1
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Zhao Z, Rudman NA, Dmochowski IJ. A Site-Specific Cross-Linker for Visible-Light Control of Proteins. ACS OMEGA 2024; 9:29331-29338. [PMID: 39005769 PMCID: PMC11238208 DOI: 10.1021/acsomega.4c00968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 07/16/2024]
Abstract
There is a need for photochemical tools that allow precise control of protein structure and function with visible light. We focus here on the s-tetrazine moiety, which can be installed at a specific protein site via the reaction between dichlorotetrazine and two adjacent sulfhydryl groups. Tetrazine's compact size enables structural mimicry of native amino acid linkages, such as an intramolecular salt bridge or disulfide bond. In this study, we investigated tetrazine installation in three different proteins, where it was confirmed that the cross-linking reaction is highly efficient in aqueous conditions and site-specific when two cysteines are located proximally: the S-S distance was 4-10 Å. As shown in maltose binding protein, the tetrazine cross-linker can replace an interdomain salt bridge crucial for xenon binding and serve as a visible-light photoswitch to modulate 129Xe NMR contrast. This work highlights the ease of aqueous tetrazine bioconjugation and its applications for protein photoregulation.
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Affiliation(s)
- Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, Pennsylvania 19104, United States
| | - Nathan A Rudman
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, Pennsylvania 19104, United States
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2
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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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3
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Lee EJ, Gladkov N, Miller JE, Yeates TO. Design of Ligand-Operable Protein-Cages That Open Upon Specific Protein Binding. ACS Synth Biol 2024; 13:157-167. [PMID: 38133598 DOI: 10.1021/acssynbio.3c00383] [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] [Indexed: 12/23/2023]
Abstract
Protein nanocages have diverse applications in medicine and biotechnology, including molecular delivery. However, although numerous studies have demonstrated the ability of protein nanocages to encapsulate various molecular species, limited methods are available for subsequently opening a nanocage for cargo release under specific conditions. A modular platform with a specific protein-target-based mechanism of nanocage opening is notably lacking. To address this important technology gap, we present a new class of designed protein cages, the Ligand-Operable Cage (LOC). LOCs primarily comprise a protein nanocage core and a fused surface binding adaptor. The geometry of the LOC is designed so that binding of a target protein ligand (or multiple copies thereof) to the surface binder is sterically incompatible with retention of the assembled state of the cage. Therefore, the tight binding of a target ligand drives cage disassembly by mass action, subsequently exposing the encapsulated cargo. LOCs are modular; direct substitution of the surface binder sequence can reprogram the nanocage to open in response to any target protein ligand of interest. We demonstrate these design principles using both a natural and a designed protein cage as the core, with different proteins acting as the triggering ligand and with different reporter readouts─fluorescence unquenching and luminescence─for cage disassembly. These developments advance the critical problem of targeted molecular delivery and detection.
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Affiliation(s)
- Eric J Lee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Nika Gladkov
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
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4
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van der Ven AM, Gyamfi H, Suttisansanee U, Ahmad MS, Su Z, Taylor RM, Poole A, Chiorean S, Daub E, Urquhart T, Honek JF. Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage. Molecules 2023; 28:4663. [PMID: 37375226 DOI: 10.3390/molecules28124663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering.
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Affiliation(s)
- Anton M van der Ven
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Hawa Gyamfi
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | - Muhammad S Ahmad
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Zhengding Su
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert M Taylor
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Amanda Poole
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisabeth Daub
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Taylor Urquhart
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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5
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Volarić J, Thallmair S, Feringa BL, Szymanski W. Photoswitchable, Water‐soluble Bis‐azobenzene Cross‐linkers with Enhanced Properties for Biological Applications. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jana Volarić
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies Frankfurt Institute for Advanced Studies GERMANY
| | - Ben L. Feringa
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Wiktor Szymanski
- University Medical Center Groningen Department of Radiology Hanzeplein 1 9747AG Groningen NETHERLANDS
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6
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Miller JE, Srinivasan Y, Dharmaraj NP, Liu A, Nguyen PL, Taylor SD, Yeates TO. Designing Protease-Triggered Protein Cages. J Am Chem Soc 2022; 144:12681-12689. [PMID: 35802879 DOI: 10.1021/jacs.2c02165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins that self-assemble into enclosed polyhedral cages, both naturally and by design, are garnering attention for their prospective utility in the fields of medicine and biotechnology. Notably, their potential for encapsulation and surface display are attractive for experiments that require protection and targeted delivery of cargo. The ability to control their opening or disassembly would greatly advance the development of protein nanocages into widespread molecular tools. Toward the development of protein cages that disassemble in a systematic manner and in response to biologically relevant stimuli, here we demonstrate a modular protein cage system that is opened by highly sequence-specific proteases, based on sequence insertions at strategically chosen loop positions in the protein cage subunits. We probed the generality of the approach in the context of protein cages built using the two prevailing methods of construction: genetic fusion between oligomeric components and (non-covalent) computational interface design between oligomeric components. Our results suggest that the former type of cage may be more amenable than the latter for endowing proteolytically controlled disassembly. We show that a successfully designed cage system, based on oligomeric fusion, is modular with regard to its triggering protease. One version of the cage is targeted by an asparagine protease implicated in cancer and Alzheimer's disease, whereas the second version is responsive to the blood-clotting protease, thrombin. The approach demonstrated here should guide future efforts to develop therapeutic vectors to treat disease states where protease induction or mis-regulation occurs.
