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Leonard AC, Friedman AJ, Chayer R, Petersen BM, Woojuh J, Xing Z, Cutler SR, Kaar JL, Shirts MR, Whitehead TA. Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS Chem Biol 2024. [PMID: 39017707 DOI: 10.1021/acschembio.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem, which could enable many practical applications of protein biosensors. In this work, we analyzed two engineered biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free-energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.
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Affiliation(s)
- Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Rachel Chayer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Brian M Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Janty Woojuh
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-9800, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Zenan Xing
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-9800, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-9800, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
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2
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Daffern N, Johansson KE, Baumer ZT, Robertson NR, Woojuh J, Bedewitz MA, Davis Z, Wheeldon I, Cutler SR, Lindorff-Larsen K, Whitehead TA. GMMA Can Stabilize Proteins Across Different Functional Constraints. J Mol Biol 2024; 436:168586. [PMID: 38663544 DOI: 10.1016/j.jmb.2024.168586] [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: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Stabilizing proteins without otherwise hampering their function is a central task in protein engineering and design. PYR1 is a plant hormone receptor that has been engineered to bind diverse small molecule ligands. We sought a set of generalized mutations that would provide stability without affecting functionality for PYR1 variants with diverse ligand-binding capabilities. To do this we used a global multi-mutant analysis (GMMA) approach, which can identify substitutions that have stabilizing effects and do not lower function. GMMA has the added benefit of finding substitutions that are stabilizing in different sequence contexts and we hypothesized that applying GMMA to PYR1 with different functionalities would identify this set of generalized mutations. Indeed, conducting FACS and deep sequencing of libraries for PYR1 variants with two different functionalities and applying a GMMA analysis identified 5 substitutions that, when inserted into four PYR1 variants that each bind a unique ligand, provided an increase of 2-6 °C in thermal inactivation temperature and no decrease in functionality.
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Affiliation(s)
- Nicolas Daffern
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zachary T Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | | | - Janty Woojuh
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Matthew A Bedewitz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Zoë Davis
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, USA; Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA; Center for Plant Cell Biology, University of California, Riverside, Riverside, CA, USA
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80305, USA.
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Leonard AC, Friedman AJ, Chayer R, Petersen BM, Kaar J, Shirts MR, Whitehead TA. Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586677. [PMID: 38586024 PMCID: PMC10996623 DOI: 10.1101/2024.03.25.586677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem which could enable many practical applications of protein biosensors. In this work, we analyzed two engineer ed biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.
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Li Z, Shen Y, Beltrán J, Tian H, Bedewitz M, Wheeldon I, Whitehead TA, Cutler SR, Zhong W. High-Performance Cannabinoid Sensor Empowered by Plant Hormone Receptors and Antifouling Magnetic Nanorods. ACS Sens 2023; 8:3914-3922. [PMID: 37737572 PMCID: PMC11288662 DOI: 10.1021/acssensors.3c01488] [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] [Indexed: 09/23/2023]
Abstract
The misuse of cannabinoids and their synthetic variants poses significant threats to public health, necessitating the development of advanced techniques for detection of these compounds in biological or environmental samples. Existing methods face challenges like lengthy sample pretreatment and laborious antifouling steps. Herein, we present a novel sensing platform using magnetic nanorods coated with zwitterionic polymers for the simple, rapid, and sensitive detection of cannabinoids in biofluids. Our technique utilizes the engineered derivatives of the plant hormone receptor Pyrabactin Resistance 1 (PYR1) as drug recognition elements and employs the chemical-induced dimerization (CID) mechanism for signal development. Additionally, the magnetic nanorods facilitate efficient target capture and reduce the assay duration. Moreover, the zwitterionic polymer coating exhibits excellent antifouling capability, preserving excellent sensor performance in complex biofluids. Our sensors detect cannabinoids in undiluted biofluids like serum, saliva, and urine with a low limit of detection (0.002 pM in saliva and few pM in urine and serum) and dynamic ranges spanning up to 9 orders of magnitude. Moreover, the PYR1 derivatives demonstrate high specificity even in the presence of multiple interfering compounds. This work opens new opportunities for sensor development, showcasing the excellent performance of antifouling magnetic nanorods that can be compatible with different recognition units, including receptors and antibodies, for detecting a variety of targets.
