1
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Frankel NW, Deng H, Yucel G, Gainer M, Leemans N, Lam A, Li Y, Hung M, Lee D, Lee CT, Banicki A, Tian M, Almudhfar N, Naitmazi L, Roguev A, Lee S, Wong W, Gordley R, Lu TK, Garrison BS. Precision off-the-shelf natural killer cell therapies for oncology with logic-gated gene circuits. Cell Rep 2024; 43:114145. [PMID: 38669141 DOI: 10.1016/j.celrep.2024.114145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive disease with a poor prognosis (5-year survival rate of 30.5% in the United States). Designing cell therapies to target AML is challenging because no single tumor-associated antigen (TAA) is highly expressed on all cancer subpopulations. Furthermore, TAAs are also expressed on healthy cells, leading to toxicity risk. To address these targeting challenges, we engineer natural killer (NK) cells with a multi-input gene circuit consisting of chimeric antigen receptors (CARs) controlled by OR and NOT logic gates. The OR gate kills a range of AML cells from leukemic stem cells to blasts using a bivalent CAR targeting FLT3 and/or CD33. The NOT gate protects healthy hematopoietic stem cells (HSCs) using an inhibitory CAR targeting endomucin, a protective antigen unique to healthy HSCs. NK cells with the combined OR-NOT gene circuit kill multiple AML subtypes and protect primary HSCs, and the circuit also works in vivo.
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MESH Headings
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Humans
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Animals
- Mice
- Receptors, Chimeric Antigen/metabolism
- Receptors, Chimeric Antigen/immunology
- Gene Regulatory Networks
- Hematopoietic Stem Cells/metabolism
- Cell Line, Tumor
- Precision Medicine/methods
- Cell- and Tissue-Based Therapy/methods
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Affiliation(s)
| | - Han Deng
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Gozde Yucel
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Marcus Gainer
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Nelia Leemans
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Alice Lam
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Yongshuai Li
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Michelle Hung
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Derrick Lee
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Chen-Ting Lee
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Andrew Banicki
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | - Mengxi Tian
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | | | | | - Assen Roguev
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA
| | | | | | | | - Timothy K Lu
- Senti Biosciences, Inc., South San Francisco, CA 94080, USA; Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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2
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Verbič A, Lebar T, Praznik A, Jerala R. Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins. ACS Synth Biol 2024; 13:792-803. [PMID: 38404221 PMCID: PMC10949250 DOI: 10.1021/acssynbio.3c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Protein degradation is a highly regulated cellular process crucial to enable the high dynamic range of the response to external and internal stimuli and to balance protein biosynthesis to maintain cell homeostasis. Within mammalian cells, hundreds of E3 ubiquitin ligases target specific protein substrates and could be repurposed for synthetic biology. Here, we present a systematic analysis of the four protein subunits of the multiprotein E3 ligase complex as scaffolds for the designed degrons. While all of them were functional, the fusion of a fragment of Skp1 with the target protein enabled the most effective degradation. Combination with heterodimerizing peptides, protease substrate sites, and chemically inducible dimerizers enabled the regulation of protein degradation. While the investigated subunits of E3 ligases showed variable degradation efficiency of the membrane and cytosolic and nuclear proteins, the bipartite SSD (SOCSbox-Skp1(ΔC111)) degron enabled fast degradation of protein targets in all tested cellular compartments, including the nucleus and plasma membrane, in different cell lines and could be chemically regulated. These subunits could be employed for research as well as for diverse applications, as demonstrated in the regulation of Cas9 and chimeric antigen receptor proteins.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | - Arne Praznik
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
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3
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Deng X, Lv H, Zhang Q, Lai EMK. Analysis and design of antithetic proportional-integral-derivative biocontrol-systems with species dilution. Comput Biol Med 2024; 171:108213. [PMID: 38422962 DOI: 10.1016/j.compbiomed.2024.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/03/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The nonlinearity and non-separability of the antithetic PID (aPID) controller have provided greater flexibility in the design of biochemical reaction networks (BCRNs), resulting in significant impacts on biocontrol-systems. Nevertheless, the dilution of control species is disregarded in designs of aPID controllers, which would lead to the failure of inhibition mechanism in the controller and loss of robust perfect adaptation (RPA)-the biological counterpart of robust steady-state tracking. Here, the impact of dilution processes on the structure of aPID is investigated in this study. It is discovered that the proportional and low-pass filters are altered when the dilution processes is present in control species, which increases the coupling between the controller parameters. Moreover, additional integrations for the reference signal and control output generated by control species dilution further leads to the loss of RPA. Subsequently, a novel aPID controller represented by BCRNs, termed quasi-aPID, has been designed to eliminate the detrimental effects of the dilution processes. In an effort to ameliorate the interdependencies among controller parameters, a degradation inhibition mechanism is employed within this controller. Furthermore, this work establishes the limiting relationship between the controller's reaction rates in order to guarantee RPA, while abstaining from the introduction of supplementary species and biochemical reactions. By using the quasi-aPID controller in both the Escherichia coli gene expression model and the whole-body cholesterol metabolism model, its effectiveness is confirmed. Simulation results demonstrate that, the quasi-aPID exhibits a smaller absolute steady-state error in both models and guarantees the RPA property.
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Affiliation(s)
- Xun Deng
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, Liaoning, China.
| | - Hui Lv
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, Liaoning, China.
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, School of Software Engineering, Dalian University, Dalian 116622, Liaoning, China.
| | - Edmund Ming Kit Lai
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
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4
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Notin P, Rollins N, Gal Y, Sander C, Marks D. Machine learning for functional protein design. Nat Biotechnol 2024; 42:216-228. [PMID: 38361074 DOI: 10.1038/s41587-024-02127-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelerating the generation of proteins for applications in biotechnology and medicine. To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more. We then highlight trends shaping the future of this field, from large-scale assays to more robust benchmarks, multimodal foundation models, enhanced sampling strategies and laboratory automation.
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Affiliation(s)
- Pascal Notin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Computer Science, University of Oxford, Oxford, UK.
| | | | - Yarin Gal
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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5
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Kortemme T. De novo protein design-From new structures to programmable functions. Cell 2024; 187:526-544. [PMID: 38306980 PMCID: PMC10990048 DOI: 10.1016/j.cell.2023.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Abstract
Methods from artificial intelligence (AI) trained on large datasets of sequences and structures can now "write" proteins with new shapes and molecular functions de novo, without starting from proteins found in nature. In this Perspective, I will discuss the state of the field of de novo protein design at the juncture of physics-based modeling approaches and AI. New protein folds and higher-order assemblies can be designed with considerable experimental success rates, and difficult problems requiring tunable control over protein conformations and precise shape complementarity for molecular recognition are coming into reach. Emerging approaches incorporate engineering principles-tunability, controllability, and modularity-into the design process from the beginning. Exciting frontiers lie in deconstructing cellular functions with de novo proteins and, conversely, constructing synthetic cellular signaling from the ground up. As methods improve, many more challenges are unsolved.