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Affiliation(s)
- Justin E Miller
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Yashes Srinivasan
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Nithin P Dharmaraj
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Andrew Liu
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Phillip L Nguyen
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Scott D Taylor
- UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Todd O Yeates
- UCLA Molecular Biology Institute, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA-DOE Institute for Genomics and Proteomics, 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States.,UCLA Department of Chemistry and Biochemistry, 611 Charles E. Young Drive East, Los Angeles, California 90095, United States
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7
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Yasuike N, Kachi-Terajima C, Karin A, Mino T, Woolley GA. Modification of proteins with azobenzene crosslinkers using reversible covalent bonds. Org Biomol Chem 2022; 20:8649-8656. [DOI: 10.1039/d2ob01656g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bis-cyanoacrylate azobenzene (BCNA) targets di-thiol peptides in the presence of mono-thiols and enables photoswitching of helical structure.
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Affiliation(s)
- Nobuo Yasuike
- Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
- JSR Corporation, 1-9-2, Higashi-Shinbashi, Minato-ku, Tokyo, 105-8640, Japan
| | - Chihiro Kachi-Terajima
- Department of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Amir Karin
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Takashi Mino
- Graduate School of Engineering, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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8
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Peverini L, Dunning K, Peralta FA, Grutter T. Photo-isomerizable tweezers to probe ionotropic receptor mechanisms. Curr Opin Pharmacol 2021; 62:109-116. [PMID: 34965483 DOI: 10.1016/j.coph.2021.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/05/2021] [Accepted: 11/18/2021] [Indexed: 12/15/2022]
Abstract
Ligand-gated ion channels (LGIC, also referred to as ionotropic receptors) are important transmembrane proteins that open to allow ions to flow across the membrane and locally modify the membrane potential in response to the binding of a ligand. For more than a decade, a tremendous effort has been carried out in the determination of many LGIC structures in high resolution, leading to an unprecedented molecular description of channel gating. However, it is sometimes difficult to classify experimentally derived structures to their corresponding functional states, and alternative methods may help resolve or refine this issue. In this review, we focus on the application of photo-isomerizable tweezers (PIT) as a powerful strategy to interrogate molecular mechanisms of LGIC while assessing their functionality by electrophysiology.
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Affiliation(s)
- Laurie Peverini
- Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015, Paris, France
| | - Kate Dunning
- CNM Team, Université de Strasbourg, Centre National de La Recherche Scientifique, CAMB UMR 7199, Faculté de Pharmacie, 67401, Illkirch, France
| | - Francisco Andres Peralta
- CNM Team, Université de Strasbourg, Centre National de La Recherche Scientifique, CAMB UMR 7199, Faculté de Pharmacie, 67401, Illkirch, France; University of Strasbourg Institute for Advanced Studies (USIAS), 67000, Strasbourg, France
| | - Thomas Grutter
- CNM Team, Université de Strasbourg, Centre National de La Recherche Scientifique, CAMB UMR 7199, Faculté de Pharmacie, 67401, Illkirch, France; University of Strasbourg Institute for Advanced Studies (USIAS), 67000, Strasbourg, France.
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9
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A photoswitchable helical peptide with light-controllable interface/transmembrane topology in lipidic membranes. iScience 2021; 24:102771. [PMID: 34286233 PMCID: PMC8273423 DOI: 10.1016/j.isci.2021.102771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/02/2021] [Accepted: 06/19/2021] [Indexed: 11/21/2022] Open
Abstract
The spontaneous insertion of helical transmembrane (TM) polypeptides into lipid bilayers is driven by three sequential equilibria: solution-to-membrane interface (MI) partition, unstructured-to-helical folding, and MI-to-TM helix insertion. A bottleneck for understanding these three steps is the lack of experimental approaches to perturb membrane-bound hydrophobic polypeptides out of equilibrium rapidly and reversibly. Here, we report on a 24-residues-long hydrophobic α-helical polypeptide, covalently coupled to an azobenzene photoswitch (KCALP-azo), which displays a light-controllable TM/MI equilibrium in hydrated lipid bilayers. FTIR spectroscopy reveals that trans KCALP-azo folds as a TM α-helix (TM topology). After trans-to-cis photoisomerization of the azobenzene moiety with UV light (reversed with blue light), the helical structure of KCALP-azo is maintained, but its helix tilt increased from 32 ± 5° to 79 ± 8°, indication of a reversible TM-to-MI transition. Further analysis indicates that this transition is incomplete, with cis KCALP-azo existing in a ∼90% TM and ∼10% MI mixture. We present an α-helical transmembrane peptide modified with a molecular photoswitch The peptide exhibits reversible photocontrol of its membrane topology A fraction moves to the membrane interface with UV and inserts back with blue light This system will be useful to address the molecular mechanism for membrane insertion
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10
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Chaperonins: Nanocarriers with Biotechnological Applications. NANOMATERIALS 2021; 11:nano11020503. [PMID: 33671209 PMCID: PMC7922521 DOI: 10.3390/nano11020503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/05/2021] [Accepted: 02/13/2021] [Indexed: 12/18/2022]
Abstract
Chaperonins are molecular chaperones found in all kingdoms of life, and as such they assist in the folding of other proteins. Structurally, chaperonins are cylinders composed of two back-to-back rings, each of which is an oligomer of ~60-kDa proteins. Chaperonins are found in two main conformations, one in which the cavity is open and ready to recognise and trap unfolded client proteins, and a "closed" form in which folding takes place. The conspicuous properties of this structure (a cylinder containing a cavity that allows confinement) and the potential to control its closure and aperture have inspired a number of nanotechnological applications that will be described in this review.
