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Collu G, Bierig T, Krebs AS, Engilberge S, Varma N, Guixà-González R, Sharpe T, Deupi X, Olieric V, Poghosyan E, Benoit RM. Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology. Structure 2021; 30:95-106.e7. [PMID: 34587504 DOI: 10.1016/j.str.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/17/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Chimeric fusion proteins are essential tools for protein nanotechnology. Non-optimized protein-protein connections are usually flexible and therefore unsuitable as structural building blocks. Here we show that the ER/K motif, a single α-helical domain (SAH), can be seamlessly fused to terminal helices of proteins, forming an extended, partially free-standing rigid helix. This enables the connection of two domains at a defined distance and orientation. We designed three constructs termed YFPnano, T4Lnano, and MoStoNano. Analysis of experimentally determined structures and molecular dynamics simulations reveals a certain degree of plasticity in the connections that allows the adaptation to crystal contact opportunities. Our data show that SAHs can be stably integrated into designed structural elements, enabling new possibilities for protein nanotechnology, for example, to improve the exposure of epitopes on nanoparticles (structural vaccinology), to engineer crystal contacts with minimal impact on construct flexibility (for the study of protein dynamics), and to design novel biomaterials.
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Affiliation(s)
- Gabriella Collu
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Tobias Bierig
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Anna-Sophia Krebs
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Sylvain Engilberge
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Niveditha Varma
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Timothy Sharpe
- Biophysics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Condensed Matter Theory Group, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Emiliya Poghosyan
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Roger M Benoit
- Laboratory of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
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Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
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Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
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Walker SP, Yallapragada VVB, Tangney M. Arming Yourself for The In Silico Protein Design Revolution. Trends Biotechnol 2020; 39:651-664. [PMID: 33139074 DOI: 10.1016/j.tibtech.2020.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/23/2022]
Abstract
Proteins mediate many essential processes of life to a degree of functional precision unmatched by any synthetic device. While engineered proteins are currently used in biotech, food, biomedicine, and material technology-based industries, the true potential of proteins is practically untapped. The emerging field of in silico protein design is predicted to provide the next quantum leap in the biotech industry. Having predictive control over protein function and the ability to redefine these functions have driven the field of protein engineering into an era of unprecedented development. This article provides a holistic analysis of protein design R&D (current state-of-the-art tools and knowhow) and commercial landscape, as well as a one-stop-shop profile of in silico protein design technology for biotechnology stakeholders.
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Affiliation(s)
- Sidney P Walker
- CancerResearch@UCC, University College Cork, Cork, Ireland; SynBioCentre, University College Cork, Cork, Ireland
| | - Venkata V B Yallapragada
- CancerResearch@UCC, University College Cork, Cork, Ireland; SynBioCentre, University College Cork, Cork, Ireland
| | - Mark Tangney
- CancerResearch@UCC, University College Cork, Cork, Ireland; SynBioCentre, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
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Do P, Perdue LA, Chyong A, Hunter R, Dougan J, Henry CJ, Porter CC, Dreaden EC. Rapid Assembly and Screening of Multivalent Immune Cell-Redirecting Therapies for Leukemia. ACS COMBINATORIAL SCIENCE 2020; 22:533-541. [PMID: 32786324 PMCID: PMC8496977 DOI: 10.1021/acscombsci.0c00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Therapies that bind with immune cells and redirect their cytotoxic activity toward diseased cells represent a promising and versatile approach to immunotherapy with applications in cancer, lupus, and other diseases; traditional methods for discovering these therapies, however, are often time-intensive and lack the throughput of related target-based discovery approaches. Inspired by the observation that the cytokine, IL-12, can enhance antileukemic activity of the clinically approved T cell redirecting therapy, blinatumomab, here we describe the structure and assembly of a chimeric immune cell-redirecting agent which redirects the lytic activity of primary human T cells toward leukemic B cells and simultaneously cotargets the delivery of T cell-stimulating IL-12. We further describe a novel method for the parallel assembly of compositionally diverse libraries of these bispecific T cell engaging cytokines (BiTEokines) and their high-throughput phenotypic screening, requiring just days for hit identification and the analysis of composition-function relationships. Using this approach, we identified CD19 × CD3 × IL12 compounds that exhibit ex vivo lytic activity comparable to current FDA-approved therapies for leukemia and correlated drug treatment with specific cell–cell contact, cytokine delivery, and leukemia cell lysis. Given the modular nature of these multivalent compounds and their rapid assembly/screening, we anticipate facile extension of this therapeutic approach to a wide range of immune cells, diseased cells, and soluble protein combinations in the future.
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Affiliation(s)
- Priscilla Do
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Lacey A Perdue
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Andrew Chyong
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Rae Hunter
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322, United States
- Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, United States
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, Georgia 30322, United States
| | - Jodi Dougan
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322, United States
- Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, United States
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, Georgia 30322, United States
| | - Curtis J Henry
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322, United States
- Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, United States
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, Georgia 30322, United States
| | - Christopher C Porter
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322, United States
- Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, United States
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, Georgia 30322, United States
| | - Erik C Dreaden
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia 30322, United States
- Winship Cancer Institute of Emory University, Atlanta, Georgia 30322, United States
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Emory School of Medicine, Atlanta, Georgia 30322, United States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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