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Affiliation(s)
- Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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6
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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7
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Gao Y, Wang L, Wang B. Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun 2023; 14:8415. [PMID: 38110405 PMCID: PMC10728147 DOI: 10.1038/s41467-023-44256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.
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Affiliation(s)
- Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lei Wang
- Center of Synthetic Biology and Integrated Bioengineering & School of Engineering, Westlake University, Hangzhou, 310030, China.
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China.
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou, 311100, China.
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8
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Wang S, Jiang W, Jin X, Qi Q, Liang Q. Genetically encoded ATP and NAD(P)H biosensors: potential tools in metabolic engineering. Crit Rev Biotechnol 2023; 43:1211-1225. [PMID: 36130803 DOI: 10.1080/07388551.2022.2103394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
To date, many metabolic engineering tools and strategies have been developed, including tools for cofactor engineering, which is a common strategy for bioproduct synthesis. Cofactor engineering is used for the regulation of pyridine nucleotides, including NADH/NAD+ and NADPH/NADP+, and adenosine triphosphate/adenosine diphosphate (ATP/ADP), which is crucial for maintaining redox and energy balance. However, the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP cannot be monitored in real time using traditional methods. Recently, many biosensors for detecting, monitoring, and regulating the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP have been developed. Although cofactor biosensors have been mainly developed for use in mammalian cells, the potential application of cofactor biosensors in metabolic engineering in bacterial and yeast cells has received recent attention. Coupling cofactor biosensors with genetic circuits is a promising strategy in metabolic engineering for optimizing the production of biochemicals. In this review, we focus on the development of biosensors for NADH/NAD+, NADPH/NADP+, and ATP/ADP and the potential application of these biosensors in metabolic engineering. We also provide critical perspectives, identify current research challenges, and provide guidance for future research in this promising field.
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Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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9
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Kumar S, Anastassov S, Aoki SK, Falkenstein J, Chang CH, Frei T, Buchmann P, Argast P, Khammash M. Diya - A universal light illumination platform for multiwell plate cultures. iScience 2023; 26:107862. [PMID: 37810238 PMCID: PMC10551653 DOI: 10.1016/j.isci.2023.107862] [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: 03/28/2023] [Revised: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Recent progress in protein engineering has established optogenetics as one of the leading external non-invasive stimulation strategies, with many optogenetic tools being designed for in vivo operation. Characterization and optimization of these tools require a high-throughput and versatile light delivery system targeting micro-titer culture volumes. Here, we present a universal light illumination platform - Diya, compatible with a wide range of cell culture plates and dishes. Diya hosts specially designed features ensuring active thermal management, homogeneous illumination, and minimal light bleedthrough. It offers light induction programming via a user-friendly custom-designed GUI. Through extensive characterization experiments with multiple optogenetic tools in diverse model organisms (bacteria, yeast, and human cell lines), we show that Diya maintains viable conditions for cell cultures undergoing light induction. Finally, we demonstrate an optogenetic strategy for in vivo biomolecular controller operation. With a custom-designed antithetic integral feedback circuit, we exhibit robust perfect adaptation and light-controlled set-point variation using Diya.
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Affiliation(s)
- Sant Kumar
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Stanislav Anastassov
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Stephanie K. Aoki
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Johannes Falkenstein
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Timothy Frei
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Peter Buchmann
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Paul Argast
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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10
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Hasiuk M, Dölz M, Marone R, Jeker LT. Leveraging microRNAs for cellular therapy. Immunol Lett 2023; 262:27-35. [PMID: 37660892 DOI: 10.1016/j.imlet.2023.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Owing to Karl Landsteiner's discovery of blood groups, blood transfusions became safe cellular therapies in the early 1900s. Since then, cellular therapy made great advances from transfusions with unmodified cells to today's commercially available chimeric antigen receptor (CAR) T cells requiring complex manufacturing. Modern cellular therapy products can be improved using basic knowledge of cell biology and molecular genetics. Emerging genome engineering tools are becoming ever more versatile and precise and thus catalyze rapid progress towards programmable therapeutic cells that compute input and respond with defined output. Despite a large body of literature describing important functions of non-coding RNAs including microRNAs (miRNAs), the vast majority of cell engineering efforts focuses on proteins. However, miRNAs form an important layer of posttranscriptional regulation of gene expression. Here, we highlight examples of how miRNAs can successfully be incorporated into engineered cellular therapies.
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Affiliation(s)
- Marko Hasiuk
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Marianne Dölz
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland.
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11
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Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 2023; 186:3810-3825.e18. [PMID: 37552983 PMCID: PMC10528910 DOI: 10.1016/j.cell.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
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Affiliation(s)
- Meghan D J Bragdon
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Nikit Patel
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James Chuang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ethan Levien
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77030, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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12
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McNamara HM, Ramm B, Toettcher JE. Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. Semin Cell Dev Biol 2023; 141:33-42. [PMID: 35484026 PMCID: PMC10332110 DOI: 10.1016/j.semcdb.2022.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
Abstract
Technological advances have driven many recent advances in developmental biology. Light sheet imaging can reveal single-cell dynamics in living three-dimensional tissues, whereas single-cell genomic methods open the door to a complete catalogue of cell types and gene expression states. An equally powerful but complementary set of approaches are also becoming available to define development processes from the bottom up. These synthetic approaches aim to reconstruct the minimal developmental patterns, signaling processes, and gene networks that produce the basic set of developmental operations: spatial polarization, morphogen interpretation, tissue movement, and cellular memory. In this review we discuss recent approaches at the intersection of synthetic biology and development, including synthetic circuits to deliver and record signaling stimuli and synthetic reconstitution of pattern formation on multicellular scales.
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Affiliation(s)
- Harold M McNamara
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA; Department of Physics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Beatrice Ramm
- Department of Physics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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13
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Zhou Z, Liu Y, Feng Y, Klepin S, Tsimring LS, Pillus L, Hasty J, Hao N. Engineering longevity-design of a synthetic gene oscillator to slow cellular aging. Science 2023; 380:376-381. [PMID: 37104589 PMCID: PMC10249776 DOI: 10.1126/science.add7631] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/03/2023] [Indexed: 04/29/2023]
Abstract
Synthetic biology enables the design of gene networks to confer specific biological functions, yet it remains a challenge to rationally engineer a biological trait as complex as longevity. A naturally occurring toggle switch underlies fate decisions toward either nucleolar or mitochondrial decline during the aging of yeast cells. We rewired this endogenous toggle to engineer an autonomous genetic clock that generates sustained oscillations between the nucleolar and mitochondrial aging processes in individual cells. These oscillations increased cellular life span through the delay of the commitment to aging that resulted from either the loss of chromatin silencing or the depletion of heme. Our results establish a connection between gene network architecture and cellular longevity that could lead to rationally designed gene circuits that slow aging.