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11
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Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions. Nat Commun 2020; 11:3770. [PMID: 32724112 PMCID: PMC7387446 DOI: 10.1038/s41467-020-17562-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2020] [Indexed: 12/24/2022] Open
Abstract
Self-assembly of molecular building blocks into higher-order structures is exploited in living systems to create functional complexity and represents a powerful strategy for constructing new materials. As nanoscale building blocks, proteins offer unique advantages, including monodispersity and atomically tunable interactions. Yet, control of protein self-assembly has been limited compared to inorganic or polymeric nanoparticles, which lack such attributes. Here, we report modular self-assembly of an engineered protein into four physicochemically distinct, precisely patterned 2D crystals via control of four classes of interactions spanning Ångström to several-nanometer length scales. We relate the resulting structures to the underlying free-energy landscape by combining in-situ atomic force microscopy observations of assembly with thermodynamic analyses of protein-protein and -surface interactions. Our results demonstrate rich phase behavior obtainable from a single, highly patchy protein when interactions acting over multiple length scales are exploited and predict unusual bulk-scale properties for protein-based materials that ensue from such control. As nanoscale building blocks, proteins offer unique advantages, including monodispersity and atomically tunable interactions, but their self-assembly is limited compared to inorganic or polymeric nanoparticles. Here, the authors show modular self-assembly of an engineered protein into four physicochemically distinct patterned 2D crystals via control of four classes of interactions.
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12
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Dalton K, Lopez T, Pande V, Frydman J. REP-X: An Evolution-guided Strategy for the Rational Design of Cysteine-less Protein Variants. Sci Rep 2020; 10:2193. [PMID: 32042106 PMCID: PMC7010797 DOI: 10.1038/s41598-020-58794-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/16/2020] [Indexed: 11/12/2022] Open
Abstract
Site-specific labeling of proteins is often a prerequisite for biophysical and biochemical characterization. Chemical modification of a unique cysteine residue is among the most facile methods for site-specific labeling of proteins. However, many proteins have multiple reactive cysteines, which must be mutated to other residues to enable labeling of unique positions. This trial-and-error process often results in cysteine-free proteins with reduced activity or stability. Herein we describe a general methodology to rationally engineer cysteine-less proteins. Briefly, natural variation across orthologues is exploited to identify suitable cysteine replacements compatible with protein activity and stability. As a proof-of-concept, we recount the successful engineering of a cysteine-less mutant of the group II chaperonin from methanogenic archaeon Methanococcus maripaludis. A webapp, REP-X (Replacement at Endogenous Positions from eXtant sequences), which enables users to design their own cysteine-less protein variants, will make this rational approach widely available.
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Affiliation(s)
- Kevin Dalton
- Biophysics Program Stanford University, Stanford, California, USA.,Department of Molecular and Cellular Biology Harvard University, Cambridge, MA, 02138, USA
| | - Tom Lopez
- Department of Biology Stanford University, Stanford, California, USA
| | - Vijay Pande
- Biophysics Program Stanford University, Stanford, California, USA.,Department of Chemistry, Stanford University, Stanford, California, USA
| | - Judith Frydman
- Biophysics Program Stanford University, Stanford, California, USA. .,Department of Biology Stanford University, Stanford, California, USA.
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13
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Engineering protein assemblies with allosteric control via monomer fold-switching. Nat Commun 2019; 10:5703. [PMID: 31836707 PMCID: PMC6911049 DOI: 10.1038/s41467-019-13686-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
The macromolecular machines of life use allosteric control to self-assemble, dissociate and change shape in response to signals. Despite enormous interest, the design of nanoscale allosteric assemblies has proven tremendously challenging. Here we present a proof of concept of allosteric assembly in which an engineered fold switch on the protein monomer triggers or blocks assembly. Our design is based on the hyper-stable, naturally monomeric protein CI2, a paradigm of simple two-state folding, and the toroidal arrangement with 6-fold symmetry that it only adopts in crystalline form. We engineer CI2 to enable a switch between the native and an alternate, latent fold that self-assembles onto hexagonal toroidal particles by exposing a favorable inter-monomer interface. The assembly is controlled on demand via the competing effects of temperature and a designed short peptide. These findings unveil a remarkable potential for structural metamorphosis in proteins and demonstrate key principles for engineering protein-based nanomachinery. The design of protein assemblies is a major thrust for biomolecular engineering and nanobiotechnology. Here the authors demonstrate a general mechanism for designing allosteric macromolecular assemblies and showcase a proof of concept for engineered allosteric protein assembly.
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14
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Kuhlman B, Bradley P. Advances in protein structure prediction and design. Nat Rev Mol Cell Biol 2019; 20:681-697. [PMID: 31417196 PMCID: PMC7032036 DOI: 10.1038/s41580-019-0163-x] [Citation(s) in RCA: 386] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
The prediction of protein three-dimensional structure from amino acid sequence has been a grand challenge problem in computational biophysics for decades, owing to its intrinsic scientific interest and also to the many potential applications for robust protein structure prediction algorithms, from genome interpretation to protein function prediction. More recently, the inverse problem - designing an amino acid sequence that will fold into a specified three-dimensional structure - has attracted growing attention as a potential route to the rational engineering of proteins with functions useful in biotechnology and medicine. Methods for the prediction and design of protein structures have advanced dramatically in the past decade. Increases in computing power and the rapid growth in protein sequence and structure databases have fuelled the development of new data-intensive and computationally demanding approaches for structure prediction. New algorithms for designing protein folds and protein-protein interfaces have been used to engineer novel high-order assemblies and to design from scratch fluorescent proteins with novel or enhanced properties, as well as signalling proteins with therapeutic potential. In this Review, we describe current approaches for protein structure prediction and design and highlight a selection of the successful applications they have enabled.