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Affiliation(s)
- Zongbo Li
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A
| | - Yuyang Shen
- Environmental Toxicology Graduate Program, University of California-Riverside, Riverside, CA 92521, U.S.A
| | - Jesús Beltrán
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, U.S.A
| | - Hao Tian
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, U.S.A
| | - Matthew Bedewitz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Ian Wheeldon
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, U.S.A
- Department of Chemical and Environmental Engineering, University of California-Riverside, Riverside, CA 92521, U.S.A
| | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sean R. Cutler
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, U.S.A
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, U.S.A
- Environmental Toxicology Graduate Program, University of California-Riverside, Riverside, CA 92521, U.S.A
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5
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Steiner PJ, Swift SD, Bedewitz M, Wheeldon I, Cutler SR, Nusinow DA, Whitehead TA. A Closed Form Model for Molecular Ratchet-Type Chemically Induced Dimerization Modules. Biochemistry 2023; 62:281-291. [PMID: 35675717 DOI: 10.1021/acs.biochem.2c00172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Chemical-induced dimerization (CID) modules enable users to implement ligand-controlled cellular and biochemical functions for a number of problems in basic and applied biology. A special class of CID modules occur naturally in plants and involve a hormone receptor that binds a hormone, triggering a conformational change in the receptor that enables recognition by a second binding protein. Two recent reports show that such hormone receptors can be engineered to sense dozens of structurally diverse compounds. As a closed form model for molecular ratchets would be of immense utility in forward engineering of biological systems, here we have developed a closed form model for these distinct CID modules. These modules, which we call molecular ratchets, are distinct from more common CID modules called molecular glues in that they engage in saturable binding kinetics and are characterized well by a Hill equation. A defining characteristic of molecular ratchets is that the sensitivity of the response can be tuned by increasing the molar ratio of the hormone receptor to the binding protein. Thus, the same molecular ratchet can have a pico- or micromolar EC50 depending on the concentration of the different receptor and binding proteins. Closed form models are derived for a base elementary reaction rate model, for ligand-independent complexation of the receptor and binding protein, and for homodimerization of the hormone receptor. Useful governing equations for a variety of in vitro and in vivo applications are derived, including enzyme-linked immunosorbent assay-like microplate assays, transcriptional activation in prokaryotes and eukaryotes, and ligand-induced split protein complementation.
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Affiliation(s)
- Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Samuel D Swift
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Matthew Bedewitz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Ian Wheeldon
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, United States.,Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Sean R Cutler
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, California 92521, United States.,Department of Botany and Plant Sciences, University of California Riverside, Riverside, California 92521, United States.,Center for Plant Cell Biology, University of California Riverside, Riverside, California 92521, United States
| | - Dmitri A Nusinow
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, United States
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
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6
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Beltrán J, Steiner PJ, Bedewitz M, Wei S, Peterson FC, Li Z, Hughes BE, Hartley Z, Robertson NR, Medina-Cucurella AV, Baumer ZT, Leonard AC, Park SY, Volkman BF, Nusinow DA, Zhong W, Wheeldon I, Cutler SR, Whitehead TA. Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds. Nat Biotechnol 2022; 40:1855-1861. [PMID: 35726092 PMCID: PMC9750858 DOI: 10.1038/s41587-022-01364-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/17/2022] [Indexed: 01/14/2023]
Abstract
A general method to generate biosensors for user-defined molecules could provide detection tools for a wide range of biological applications. Here, we describe an approach for the rapid engineering of biosensors using PYR1 (Pyrabactin Resistance 1), a plant abscisic acid (ABA) receptor with a malleable ligand-binding pocket and a requirement for ligand-induced heterodimerization, which facilitates the construction of sense-response functions. We applied this platform to evolve 21 sensors with nanomolar to micromolar sensitivities for a range of small molecules, including structurally diverse natural and synthetic cannabinoids and several organophosphates. X-ray crystallography analysis revealed the mechanistic basis for new ligand recognition by an evolved cannabinoid receptor. We demonstrate that PYR1-derived receptors are readily ported to various ligand-responsive outputs, including enzyme-linked immunosorbent assay (ELISA)-like assays, luminescence by protein-fragment complementation and transcriptional circuits, all with picomolar to nanomolar sensitivity. PYR1 provides a scaffold for rapidly evolving new biosensors for diverse sense-response applications.
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Affiliation(s)
- Jesús Beltrán
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Paul J Steiner
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Matthew Bedewitz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Shuang Wei
- Department of Biochemistry, University of California, Riverside, Riverside, CA, USA
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Zongbo Li
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Brigid E Hughes
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Zachary Hartley
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Nicholas R Robertson
- Department of Bioengineering, University of California, Riverside, Riverside, USA
| | | | - Zachary T Baumer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
| | - Sang-Youl Park
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA.
| | - Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
- Center for Plant Cell Biology, University of California, Riverside, Riverside, CA, USA.
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA.
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