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Affiliation(s)
- Zhen Zhou
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yuting Liu
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yushen Feng
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lev S. Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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14
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Anastassov S, Filo M, Chang CH, Khammash M. A cybergenetic framework for engineering intein-mediated integral feedback control systems. Nat Commun 2023; 14:1337. [PMID: 36906662 PMCID: PMC10008564 DOI: 10.1038/s41467-023-36863-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/21/2023] [Indexed: 03/13/2023] Open
Abstract
The ability of biological systems to tightly regulate targeted variables, despite external and internal disturbances, is known as Robust Perfect Adaptation (RPA). Achieved frequently through biomolecular integral feedback controllers at the cellular level, RPA has important implications for biotechnology and its various applications. In this study, we identify inteins as a versatile class of genetic components suitable for implementing these controllers and present a systematic approach for their design. We develop a theoretical foundation for screening intein-based RPA-achieving controllers and a simplified approach for modeling them. We then genetically engineer and test intein-based controllers using commonly used transcription factors in mammalian cells and demonstrate their exceptional adaptation properties over a wide dynamic range. The small size, flexibility, and applicability of inteins across life forms allow us to create a diversity of genetic RPA-achieving integral feedback control systems that can be used in various applications, including metabolic engineering and cell-based therapy.
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Affiliation(s)
- Stanislav Anastassov
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland.
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15
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d'Amone L, Matzeu G, Quijano-Rubio A, Callahan GP, Napier B, Baker D, Omenetto FG. Reshaping de Novo Protein Switches into Bioresponsive Materials for Biomarker, Toxin, and Viral Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208556. [PMID: 36493355 DOI: 10.1002/adma.202208556] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/14/2022] [Indexed: 06/17/2023]
Abstract
De novo designed protein switches are powerful tools to specifically and sensitively detect diverse targets with simple chemiluminescent readouts. Finding an appropriate material host for de novo designed protein switches without altering their thermodynamics while preserving their intrinsic stability over time would enable the development of a variety of sensing formats to monitor exposure to pathogens, toxins, and for disease diagnosis. Here, a de novo protein-biopolymer hybrid that maintains the detection capabilities induced by the conformational change of the incorporated proteins in response to analytes of interest is generated in multiple, shelf-stable material formats without the need of refrigerated storage conditions. A set of functional demonstrator devices including personal protective equipment such as masks and laboratory gloves, free-standing films, air quality monitors, and wearable devices is presented to illustrate the versatility of the approach. Such formats are designed to be responsive to human epidermal growth factor receptor (HER2), anti-hepatitis B (HBV) antibodies, Botulinum neurotoxin B (BoNT/B), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This combination of form and function offers wide opportunities for ubiquitous sensing in multiple environments by enabling a large class of bio-responsive interfaces of broad utility.
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Affiliation(s)
- Luciana d'Amone
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Giusy Matzeu
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Alfredo Quijano-Rubio
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Gregory P Callahan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Bradley Napier
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - David Baker
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Fiorenzo G Omenetto
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
- Department of Physics, Tufts University, Medford, MA, 02155, USA
- Laboratory for Living Devices, Tufts University, Medford, MA, 02155, USA
- Department of Electrical and Computer Engineering, Tufts University, Medford, MA, 02155, USA
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16
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Biomolecular feedback controllers: from theory to applications. Curr Opin Biotechnol 2023; 79:102882. [PMID: 36638743 DOI: 10.1016/j.copbio.2022.102882] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/07/2022] [Indexed: 01/13/2023]
Abstract
Billions of years of evolution have led to the creation of sophisticated genetic regulatory mechanisms that control various biological processes in a timely and precise fashion, despite their uncertain and noisy environments. Understanding such naturally existing mechanisms and even designing novel ones will have direct implications in various fields such as biotechnology, medicine, and synthetic biology. In particular, many studies have revealed that feedback-based control mechanisms inside the living cells endow the overall system with multiple attractive features, including homeostasis, noise reduction, and high dynamic performance. The remarkable interdisciplinary nature of these studies has brought together disparate disciplines such as systems/synthetic biology and control theory in an effort to design and build more powerful and reliable biomolecular control systems. Here, we review various biomolecular feedback controllers, highlight their characteristics, and point out their promising impact.
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17
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Abstract
AbstractComputational properties of neuronal networks have been applied to computing systems using simplified models comprising repeated connected nodes, e.g., perceptrons, with decision-making capabilities and flexible weighted links. Analogously to their revolutionary impact on computing, neuro-inspired models can transform synthetic gene circuit design in a manner that is reliable, efficient in resource utilization, and readily reconfigurable for different tasks. To this end, we introduce the perceptgene, a perceptron that computes in the logarithmic domain, which enables efficient implementation of artificial neural networks in Escherichia coli cells. We successfully modify perceptgene parameters to create devices that encode a minimum, maximum, and average of analog inputs. With these devices, we create multi-layer perceptgene circuits that compute a soft majority function, perform an analog-to-digital conversion, and implement a ternary switch. We also create a programmable perceptgene circuit whose computation can be modified from OR to AND logic using small molecule induction. Finally, we show that our approach enables circuit optimization via artificial intelligence algorithms.
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18
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Niu L, Cheng B, Huang G, Nan K, Han S, Ren H, Liu N, Li Y, Genin GM, Xu F. A positive mechanobiological feedback loop controls bistable switching of cardiac fibroblast phenotype. Cell Discov 2022; 8:84. [PMID: 36068215 PMCID: PMC9448780 DOI: 10.1038/s41421-022-00427-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/28/2022] [Indexed: 12/15/2022] Open
Abstract
Cardiac fibrosis is associated with activation of cardiac fibroblasts (CFs), a pathological, phenotypic transition that is widely believed to be irreversible in the late stages of disease development. Sensing of a stiffened mechanical environment through regulation of integrin-based adhesion plaques and activation of the Piezo1 mechanosensitive ion channel is known to factor into this transition. Here, using integrated in vitro and in silico models, we discovered a mutually reinforcing, mechanical positive feedback loop between integrin β1 and Piezo1 activation that forms a bistable switch. The bistable switch is initiated by perturbations in matrix elastic modulus that amplify to trigger downstream signaling involving Ca2+ and YAP that, recursively, leads fibroblasts to further stiffen their environment. By simultaneously interfering with the newly identified mechanical positive feedback loop and modulating matrix elastic modulus, we reversed markers of phenotypical transition of CF, suggesting new therapeutic targets for fibrotic disease.
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Affiliation(s)
- Lele Niu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Cheng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Guoyou Huang
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, China
| | - Kai Nan
- Department of Orthopedics Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuang Han
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Honghui Hospital, Xi'an, Shaanxi, China
| | - Hui Ren
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Na Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yan Li
- Department of Cardiology, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Guy M Genin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Mechanical Engineering & Materials Science, Washington University in St. Louis, St. Louis, MO, USA.,NSF Science and Technology Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China. .,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, China.