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Affiliation(s)
- Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Philip Bradley
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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15
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Affiliation(s)
- Aleksei Solomonov
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces Weizmann Institute of Science 7610001 Rehovot Israel
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16
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Akbar Ali M, Alam MA. Novel photoresponsive cyclicparaphenylenediazenes: structure, strain energy, cis-trans isomerization, and electronic properties. Photochem Photobiol Sci 2019; 18:1185-1196. [PMID: 30810558 DOI: 10.1039/c8pp00502h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A series of cis-trans isomers of cyclicparaphenylenediazenes (CPPDs) have been designed to explore their potential applications in solar thermal fuels and photoswitchable devices. In this work, three isomers of cis-trans-[3]CPPD, seven isomers of cis-trans-[4]CPPD, eleven isomers of cis-trans-[5]CPPD, and sixteen isomers of cis-trans-[6]CPPD have been proposed using density functional theory (DFT) at the B3LYP/6-31+G(d,p) level of theory. The stability of these CPPDs has been quantified by the homodesmotic reaction approach. Strain energies (SE) indicate that 3-cct, 4-ctct-anti, 5-cctct-anti, and 6-cttttc-anti are stable molecules in their respective CPPDs. The SE and heats of formation of cis-trans-CPPDs were also compared with those of all-cis-CPPDs and all-trans-CPPD isomers. The calculations suggest that cis-trans-CPPDs are more stable than all-cis and all-trans-CPPDs. The SE and also suggest that 3-cct, 4-ctct-anti, 5-cctct-anti, and 6-cttttc-anti are important candidates for laboratory test. The calculated highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) energy gaps of cis-trans-CPPDs indicate that these oligomers are potential materials for the construction of solar cells. Time-dependent (TD) DFT calculations of CPPDs show a characteristic peak in the range of 450 nm to 600 nm, which is consistent with previous studies. The predicted structures, and thermochemical and electronic properties can be a good starting point for the synthesis of CPPD-based photoswitchable and solar fuel cell devices.
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Affiliation(s)
- Mohamad Akbar Ali
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.
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17
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Cannon KA, Ochoa JM, Yeates TO. High-symmetry protein assemblies: patterns and emerging applications. Curr Opin Struct Biol 2019; 55:77-84. [PMID: 31005680 DOI: 10.1016/j.sbi.2019.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/06/2019] [Indexed: 12/28/2022]
Abstract
The accelerated elucidation of three-dimensional structures of protein complexes, both natural and designed, is providing new examples of large supramolecular assemblies with intriguing shapes. Those with high symmetry - based on the geometries of the Platonic solids - are particularly notable as their innately closed forms create interior spaces with varying degrees of enclosure. We survey known protein assemblies of this type and discuss their geometric features. The results bear on issues of protein function and evolution, while also guiding novel bioengineering applications. Recent successes using high-symmetry protein assemblies for applications in interior encapsulation and exterior display are highlighted.
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Affiliation(s)
- Kevin A Cannon
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States
| | - Jessica M Ochoa
- UCLA Department of Chemistry and Biochemistry, United States; UCLA Molecular Biology Institute, United States
| | - Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States; UCLA Molecular Biology Institute, United States.
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18
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Majerle A, Schmieden DT, Jerala R, Meyer AS. Synthetic Biology for Multiscale Designed Biomimetic Assemblies: From Designed Self-Assembling Biopolymers to Bacterial Bioprinting. Biochemistry 2019; 58:2095-2104. [PMID: 30957491 DOI: 10.1021/acs.biochem.8b00922] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nature is based on complex self-assembling systems that span from the nanoscale to the macroscale. We have already begun to design biomimetic systems with properties that have not evolved in nature, based on designed molecular interactions and regulation of biological systems. Synthetic biology is based on the principle of modularity, repurposing diverse building modules to design new types of molecular and cellular assemblies. While we are currently able to use techniques from synthetic biology to design self-assembling molecules and re-engineer functional cells, we still need to use guided assembly to construct biological assemblies at the macroscale. We review the recent strategies for designing biological systems ranging from molecular assemblies based on self-assembly of (poly)peptides to the guided assembly of patterned bacteria, spanning 7 orders of magnitude.
