)
- Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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