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19
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CoRa-A general approach for quantifying biological feedback control. Proc Natl Acad Sci U S A 2022; 119:e2206825119. [PMID: 36037352 PMCID: PMC9457221 DOI: 10.1073/pnas.2206825119] [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] [Indexed: 11/21/2022] Open
Abstract
Feedback control is a fundamental underpinning of life, underlying homeostasis of biological processes at every scale of organization, from cells to ecosystems. The ability to evaluate the contribution and limitations of feedback control mechanisms operating in cells is a critical step for understanding and ultimately designing feedback control systems with biological molecules. Here, we introduce CoRa—or Control Ratio—a general framework that quantifies the contribution of a biological feedback control mechanism to adaptation using a mathematically controlled comparison to an identical system that does not contain the feedback. CoRa provides a simple and intuitive metric with broad applicability to biological feedback systems.
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20
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Li L, Chen G. Precise Assembly of Proteins and Carbohydrates for Next-Generation Biomaterials. J Am Chem Soc 2022; 144:16232-16251. [PMID: 36044681 DOI: 10.1021/jacs.2c04418] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complexity and diversity of biomacromolecules make them a unique class of building blocks for generating precise assemblies. They are particularly available to a new generation of biomaterials integrated with living systems due to their intrinsic properties such as accurate recognition, self-organization, and adaptability. Therefore, many excellent approaches have been developed, leading to a variety of quite practical outcomes. Here, we review recent advances in the fabrication and application of artificially precise assemblies by employing proteins and carbohydrates as building blocks, followed by our perspectives on some of new challenges, goals, and opportunities for the future research directions in this field.
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Affiliation(s)
- Long Li
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, People's Republic of China.,Multiscale Research Institute for Complex Systems, Fudan University, Shanghai 200433, People's Republic of China
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21
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Garabedian MV, Su Z, Dabdoub J, Tong M, Deiters A, Hammer DA, Good MC. Protein Condensate Formation via Controlled Multimerization of Intrinsically Disordered Sequences. Biochemistry 2022; 61:2470-2481. [PMID: 35918061 DOI: 10.1021/acs.biochem.2c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many proteins harboring low complexity or intrinsically disordered sequences (IDRs) are capable of undergoing liquid-liquid phase separation to form mesoscale condensates that function as biochemical niches with the ability to concentrate or sequester macromolecules and regulate cellular activity. Engineered disordered proteins have been used to generate programmable synthetic membraneless organelles in cells. Phase separation is governed by the strength of interactions among polypeptides with multivalency enhancing phase separation at lower concentrations. Previously, we and others demonstrated enzymatic control of IDR valency from multivalent precursors to dissolve condensed phases. Here, we develop noncovalent strategies to multimerize an individual IDR, the RGG domain of LAF-1, using protein interaction domains to regulate condensate formation in vitro and in living cells. First, we characterize modular dimerization of RGG domains at either terminus using cognate high-affinity coiled-coil pairs to form stable condensates in vitro. Second, we demonstrate temporal control over phase separation of RGG domains fused to FRB and FKBP in the presence of dimerizer. Further, using a photocaged dimerizer, we achieve optically induced condensation both in cell-sized emulsions and within live cells. Collectively, these modular tools allow multiple strategies to promote phase separation of a common core IDR for tunable control of condensate assembly.
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Affiliation(s)
- Mikael V Garabedian
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhihui Su
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jorge Dabdoub
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michelle Tong
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Philadelphia, Pennsylvania 15260, United States
| | - Daniel A Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Matthew C Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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22
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Li J, Wang JL, Zhang WL, Tu Z, Cai XF, Wang YW, Gan CY, Deng HJ, Cui J, Shu ZC, Long QX, Chen J, Tang N, Hu X, Huang AL, Hu JL. Protein sensors combining both on-and-off model for antibody homogeneous assay. Biosens Bioelectron 2022; 209:114226. [PMID: 35413624 PMCID: PMC8968183 DOI: 10.1016/j.bios.2022.114226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 01/03/2023]
Abstract
Protein sensors based on allosteric enzymes responding to target binding with rapid changes in enzymatic activity are potential tools for homogeneous assays. However, a high signal-to-noise ratio (S/N) is difficult to achieve in their construction. A high S/N is critical to discriminate signals from the background, a phenomenon that might largely vary among serum samples from different individuals. Herein, based on the modularized luciferase NanoLuc, we designed a novel biosensor called NanoSwitch. This sensor allows direct detection of antibodies in 1 μl serum in 45 min without washing steps. In the detection of Flag and HA antibodies, NanoSwitches respond to antibodies with S/N ratios of 33-fold and 42-fold, respectively. Further, we constructed a NanoSwitch for detecting SARS-CoV-2-specific antibodies, which showed over 200-fold S/N in serum samples. High S/N was achieved by a new working model, combining the turn-off of the sensor with human serum albumin and turn-on with a specific antibody. Also, we constructed NanoSwitches for detecting antibodies against the core protein of hepatitis C virus (HCV) and gp41 of the human immunodeficiency virus (HIV). Interestingly, these sensors demonstrated a high S/N and good performance in the assays of clinical samples; this was partly attributed to the combination of off-and-on models. In summary, we provide a novel type of protein sensor and a working model that potentially guides new sensor design with better performance.
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23
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McCue AC, Yao Z, Kuhlman B. Advances in modular control of CAR-T therapy with adapter-mediated CARs. Adv Drug Deliv Rev 2022; 187:114358. [PMID: 35618140 PMCID: PMC9939278 DOI: 10.1016/j.addr.2022.114358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/01/2022]
Abstract
Protein engineering has contributed to successes in the field of T cell-based immunotherapy, including chimeric antigen receptor (CAR) T cell therapy. CAR T cell therapy has become a pillar of cancer immunotherapy, demonstrating clinical effectiveness against B cell malignancies by targeting the B cell antigen CD19. Current gene editing techniques have limited safety controls over CAR T cell activity, which presents a hurdle for control of CAR T cells in patients. Alternatively, CAR T cell activity can be controlled by engineering CARs to bind soluble adapter molecules that direct the interaction between the CAR T cell and target cell. The flexibility in this adapter-mediated approach overcomes the rigid specificity of traditional CAR T cells to allow targeting of multiple cell types. Here we describe adapter CAR T technologies and how these methods emphasize the growing role of protein engineering in the design of programmable tools for T cell therapies.
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Affiliation(s)
- Amelia C McCue
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Zhiyuan Yao
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27514, USA.