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Affiliation(s)
- Andreja Majerle
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Dominik T Schmieden
- Department of Bionanoscience, Kavli Institute of Nanoscience , Delft University of Technology , 2629 HZ Delft , The Netherlands
| | - Roman Jerala
- Department of Synthetic Biology and Immunology , National Institute of Chemistry , Hajdrihova 19 , 1000 Ljubljana , Slovenia
| | - Anne S Meyer
- Department of Biology , University of Rochester , Rochester , New York 14627 , United States
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19
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Heu W, Choi JM, Kyeong HH, Choi Y, Kim HY, Kim HS. Repeat Module-Based Rational Design of a Photoswitchable Protein for Light-Driven Control of Biological Processes. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Woosung Heu
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Jung Min Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hyun-Ho Kyeong
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Yoonjoo Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hee Yeon Kim
- Graduate school of Nanoscience and Technology; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hak-Sung Kim
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
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20
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Heu W, Choi JM, Kyeong HH, Choi Y, Kim HY, Kim HS. Repeat Module-Based Rational Design of a Photoswitchable Protein for Light-Driven Control of Biological Processes. Angew Chem Int Ed Engl 2018; 57:10859-10863. [DOI: 10.1002/anie.201803993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Woosung Heu
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Jung Min Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hyun-Ho Kyeong
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Yoonjoo Choi
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hee Yeon Kim
- Graduate school of Nanoscience and Technology; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
| | - Hak-Sung Kim
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Korea
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21
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Abstract
The last few years have witnessed significant advances in the use of light as a stimulus to control biomolecular interactions. Great efforts have been devoted to the development of genetically encoded optobiological and small photochromic switches. Newly discovered small molecules now allow researchers to build molecular systems that are sensitive to a wider range of wavelengths of light than ever before with improved switching fidelities and increased lifetimes of the photoactivated states. Because these molecules are relatively small and adopt predictable conformations they are well suited as tools to interrogate cellular function in a spatially and temporally contolled fashion and for applications in photopharmacology.
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Affiliation(s)
- Robert J Mart
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry & Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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22
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Wood CW, Woolfson DN. CCBuilder 2.0: Powerful and accessible coiled-coil modeling. Protein Sci 2017; 27:103-111. [PMID: 28836317 PMCID: PMC5734305 DOI: 10.1002/pro.3279] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 01/06/2023]
Abstract
The increased availability of user-friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α-helical coiled coil provides one such example, which represents ≈ 3-5% of all known protein-encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy-to-use web application, called CCBuilder 2.0, for modeling and optimizing both α-helical coiled coils and polyproline-based collagen triple helices. This has many applications from providing models to aid molecular replacement for X-ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo "dark matter" protein structures. CCBuilder 2.0 is available as a web-based application, the code for which is open-source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. LAY SUMMARY We have created CCBuilder 2.0, an easy to use web-based application that can model structures for a whole class of proteins, the α-helical coiled coil, which is estimated to account for 3-5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more-applied research including designing and engineering novel proteins that have potential applications in biotechnology.
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Affiliation(s)
- Christopher W Wood
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom.,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom
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23
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Let there be light: how to use photoswitchable cross-linker to reprogram proteins. Biochem Soc Trans 2017; 45:831-837. [PMID: 28620044 DOI: 10.1042/bst20160386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 04/04/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022]
Abstract
Azobenzene is a photo-isomerizing molecule whose end-to-end distance changes upon external illumination. When combined with site-specific reactive groups, it can be used as molecular tweezers to remote-control the structure and function of protein targets. The present study gives a brief overview over the rational design strategies that use an azobenzene-based photoswitchable cross-linker to engineer ON/OFF switches into functional proteins or to reprogram proteins for novel functions. The re-engineered proteins may be used as remote controls for cellular pathways, as light-gated drug delivery platforms or as light-powered machinery of synthetic cells and micro-scaled factories.
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24
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Wang C, Zhang Q, Wang X, Chang H, Zhang S, Tang Y, Xu J, Qi R, Cheng Y. Dynamic Modulation of Enzyme Activity by Near-Infrared Light. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700968] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Changping Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Qiang Zhang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Xinyu Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Hong Chang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Yuankai Tang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Ruijuan Qi
- Key Laboratory of Polar Materials and Devices; East China Normal University; Shanghai China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
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25
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Wang C, Zhang Q, Wang X, Chang H, Zhang S, Tang Y, Xu J, Qi R, Cheng Y. Dynamic Modulation of Enzyme Activity by Near-Infrared Light. Angew Chem Int Ed Engl 2017; 56:6767-6772. [DOI: 10.1002/anie.201700968] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/04/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Changping Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Qiang Zhang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Xinyu Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Hong Chang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Yuankai Tang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Ruijuan Qi
- Key Laboratory of Polar Materials and Devices; East China Normal University; Shanghai China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
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26
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Khersonsky O, Fleishman SJ. Incorporating an allosteric regulatory site in an antibody through backbone design. Protein Sci 2017; 26:807-813. [PMID: 28142198 DOI: 10.1002/pro.3126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 12/17/2022]
Abstract
Allosteric regulation underlies living cells' ability to sense changes in nutrient and signaling-molecule concentrations, but the ability to computationally design allosteric regulation into non-allosteric proteins has been elusive. Allosteric-site design is complicated by the requirement to encode the relative stabilities of active and inactive conformations of the same protein in the presence and absence of both ligand and effector. To address this challenge, we used Rosetta to design the backbone of the flexible heavy-chain complementarity-determining region 3 (HCDR3), and used geometric matching and sequence optimization to place a Zn2+ -coordination site in a fluorescein-binding antibody. We predicted that due to HCDR3's flexibility, the fluorescein-binding pocket would configure properly only upon Zn2+ application. We found that regulation by Zn2+ was reversible and sensitive to the divalent ion's identity, and came at the cost of reduced antibody stability and fluorescein-binding affinity. Fluorescein bound at an order of magnitude higher affinity in the presence of Zn2+ than in its absence, and the increase in fluorescein affinity was due almost entirely to faster fluorescein on-rate, suggesting that Zn2+ preorganized the antibody for fluorescein binding. Mutation analysis demonstrated the extreme sensitivity of Zn2+ regulation on the atomic details in and around the metal-coordination site. The designed antibody could serve to study how allosteric regulation evolved from non-allosteric binding proteins, and suggests a way to designing molecular sensors for environmental and biomedical targets.
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Affiliation(s)
- Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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27
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Abstract
This review highlights relevant studies of light-controlled molecular containers able to catch and release small molecules.
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Affiliation(s)
- Alejandro Díaz-Moscoso
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- Tarragona
- Spain
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- Tarragona
- Spain
- ICREA
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28
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Ali MA, Alam MA. Theoretical studies on the structure and thermochemistry of cyclicparaphenylenediazenes. RSC Adv 2017. [DOI: 10.1039/c7ra06409h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Comparison of thermochemistry of carbon nanoring structures.
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Affiliation(s)
| | - Mohammad A. Alam
- Department of Chemistry and Physics
- College of Science and Mathematics
- Arkansas State University
- Jonesboro
- USA
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29
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Lai YT, Hura GL, Dyer KN, Tang HYH, Tainer JA, Yeates TO. Designing and defining dynamic protein cage nanoassemblies in solution. SCIENCE ADVANCES 2016; 2:e1501855. [PMID: 27990489 PMCID: PMC5156514 DOI: 10.1126/sciadv.1501855] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 11/11/2016] [Indexed: 05/13/2023]
Abstract
Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. We created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. These methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.
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Affiliation(s)
- Yen-Ting Lai
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Greg L. Hura
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kevin N. Dyer
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - John A. Tainer
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Corresponding author. (T.O.Y.); (J.A.T.)
| | - Todd O. Yeates
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Corresponding author. (T.O.Y.); (J.A.T.)
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30
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Zhou Q, Fursule I, Berron BJ, Beck MJ. Toward Spatiotemporally Controlled Synthesis of Photoresponsive Polymers: Computational Design of Azobenzene-Containing Monomers for Light-Mediated ROMP. J Phys Chem A 2016; 120:7101-11. [DOI: 10.1021/acs.jpca.6b05807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qunfei Zhou
- Department of Chemical and Materials Engineering and ‡Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Ishan Fursule
- Department of Chemical and Materials Engineering and ‡Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Brad J. Berron
- Department of Chemical and Materials Engineering and ‡Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Matthew J. Beck
- Department of Chemical and Materials Engineering and ‡Center for Computational
Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
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31
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Zhang Y, Ardejani MS, Orner BP. Design and Applications of Protein-Cage-Based Nanomaterials. Chem Asian J 2016; 11:2814-2828. [DOI: 10.1002/asia.201600769] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Zhang
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals; College of Chemical Engineering; Nanjing Forestry University; Nanjing 210037 P.R. China
| | - Maziar S. Ardejani
- Department of Chemistry; The Scripps Research Institute; La Jolla CA 92037 United States
| | - Brendan P. Orner
- Department of Chemistry; King's College London; London SE1 1DB United Kingdom
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32
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Fernández-Fernández MR, Sot B, Valpuesta JM. Molecular chaperones: functional mechanisms and nanotechnological applications. NANOTECHNOLOGY 2016; 27:324004. [PMID: 27363314 DOI: 10.1088/0957-4484/27/32/324004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular chaperones are a group of proteins that assist in protein homeostasis. They not only prevent protein misfolding and aggregation, but also target misfolded proteins for degradation. Despite differences in structure, all types of chaperones share a common general feature, a surface that recognizes and interacts with the misfolded protein. This and other, more specialized properties can be adapted for various nanotechnological purposes, by modification of the original biomolecules or by de novo design based on artificial structures.
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Affiliation(s)
- M Rosario Fernández-Fernández
- Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de la Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
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33
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Hoersch D. Engineering a light-controlled F1 ATPase using structure-based protein design. PeerJ 2016; 4:e2286. [PMID: 27547581 PMCID: PMC4974930 DOI: 10.7717/peerj.2286] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/04/2016] [Indexed: 12/03/2022] Open
Abstract
The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered the active site of E.coli F1 ATPase with a structure-based protein design approach: by incorporation of a site-specific, photoswitchable crosslinker, whose end-to-end distance can be modulated by illumination with light of two different wavelengths, a dynamic constraint was imposed on the inter-atomic distances of the α and β subunits. Crosslinking reduced the ATP hydrolysis activity of four designs tested in vitro and in one case created a synthetic ATPase whose activity can be reversibly modulated by subsequent illumination with near UV and blue light. The work is a first step into the direction of the long-term goal to design nanoscaled machines based on biological parts that can be precisely controlled by light.
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Affiliation(s)
- Daniel Hoersch
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin , Berlin , Germany
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34
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Hoersch D, Kortemme T. A Model for the Molecular Mechanism of an Engineered Light-Driven Protein Machine. Structure 2016; 24:576-584. [PMID: 27021162 DOI: 10.1016/j.str.2016.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 01/28/2023]
Abstract
Controllable protein-based machines and materials are of considerable interest for diverse biotechnological applications. We previously re-engineered an ATP-driven protein machine, a group II chaperonin, to function as a light-gated nanocage. Here we develop and test a model for the molecular mechanism of the re-engineered chaperonin, which undergoes a large-scale closed to open conformational change triggered by reversible photo-isomerization of a site-specifically attached azobenzene crosslinker. In silico experiments using all-atom simulations suggest that rigid body motions of protein subdomains couple the length changes of the crosslinker to rearrangements of the nucleotide-binding pocket, leading to cage opening. We tested this model by designing a mutant for which the orientation of the two protein subdomains forming the nucleotide-binding pocket is directly controlled by the crosslinker, and confirmed successful reversible photoswitching in vitro. The model probes the conformational cycle of group II chaperonins and offers a design principle for engineering other light-driven protein-based molecular machines.