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24
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Qin L, Liu X, Xu K, Li C. Mining and design of biosensors for engineering microbial cell factory. Curr Opin Biotechnol 2022; 75:102694. [DOI: 10.1016/j.copbio.2022.102694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
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25
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Dishman AF, Volkman BF. Design and discovery of metamorphic proteins. Curr Opin Struct Biol 2022; 74:102380. [PMID: 35561475 PMCID: PMC9664977 DOI: 10.1016/j.sbi.2022.102380] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/03/2022]
Abstract
Metamorphic proteins are single amino acid sequences that reversibly interconvert between multiple, dramatically different native structures, often with distinct functions. Since the discovery of the first metamorphic proteins in the early 2000s, several additional metamorphic proteins have been identified, and it was suggested that up to 4% of proteins in the PDB may switch folds. Metamorphic proteins have been found to share common features such as marginal thermostability and inconsistencies in predicted secondary structures. Outstanding challenges in the field include the search for more metamorphic proteins and the design of new proteins that switch folds. Identification of novel metamorphic proteins in nature will improve therapeutic targeting of fold-switching proteins involved in human pathology and will enhance the design of protein-based therapies. Designed fold switching proteins have applications as biosensors, molecular switches, molecular machines, and self-assembling systems.
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Affiliation(s)
- Acacia F Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA; Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA. https://twitter.com/@cacidish
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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26
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Khan A, Saha G, Pal RK. Controlling the Effects of External Perturbations on a Gene Regulatory Network Using Proportional-Integral-Derivative Controller. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1531-1544. [PMID: 33206608 DOI: 10.1109/tcbb.2020.3039038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene regulatory networks are biologically robust, which imparts resilience to living systems against most external perturbations affecting them. However, there is a limit to this and disturbances beyond this limit can impart unwanted signalling on one or more master regulators in a network. Certain disturbances may affect the functioning of other constituent genes of the same network. In most cases, this phenomenon can have some effect on the functioning of the living organism. In this investigation, we have proposed a methodology to mitigate the effects of external perturbations on a genetic network using a proportional-integral-derivative controller. The proposed controller has been used to perturb one or more of the other unaffected master regulators such that the most affected gene/s of the network revert to their normal state. The only required condition of such type of manoeuvring is that there should be multiple master regulators in a network. The proposed technique has been experimented on a 10-gene DREAM4 benchmark network and also on a larger 20-gene network, where only downregulation has been considered due to data constraints. Simulation results indicate that the most vulnerable genes can be reverted to their normal expression levels in 10 out of the 16 simulations performed.
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27
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Kretschmer S, Kortemme T. Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2022; 110:659-674. [PMID: 36531560 PMCID: PMC9754107 DOI: 10.1109/jproc.2022.3157898] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Synthetic biology approaches living systems with an engineering perspective and promises to deliver solutions to global challenges in healthcare and sustainability. A critical component is the design of biomolecular circuits with programmable input-output behaviors. Such circuits typically rely on a sensor module that recognizes molecular inputs, which is coupled to a functional output via protein-level circuits or regulating the expression of a target gene. While gene expression outputs can be customized relatively easily by exchanging the target genes, sensing new inputs is a major limitation. There is a limited repertoire of sensors found in nature, and there are often difficulties with interfacing them with engineered circuits. Computational protein design could be a key enabling technology to address these challenges, as it allows for the engineering of modular and tunable sensors that can be tailored to the circuit's application. In this article, we review recent computational approaches to design protein-based sensors for small-molecule inputs with particular focus on those based on the widely used Rosetta software suite. Furthermore, we review mechanisms that have been harnessed to couple ligand inputs to functional outputs. Based on recent literature, we illustrate how the combination of protein design and synthetic biology enables new sensors for diverse applications ranging from biomedicine to metabolic engineering. We conclude with a perspective on how strategies to address frontiers in protein design and cellular circuit design may enable the next generation of sense-response networks, which may increasingly be assembled from de novo components to display diverse and engineerable input-output behaviors.
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Affiliation(s)
- Simon Kretschmer
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158 USA, and affiliated with the California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158 USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158 USA, and affiliated with the California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158 USA
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28
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Filo M, Kumar S, Khammash M. A hierarchy of biomolecular proportional-integral-derivative feedback controllers for robust perfect adaptation and dynamic performance. Nat Commun 2022; 13:2119. [PMID: 35440114 PMCID: PMC9018779 DOI: 10.1038/s41467-022-29640-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 03/25/2022] [Indexed: 01/05/2023] Open
Abstract
Proportional-Integral-Derivative (PID) feedback controllers are the most widely used controllers in industry. Recently, the design of molecular PID-controllers has been identified as an important goal for synthetic biology and the field of cybergenetics. In this paper, we consider the realization of PID-controllers via biomolecular reactions. We propose an array of topologies offering a compromise between simplicity and high performance. We first demonstrate that different biomolecular PI-controllers exhibit different performance-enhancing capabilities. Next, we introduce several derivative controllers based on incoherent feedforward loops acting in a feedback configuration. Alternatively, we show that differentiators can be realized by placing molecular integrators in a negative feedback loop, which can be augmented by PI-components to yield PID-controllers. We demonstrate that PID-controllers can enhance stability and dynamic performance, and can also reduce stochastic noise. Finally, we provide an experimental demonstration using a hybrid setup where in silico PID-controllers regulate a genetic circuit in single yeast cells.
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Affiliation(s)
- Maurice Filo
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sant Kumar
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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29
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Jones RD, Qian Y, Ilia K, Wang B, Laub MT, Del Vecchio D, Weiss R. Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles. Nat Commun 2022; 13:1720. [PMID: 35361767 PMCID: PMC8971529 DOI: 10.1038/s41467-022-29338-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Engineered signaling networks can impart cells with new functionalities useful for directing differentiation and actuating cellular therapies. For such applications, the engineered networks must be tunable, precisely regulate target gene expression, and be robust to perturbations within the complex context of mammalian cells. Here, we use bacterial two-component signaling proteins to develop synthetic phosphoregulation devices that exhibit these properties in mammalian cells. First, we engineer a synthetic covalent modification cycle based on kinase and phosphatase proteins derived from the bifunctional histidine kinase EnvZ, enabling analog tuning of gene expression via its response regulator OmpR. By regulating phosphatase expression with endogenous miRNAs, we demonstrate cell-type specific signaling responses and a new strategy for accurate cell type classification. Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. Our work lays the foundation for establishing tunable, precise, and robust control over cell behavior with synthetic signaling networks.