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Affiliation(s)
- Daniel Hoersch
- Department of Physics, Freie Universität Berlin, Berlin 14195, Germany; Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
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35
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Construction and application of photoresponsive smart nanochannels. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2016. [DOI: 10.1016/j.jphotochemrev.2015.12.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nat Commun 2016; 7:10591. [PMID: 26830310 PMCID: PMC4740900 DOI: 10.1038/ncomms10591] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/02/2016] [Indexed: 12/23/2022] Open
Abstract
Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate at the nanometre scale or below. Translating controlled operation of individual molecular machines to a larger dimension, for example, to 10-100 nm, which features many practical applications, is highly important but remains challenging. Here we demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through the host nanostructure and consequently translate it into reversible chiroptical function with large amplitude modulation. Light is exploited as both energy source and information probe. Our plasmonic nanosystem bears unique features of optical addressability, reversibility and modulability, which are crucial for developing all-optical molecular devices with desired functionalities.
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37
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Kim YN, Jung Y. Artificial supramolecular protein assemblies as functional high-order protein scaffolds. Org Biomol Chem 2016; 14:5352-6. [DOI: 10.1039/c6ob00116e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Artificial supramolecular protein assemblies can serve as novel high-order scaffolds that can display various functional proteins with defined valencies and organization, offering unprecedented functional bio-architectures.
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Affiliation(s)
- Yu-na Kim
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 305-701
- Korea
| | - Yongwon Jung
- Department of Chemistry
- Korea Advanced Institute of Science and Technology
- Daejeon 305-701
- Korea
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38
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Ritterson RS, Hoersch D, Barlow KA, Kortemme T. Design of Light-Controlled Protein Conformations and Functions. Methods Mol Biol 2016; 1414:197-211. [PMID: 27094293 DOI: 10.1007/978-1-4939-3569-7_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In recent years, interest in controlling protein function with light has increased. Light offers a number of unique advantages over other methods, including spatial and temporal control and high selectivity. Here, we describe a general protocol for engineering a protein to be controllable with light via reaction with an exogenously introduced photoisomerizable small molecule and illustrate our protocol with two examples from the literature: the engineering of the calcium affinity of the cell-cell adhesion protein cadherin, which is an example of a protein that switches from a native to a disrupted state (Ritterson et al. J Am Chem Soc (2013) 135:12516-12519), and the engineering of the opening and closing of the chaperonin Mm-cpn, an example of a switch between two functional states (Hoersch et al.: Nat Nanotechn (2013) 8:928-932). This protocol guides the user from considering which proteins may be most amenable to this type of engineering, to considerations of how and where to make the desired changes, to the assays required to test for functionality.
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Affiliation(s)
- Ryan S Ritterson
- California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA
| | - Daniel Hoersch
- California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Kyle A Barlow
- Graduate Program in Bioinformatics, California Institute for Quantitative Biomedical Research, and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA
| | - Tanja Kortemme
- California Institute for Quantitative Biomedical Research and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, Byers Hall 308 E, San Francisco, CA, 94158, USA.
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Tobin PH, Richards DH, Callender RA, Wilson CJ. Protein engineering: a new frontier for biological therapeutics. Curr Drug Metab 2015; 15:743-56. [PMID: 25495737 DOI: 10.2174/1389200216666141208151524] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/27/2014] [Accepted: 12/07/2014] [Indexed: 12/14/2022]
Abstract
Protein engineering holds the potential to transform the metabolic drug landscape through the development of smart, stimulusresponsive drug systems. Protein therapeutics are a rapidly expanding segment of Food and Drug Administration approved drugs that will improve clinical outcomes over the long run. Engineering of protein therapeutics is still in its infancy, but recent general advances in protein engineering capabilities are being leveraged to yield improved control over both pharmacokinetics and pharmacodynamics. Stimulus- responsive protein therapeutics are drugs which have been designed to be metabolized under targeted conditions. Protein engineering is being utilized to develop tailored smart therapeutics with biochemical logic. This review focuses on applications of targeted drug neutralization, stimulus-responsive engineered protein prodrugs, and emerging multicomponent smart drug systems (e.g., antibody-drug conjugates, responsive engineered zymogens, prospective biochemical logic smart drug systems, drug buffers, and network medicine applications).
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Affiliation(s)
| | | | | | - Corey J Wilson
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520-8286, USA.
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Kim Y, Kang J, Shen B, Wang Y, He Y, Lee M. Open-closed switching of synthetic tubular pores. Nat Commun 2015; 6:8650. [PMID: 26456695 PMCID: PMC4633957 DOI: 10.1038/ncomms9650] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/16/2015] [Indexed: 01/28/2023] Open
Abstract
While encouraging progress has been made on switchable nanopores to mimic biological channels and pores, it remains a great challenge to realize long tubular pores with a dynamic open-closed motion. Here we report μm-long, dynamic tubular pores that undergo rapid switching between open and closed states in response to a thermal signal in water. The tubular walls consist of laterally associated primary fibrils stacked from disc-shaped molecules in which the discs readily tilt by means of thermally regulated dehydration of the oligoether chains placed on the wall surfaces. Notably, this pore switching mediates a controlled water-pumping catalytic action for the dehydrative cyclization of adenosine monophosphate to produce metabolically active cyclic adenosine monophosphate. We believe that our work may allow the creation of a variety of dynamic pore structures with complex functions arising from open-closed motion.
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Affiliation(s)
- Yongju Kim
- State Key Laboratory for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiheong Kang
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Bowen Shen
- State Key Laboratory for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Yanqiu Wang
- State Key Laboratory for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Ying He
- State Key Laboratory for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Myongsoo Lee
- State Key Laboratory for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
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Green fluorescent protein nanopolygons as monodisperse supramolecular assemblies of functional proteins with defined valency. Nat Commun 2015; 6:7134. [PMID: 25972078 PMCID: PMC4479010 DOI: 10.1038/ncomms8134] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/08/2015] [Indexed: 02/08/2023] Open
Abstract
Supramolecular protein assemblies offer novel nanoscale architectures with molecular precision and unparalleled functional diversity. A key challenge, however, is to create precise nano-assemblies of functional proteins with both defined structures and a controlled number of protein-building blocks. Here we report a series of supramolecular green fluorescent protein oligomers that are assembled in precise polygonal geometries and prepared in a monodisperse population. Green fluorescent protein is engineered to be self-assembled in cells into oligomeric assemblies that are natively separated in a single-protein resolution by surface charge manipulation, affording monodisperse protein (nano)polygons from dimer to decamer. Several functional proteins are multivalently displayed on the oligomers with controlled orientations. Spatial arrangements of protein oligomers and displayed functional proteins are directly visualized by a transmission electron microscope. By employing our functional protein assemblies, we provide experimental insight into multivalent protein–protein interactions and tools to manipulate receptor clustering on live cell surfaces. Supramolecular protein assemblies can provide novel nano-architectures with diverse structures and functions. Here, the authors report a fabrication strategy for a series of monodisperse protein oligomers, which allows valency-controlled display of various functional proteins.
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Yamashita H, Ikezawa T, Kobayashi Y, Abe J. Photochromic Phenoxyl-Imidazolyl Radical Complexes with Decoloration Rates from Tens of Nanoseconds to Seconds. J Am Chem Soc 2015; 137:4952-5. [DOI: 10.1021/jacs.5b02353] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hiroaki Yamashita
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Takahiro Ikezawa
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Yoichi Kobayashi
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Jiro Abe
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
- CREST, Japan Science and Technology Agency (JST), K’s Gobancho, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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Kundu PK, Klajn R. Watching single molecules move in response to light. ACS NANO 2014; 8:11913-11916. [PMID: 25474733 DOI: 10.1021/nn506656r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nature has long inspired scientists with its seemingly unlimited ability to harness solar energy and to utilize it to drive various physiological processes. With the help of man-made molecular photoswitches, we now have the potential to outperform natural systems in many ways, with the ultimate goal of fabricating multifunctional materials that operate at different light wavelengths. An important challenge in developing light-controlled artificial molecular machines lies in attaining a detailed understanding of the photoisomerization-coupled conformational changes that occur in macromolecules and molecular assemblies. In this issue of ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting insights into the behavior of individual photoresponsive molecules and to identify contraction, extension, and crawling events accompanying light-induced isomerization.
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Affiliation(s)
- Pintu K Kundu
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
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Horstmann B, Korbus M, Friedmann T, Wolff C, Thiele CM, Meyer-Almes FJ. Synthesis of azobenzenealkylmaleimide probes to photocontrol the enzyme activity of a bacterial histone deacetylase-like amidohydrolase. Bioorg Chem 2014; 57:155-161. [PMID: 25462992 DOI: 10.1016/j.bioorg.2014.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/06/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022]
Abstract
A series of azobenzenealkylmaleimides (AMDs) with different spacer length was synthesized and coupled via Michael-Addition to a specific mutant of a bacterial histone deacetylase-like amidohydrolase (HDAH). Michaelis-Menten parameters (Vmax and Km) were employed to characterize the effect of both, the spacer length and the configuration (cis vs. trans) of the attached azobenzene moiety, on the HDAH enzyme activity. The photoswitch behavior of the AMD/enzyme conjugate activity was clearly influenced by the AMD spacer length. This study highlights the importance of steric rearrangement of the photoswitch with respect to the active site and describes a strategy to optimize the photocontrol of HDAH.
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Affiliation(s)
- Benjamin Horstmann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64287 Darmstadt, Germany
| | - Michael Korbus
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64287 Darmstadt, Germany
| | - Tatjana Friedmann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64287 Darmstadt, Germany
| | - Christiane Wolff
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Christina Marie Thiele
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, 64287 Darmstadt, Germany.
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Shima K, Mutoh K, Kobayashi Y, Abe J. Enhancing the Versatility and Functionality of Fast Photochromic Bridged Imidazole Dimers by Flipping Imidazole Rings. J Am Chem Soc 2014; 136:3796-9. [DOI: 10.1021/ja501028v] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kentaro Shima
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Katsuya Mutoh
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Yoichi Kobayashi
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Jiro Abe
- Department
of Chemistry, School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
- CREST, Japan Science and Technology Agency (JST), K’s Gobancho, 7 Gobancho, Chiyoda-ku,
Tokyo 102-0076, Japan
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46
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Affiliation(s)
- G Andrew Woolley
- Department of Chemistry, University of Toronto, Ontario M5S 3H6, Canada
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