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Affiliation(s)
- Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yili Qian
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Katherine Ilia
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Benjamin Wang
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Michael T Laub
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Domitilla Del Vecchio
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Electrical Engineering and Computer Science Department, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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30
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Abstract
The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His3-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pKa of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
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31
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Billerbeck S, Cornish VW. Peptide-Dependent Growth in Yeast via Fine-Tuned Peptide/GPCR-Activated Essential Gene Expression. Biochemistry 2022; 61:150-159. [PMID: 35023728 PMCID: PMC8811955 DOI: 10.1021/acs.biochem.1c00661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AB Groningen, The Netherlands
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Virginia W. Cornish
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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32
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May MP, Munsky B. Exploiting Noise, Non-Linearity, and Feedback for Differential Control of Multiple Synthetic Cells with a Single Optogenetic Input. ACS Synth Biol 2021; 10:3396-3410. [PMID: 34793137 PMCID: PMC9875732 DOI: 10.1021/acssynbio.1c00341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Synthetic biology seeks to develop modular biocircuits that combine to produce complex, controllable behaviors. These designs are often subject to noisy fluctuations and uncertainties, and most modern synthetic biology design processes have focused to create robust components to mitigate the noise of gene expression and reduce the heterogeneity of single-cell responses. However, a deeper understanding of noise can achieve control goals that would otherwise be impossible. We explore how an "Optogenetic Maxwell Demon" could selectively amplify noise to control multiple cells using single-input-multiple-output (SIMO) feedback. Using data-constrained stochastic model simulations and theory, we show how an appropriately selected stochastic SIMO controller can drive multiple different cells to different user-specified configurations irrespective of initial conditions. We explore how controllability depends on cells' regulatory structures, the amount of information available to the controller, and the accuracy of the model used. Our results suggest that gene regulation noise, when combined with optogenetic feedback and non-linear biochemical auto-regulation, can achieve synergy to enable precise control of complex stochastic processes.
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Affiliation(s)
- Michael P May
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA, 80523
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA, 80523,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA, 80523
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33
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Abstract
Synthetic biology increasingly enables the construction of sophisticated functions in mammalian cells. A particularly promising frontier combines concepts drawn from industrial process control engineering-which is used to confer and balance properties such as stability and efficiency-with understanding as to how living systems have evolved to perform similar tasks with biological components. In this review, we first survey the state-of-the-art for both technologies and strategies available for genetic programming in mammalian cells. We then discuss recent progress in implementing programming objectives inspired by engineered and natural control mechanisms. Finally, we consider the transformative role of model-guided design in the present and future construction of customized mammalian cell functions for applications in biotechnology, medicine, and fundamental research.
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34
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Alberstein RG, Guo AB, Kortemme T. Design principles of protein switches. Curr Opin Struct Biol 2021; 72:71-78. [PMID: 34537489 DOI: 10.1016/j.sbi.2021.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 01/14/2023]
Abstract
Protein switches perform essential roles in many biological processes and are exciting targets for de novo protein design, which aims to produce proteins of arbitrary shape and functionality. However, the biophysical requirements for switch function - multiple conformational states, fine-tuned energetics, and stimuli-responsiveness - pose a formidable challenge for design by computation (or intuition). A variety of methods have been developed toward tackling this challenge, usually taking inspiration from the wealth of sequence and structural information available for naturally occurring protein switches. More recently, modular switches have been designed computationally, and new methods have emerged for sampling unexplored structure space, providing promising new avenues toward the generation of purpose-built switches and de novo signaling systems for cellular engineering.
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Affiliation(s)
- Robert G Alberstein
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Amy B Guo
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
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35
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Woodall NB, Weinberg Z, Park J, Busch F, Johnson RS, Feldbauer MJ, Murphy M, Ahlrichs M, Yousif I, MacCoss MJ, Wysocki VH, El-Samad H, Baker D. De novo design of tyrosine and serine kinase-driven protein switches. Nat Struct Mol Biol 2021; 28:762-770. [PMID: 34518698 PMCID: PMC8601088 DOI: 10.1038/s41594-021-00649-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Kinases play central roles in signaling cascades, relaying information from the outside to the inside of mammalian cells. De novo designed protein switches capable of interfacing with tyrosine kinase signaling pathways would open new avenues for controlling cellular behavior, but, so far, no such systems have been described. Here we describe the de novo design of two classes of protein switch that link phosphorylation by tyrosine and serine kinases to protein-protein association. In the first class, protein-protein association is required for phosphorylation by the kinase, while in the second class, kinase activity drives protein-protein association. We design systems that couple protein binding to kinase activity on the immunoreceptor tyrosine-based activation motif central to T-cell signaling, and kinase activity to reconstitution of green fluorescent protein fluorescence from fragments and the inhibition of the protease calpain. The designed switches are reversible and function in vitro and in cells with up to 40-fold activation of switching by phosphorylation.
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Affiliation(s)
- Nicholas B Woodall
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Zara Weinberg
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jesslyn Park
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Florian Busch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Issa Yousif
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Hana El-Samad
- Department of Biochemistry & Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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36
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Beuvin F, de Givry S, Schiex T, Verel S, Simoncini D. Iterated local search with partition crossover for computational protein design. Proteins 2021; 89:1522-1529. [PMID: 34228826 DOI: 10.1002/prot.26174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/25/2021] [Indexed: 11/06/2022]
Abstract
Structure-based computational protein design (CPD) refers to the problem of finding a sequence of amino acids which folds into a specific desired protein structure, and possibly fulfills some targeted biochemical properties. Recent studies point out the particularly rugged CPD energy landscape, suggesting that local search optimization methods should be designed and tuned to easily escape local minima attraction basins. In this article, we analyze the performance and search dynamics of an iterated local search (ILS) algorithm enhanced with partition crossover. Our algorithm, PILS, quickly finds local minima and escapes their basins of attraction by solution perturbation. Additionally, the partition crossover operator exploits the structure of the residue interaction graph in order to efficiently mix solutions and find new unexplored basins. Our results on a benchmark of 30 proteins of various topology and size show that PILS consistently finds lower energy solutions compared to Rosetta fixbb and a classic ILS, and that the corresponding sequences are mostly closer to the native.
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Affiliation(s)
- François Beuvin
- IRIT UMR 5505-CNRS, Université de Toulouse I Capitole, Toulouse, France.,Artificial and Natural Intelligence Toulouse Institute, ANITI, Toulouse, France
| | - Simon de Givry
- Artificial and Natural Intelligence Toulouse Institute, ANITI, Toulouse, France.,MIAT, Université de Toulouse, INRAE, UR 875, Toulouse, France
| | - Thomas Schiex
- Artificial and Natural Intelligence Toulouse Institute, ANITI, Toulouse, France.,MIAT, Université de Toulouse, INRAE, UR 875, Toulouse, France
| | | | - David Simoncini
- IRIT UMR 5505-CNRS, Université de Toulouse I Capitole, Toulouse, France.,Artificial and Natural Intelligence Toulouse Institute, ANITI, Toulouse, France
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37
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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38
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Xu Y, Wu Y, Lv X, Sun G, Zhang H, Chen T, Du G, Li J, Liu L. Design and construction of novel biocatalyst for bioprocessing: Recent advances and future outlook. BIORESOURCE TECHNOLOGY 2021; 332:125071. [PMID: 33826982 DOI: 10.1016/j.biortech.2021.125071] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Bioprocess, a biocatalysis-based technology, is becoming popular in many research fields and widely applied in industrial manufacturing. However, low bioconversion, low productivity, and high costs during industrial processes are usually the limitation in bioprocess. Therefore, many biocatalyst strategies have been developed to meet these challenges in recent years. In this review, we firstly discuss protein engineering strategies, which are emerged for improving the biocatalysis activity of biocatalysts. Then, we summarize metabolic engineering strategies that are promoting the development of microbial cell factories. Next, we illustrate the necessity of using the combining strategy of protein engineering and metabolic engineering for efficient biocatalysts. Lastly, future perspectives about the development and application of novel biocatalyst strategies are discussed. This review provides theoretical guidance for the development of efficient, sustainable, and economical bioprocesses mediated by novel biocatalysts.
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Affiliation(s)
- Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co., Ltd., Tai'an 271000, PR China
| | - Taichi Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China.
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39
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Shakiba N, Jones RD, Weiss R, Del Vecchio D. Context-aware synthetic biology by controller design: Engineering the mammalian cell. Cell Syst 2021; 12:561-592. [PMID: 34139166 PMCID: PMC8261833 DOI: 10.1016/j.cels.2021.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
The rise of systems biology has ushered a new paradigm: the view of the cell as a system that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides a complementary approach, allowing us to program cell behavior through the addition of synthetic genetic devices into the cellular processor. These devices, and the complex genetic circuits they compose, are engineered using a design-prototype-test cycle, allowing for predictable device performance to be achieved in a context-dependent manner. Within mammalian cells, context effects impact device performance at multiple scales, including the genetic, cellular, and extracellular levels. In order for synthetic genetic devices to achieve predictable behaviors, approaches to overcome context dependence are necessary. Here, we describe control systems approaches for achieving context-aware devices that are robust to context effects. We then consider cell fate programing as a case study to explore the potential impact of context-aware devices for regenerative medicine applications.
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Affiliation(s)
- Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Domitilla Del Vecchio
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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40
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ElGamacy M, Hernandez Alvarez B. Expanding the versatility of natural and de novo designed coiled coils and helical bundles. Curr Opin Struct Biol 2021; 68:224-234. [PMID: 33964630 DOI: 10.1016/j.sbi.2021.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Natural helical bundles (HBs) constitute a ubiquitous class of protein folds built of two or more longitudinally arranged α-helices. They adopt topologies that include symmetric, highly regular assemblies all the way to asymmetric, loosely packed domains. The diverse functional spectrum of HBs ranges from structural scaffolds to complex and dynamic effectors as molecular motors, signaling and sensing molecules, enzymes, and molecular switches. Symmetric HBs, particularly coiled coils, offer simple model systems providing an ideal entry point for protein folding and design studies. Herein, we review recent progress unveiling new structural features and functional mechanisms in natural HBs and cover staggering advances in the de novo design of HBs, giving rise to exotic structures and the creation of novel functions.
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Affiliation(s)
- Mohammad ElGamacy
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen, 72076, Germany; Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller-Strasse 10, Tübingen, 72076, Germany; Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany.
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41
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Chen Z, Elowitz MB. Programmable protein circuit design. Cell 2021; 184:2284-2301. [PMID: 33848464 PMCID: PMC8087657 DOI: 10.1016/j.cell.2021.03.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022]
Abstract
A fundamental challenge in synthetic biology is to create molecular circuits that can program complex cellular functions. Because proteins can bind, cleave, and chemically modify one another and interface directly and rapidly with endogenous pathways, they could extend the capabilities of synthetic circuits beyond what is possible with gene regulation alone. However, the very diversity that makes proteins so powerful also complicates efforts to harness them as well-controlled synthetic circuit components. Recent work has begun to address this challenge, focusing on principles such as orthogonality and composability that permit construction of diverse circuit-level functions from a limited set of engineered protein components. These approaches are now enabling the engineering of circuits that can sense, transmit, and process information; dynamically control cellular behaviors; and enable new therapeutic strategies, establishing a powerful paradigm for programming biology.
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Affiliation(s)
- Zibo Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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42
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Weinberg ZY, Hilburger CE, Kim M, Cao L, Khalid M, Elmes S, Diwanji D, Hernandez E, Lopez J, Schaefer K, Smith AM, Zhou F, Kumar GR, Ott M, Baker D, El-Samad H. Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.20.440678. [PMID: 33907743 PMCID: PMC8077567 DOI: 10.1101/2021.04.20.440678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic has demonstrated the need for exploring different diagnostic and therapeutic modalities to tackle future viral threats. In this vein, we propose the idea of sentinel cells, cellular biosensors capable of detecting viral antigens and responding to them with customizable responses. Using SARS-CoV-2 as a test case, we developed a live cell sensor (SARSNotch) using a de novo-designed protein binder against the SARS-CoV-2 Spike protein. SARSNotch is capable of driving custom genetically-encoded payloads in immortalized cell lines or in primary T lymphocytes in response to purified SARS-CoV-2 Spike or in the presence of Spike-expressing cells. Furthermore, SARSNotch is functional in a cellular system used in directed evolution platforms for development of better binders or therapeutics. In keeping with the rapid dissemination of scientific knowledge that has characterized the incredible scientific response to the ongoing pandemic, we extend an open invitation for others to make use of and improve SARSNotch sentinel cells in the hopes of unlocking the potential of the next generation of smart antiviral therapeutics.
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Affiliation(s)
- Zara Y. Weinberg
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Claire E. Hilburger
- The UC Berkeley-UCSF Graduate Program in Bioengineering, UC Berkeley, Berkeley, CA
| | - Matthew Kim
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA
- Institute for Protein Design, University of Washington, Seattle, WA
| | - Mir Khalid
- Gladstone Institute of Virology, San Francisco, CA
| | - Sarah Elmes
- Laboratory for Cell Analysis, University of California, San Francisco, CA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, CA
- Medical Scientist Training Program, University of California San Francisco, CA
| | - Evelyn Hernandez
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Jocelyne Lopez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - Kaitlin Schaefer
- Department of Pharmacology, University of California, San Francisco, CA
| | - Amber M. Smith
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Fengbo Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA
| | - QCRG Structural Biology Consortium
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San, Francisco, San Francisco, CA
| | | | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA
- Department of Medicine, University of California San, Francisco, San Francisco, CA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA
- Institute for Protein Design, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
- Cell Design Initiative, University of California, San Francisco, CA
- Chan-Zuckerberg Biohub, San Francisco, CA
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43
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English MA, Gayet RV, Collins JJ. Designing Biological Circuits: Synthetic Biology Within the Operon Model and Beyond. Annu Rev Biochem 2021; 90:221-244. [PMID: 33784178 DOI: 10.1146/annurev-biochem-013118-111914] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In 1961, Jacob and Monod proposed the operon model of gene regulation. At the model's core was the modular assembly of regulators, operators, and structural genes. To illustrate the composability of these elements, Jacob and Monod linked phenotypic diversity to the architectures of regulatory circuits. In this review, we examine how the circuit blueprints imagined by Jacob and Monod laid the foundation for the first synthetic gene networks that launched the field of synthetic biology in 2000. We discuss the influences of the operon model and its broader theoretical framework on the first generation of synthetic biological circuits, which were predominantly transcriptional and posttranscriptional circuits. We also describe how recent advances in molecular biology beyond the operon model-namely, programmable DNA- and RNA-binding molecules as well as models of epigenetic and posttranslational regulation-are expanding the synthetic biology toolkit and enabling the design of more complex biological circuits.
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Affiliation(s)
- Max A English
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; .,Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Raphaël V Gayet
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; .,Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.,Microbiology Graduate Program, MIT, Cambridge, Massachusetts 02139, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; .,Institute for Medical Engineering and Science, MIT, Cambridge, Massachusetts 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.,Synthetic Biology Center, MIT, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard-MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
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44
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Lormeau C, Rudolf F, Stelling J. A rationally engineered decoder of transient intracellular signals. Nat Commun 2021; 12:1886. [PMID: 33767179 PMCID: PMC7994635 DOI: 10.1038/s41467-021-22190-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/05/2021] [Indexed: 12/20/2022] Open
Abstract
Cells can encode information about their environment by modulating signaling dynamics and responding accordingly. Yet, the mechanisms cells use to decode these dynamics remain unknown when cells respond exclusively to transient signals. Here, we approach design principles underlying such decoding by rationally engineering a synthetic short-pulse decoder in budding yeast. A computational method for rapid prototyping, TopoDesign, allowed us to explore 4122 possible circuit architectures, design targeted experiments, and then rationally select a single circuit for implementation. This circuit demonstrates short-pulse decoding through incoherent feedforward and positive feedback. We predict incoherent feedforward to be essential for decoding transient signals, thereby complementing proposed design principles of temporal filtering, the ability to respond to sustained signals, but not to transient signals. More generally, we anticipate TopoDesign to help designing other synthetic circuits with non-intuitive dynamics, simply by assembling available biological components.
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Affiliation(s)
- Claude Lormeau
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Mattenstrasse 26, CH 4058, Basel, Switzerland
- Life Science Zurich Graduate School, Interdisciplinary PhD Program Systems Biology, Zurich, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Mattenstrasse 26, CH 4058, Basel, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Mattenstrasse 26, CH 4058, Basel, Switzerland.
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45
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De novo design of a reversible phosphorylation-dependent switch for membrane targeting. Nat Commun 2021; 12:1472. [PMID: 33674566 PMCID: PMC7935970 DOI: 10.1038/s41467-021-21622-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells. The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.
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46
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Makhlynets OV, Caputo GA. Characteristics and therapeutic applications of antimicrobial peptides. BIOPHYSICS REVIEWS 2021; 2:011301. [PMID: 38505398 PMCID: PMC10903410 DOI: 10.1063/5.0035731] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
The demand for novel antimicrobial compounds is rapidly growing due to the phenomenon of antibiotic resistance in bacteria. In response, numerous alternative approaches are being taken including use of polymers, metals, combinatorial approaches, and antimicrobial peptides (AMPs). AMPs are a naturally occurring part of the immune system of all higher organisms and display remarkable broad-spectrum activity and high selectivity for bacterial cells over host cells. However, despite good activity and safety profiles, AMPs have struggled to find success in the clinic. In this review, we outline the fundamental properties of AMPs that make them effective antimicrobials and extend this into three main approaches being used to help AMPs become viable clinical options. These three approaches are the incorporation of non-natural amino acids into the AMP sequence to impart better pharmacological properties, the incorporation of AMPs in hydrogels, and the chemical modification of surfaces with AMPs for device applications. These approaches are being developed to enhance the biocompatibility, stability, and/or bioavailability of AMPs as clinical options.
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Affiliation(s)
- Olga V. Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
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47
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Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
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Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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48
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Cuba Samaniego C, Franco E. Ultrasensitive molecular controllers for quasi-integral feedback. Cell Syst 2021; 12:272-288.e3. [PMID: 33539724 DOI: 10.1016/j.cels.2021.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 09/22/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022]
Abstract
Feedback control has enabled the success of automated technologies by mitigating the effects of variability, unknown disturbances, and noise. While it is known that biological feedback loops reduce the impact of noise and help shape kinetic responses, many questions remain about how to design molecular integral controllers. Here, we propose a modular strategy to build molecular quasi-integral feedback controllers, which involves following two design principles. The first principle is to utilize an ultrasensitive response, which determines the gain of the controller and influences the steady-state error. The second is to use a tunable threshold of the ultrasensitive response, which determines the equilibrium point of the system. We describe a reaction network, named brink controller, that satisfies these conditions by combining molecular sequestration and an activation/deactivation cycle. With computational models, we examine potential biological implementations of brink controllers, and we illustrate different example applications.
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Affiliation(s)
- Christian Cuba Samaniego
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA; Bioengineering, University of California at Los Angeles, Los Angeles, CA 90095, USA; Mechanical Engineering, University of California at Riverside, Riverside, CA 92521, USA.
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49
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Dishman AF, Tyler RC, Fox JC, Kleist AB, Prehoda KE, Babu MM, Peterson FC, Volkman BF. Evolution of fold switching in a metamorphic protein. Science 2021; 371:86-90. [PMID: 33384377 PMCID: PMC8017559 DOI: 10.1126/science.abd8700] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022]
Abstract
Metamorphic proteins switch between different folds, defying the protein folding paradigm. It is unclear how fold switching arises during evolution. With ancestral reconstruction and nuclear magnetic resonance, we studied the evolution of the metamorphic human protein XCL1, which has two distinct folds with different functions, making it an unusual member of the chemokine family, whose members generally adopt one conserved fold. XCL1 evolved from an ancestor with the chemokine fold. Evolution of a dimer interface, changes in structural constraints and molecular strain, and alteration of intramolecular protein contacts drove the evolution of metamorphosis. Then, XCL1 likely evolved to preferentially populate the noncanonical fold before reaching its modern-day near-equal population of folds. These discoveries illuminate how one sequence has evolved to encode multiple structures, revealing principles for protein design and engineering.
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Affiliation(s)
- Acacia F Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert C Tyler
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jamie C Fox
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kenneth E Prehoda
- Institute of Molecular Biology, Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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50
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Kimchi O, Goodrich CP, Courbet A, Curatolo AI, Woodall NB, Baker D, Brenner MP. Self-assembly-based posttranslational protein oscillators. SCIENCE ADVANCES 2020; 6:6/51/eabc1939. [PMID: 33328225 PMCID: PMC7744077 DOI: 10.1126/sciadv.abc1939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems.
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Affiliation(s)
- Ofer Kimchi
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA.
| | - Carl P Goodrich
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Agnese I Curatolo
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA
| | - Nicholas B Woodall
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Michael P Brenner
- Harvard University School of Engineering and Applied Sciences, Cambridge, MA 02138, USA
- Kavli Institute for Bionano Science and Technology Harvard University, Cambridge, MA 02138, USA
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