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Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals. CHEMISTRY 2022. [DOI: 10.3390/chemistry4030059] [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] Open
Abstract
Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.
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Zavarzina DG, Prokofeva MI, Pikhtereva VA, Klyukina AA, Maslov AA, Merkel AY, Gavrilov SN. Deferrivibrio essentukiensis sp. nov., gen. nov., a Representative of Deferrivibrionaceae fam. nov., Isolated from the Subsurface Aquifer of Caucasian Mineral Drinking Waters. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Abstract
Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O2-dependent oxidases, fast hydrolases, and multi-proton/multi-electron reductases, have been created. In addition, proteins can now be designed using xeno-biological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.
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Affiliation(s)
- Matthew J. Chalkley
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - Samuel I. Mann
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, (CA), USA
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4
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Mylemans B, Lee XY, Laier I, Helsen C, Voet ARD. Structure and stability of the designer protein WRAP-T and its permutants. Sci Rep 2021; 11:18867. [PMID: 34552189 PMCID: PMC8458387 DOI: 10.1038/s41598-021-98391-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/01/2021] [Indexed: 11/29/2022] Open
Abstract
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\begin{document}$$\beta $$\end{document}β-Propeller proteins are common natural disc-like pseudo-symmetric proteins that contain multiple repeats (‘blades’) each consisting of a 4-stranded anti-parallel \documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β-sheet. So far, 4- to 12-bladed \documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β-propellers have been discovered in nature showing large functional and sequential variation. Using computational design approaches, we created perfectly symmetric \documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β-propellers out of natural pseudo-symmetric templates. These proteins are useful tools to study protein evolution of this very diverse fold. While the 7-bladed architecture is the most common, no symmetric 7-bladed monomer has been created and characterized so far. Here we describe such a engineered protein, based on a highly symmetric natural template, and test the effects of circular permutation on its stability. Geometrical analysis of this protein and other artificial symmetrical proteins reveals no systematic constraint that could be used to help in engineering of this fold, and suggests sequence constraints unique to each \documentclass[12pt]{minimal}
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\begin{document}$$\beta $$\end{document}β-propeller sub-family.
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Affiliation(s)
- Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Xiao Yin Lee
- Laboratory of Molecular Endocrinology, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Ina Laier
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Christine Helsen
- Laboratory of Molecular Endocrinology, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium.
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5
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Jung SM, Lee J, Song WJ. Design of artificial metalloenzymes with multiple inorganic elements: The more the merrier. J Inorg Biochem 2021; 223:111552. [PMID: 34332336 DOI: 10.1016/j.jinorgbio.2021.111552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/21/2021] [Accepted: 07/15/2021] [Indexed: 11/27/2022]
Abstract
A large fraction of metalloenzymes harbors multiple metal-centers that are electronically and/or functionally arranged within their proteinaceous environments. To explore the orchestration of inorganic and biochemical components and to develop bioinorganic catalysts and materials, we have described selected examples of artificial metalloproteins having multiple metallocofactors that were grouped depending on their initial protein scaffolds, the nature of introduced inorganic moieties, and the method used to propagate the number of metal ions within a protein. They demonstrated that diverse inorganic moieties can be selectively grafted and modulated in protein environments, providing a retrosynthetic bottom-up approach in the design of versatile and proficient biocatalysts and biomimetic model systems to explore fundamental questions in bioinorganic chemistry.
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Affiliation(s)
- Se-Min Jung
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehee Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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6
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Biophysical reviews 'meet the editor series'-Jeremy R. H. Tame. Biophys Rev 2021; 13:295-301. [PMID: 34178167 DOI: 10.1007/s12551-021-00798-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 10/21/2022] Open
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7
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Vrancken JPM, Noguchi H, Zhang KYJ, Tame JRH, Voet ARD. The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins 2021; 89:945-951. [PMID: 33713051 DOI: 10.1002/prot.26072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 01/17/2023]
Abstract
Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium-chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β-propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
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8
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Mylemans B, Noguchi H, Deridder E, Lescrinier E, Tame JRH, Voet ARD. Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein. Protein Sci 2020; 29:2375-2386. [PMID: 33006397 DOI: 10.1002/pro.3961] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 11/09/2022]
Abstract
The β-propeller fold is adopted by a sequentially diverse family of repeat proteins with apparent rotational symmetry. While the structure is mostly stabilized by hydrophobic interactions, an additional stabilization is provided by hydrogen bonds between the N-and C-termini, which are almost invariably part of the same β-sheet. This feature is often referred to as the "Velcro" closure. The positioning of the termini within a blade is variable and depends on the protein family. In order to investigate the influence of this location on protein structure, folding and stability, we created different circular permutants, and a circularized version, of the designer propeller protein named Pizza. This protein is perfectly symmetrical, possessing six identical repeats. While all mutants adopt the same structure, the proteins lacking the "Velcro" closure were found to be significantly less resistant to thermal and chemical denaturation. This could explain why such proteins are rarely observed in nature. Interestingly the most common "Velcro" configuration for this protein family was not the most stable among the Pizza variants tested. The circularized version shows dramatically improved stability, which could have implications for future applications.
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Affiliation(s)
| | | | - Els Deridder
- Department of Chemistry, KU Leuven, Leuven, Belgium
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9
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Abstract
Recently an artificial protein named Pizza6 was reported, which possesses six identical tandem repeats and adopts a monomeric β -propeller fold with sixfold structural symmetry. Pizza2, a truncated form that consists of a double tandem repeat, self-assembles into a trimer reconstructing the same propeller architecture as Pizza6. The ability of pizza proteins to self-assemble to form complete propellers makes them interesting building blocks to engineer larger symmetrical protein complexes such as symmetric nanoparticles. Here we have explored the self-assembly of Pizza2 fused to homo-oligomerizing peptides. In total, we engineered five different fusion proteins, of which three appeared to assemble successfully into larger complexes. Further characterization of these proteins showed one monodisperse designer protein with a structure close to the intended design. This protein was further fused to eGFP to investigate functionalization of the nanoparticle. The fusion protein was stable and could be expressed in high yield, showing that Pizza-based nanoparticles may be further decorated with functional domains.
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10
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Hishikawa Y, Maity B, Ito N, Abe S, Lu D, Ueno T. Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage. CHEM LETT 2020. [DOI: 10.1246/cl.200217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuki Hishikawa
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Nozomi Ito
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Diannan Lu
- Department of Chemical Engineering, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing 100-084, P. R. China
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B55 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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11
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Kaushik R, Zhang KYJ. A protein sequence fitness function for identifying natural and nonnatural proteins. Proteins 2020; 88:1271-1284. [PMID: 32415863 DOI: 10.1002/prot.25900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/26/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The infinitesimally small sequence space naturally scouted in the millions of years of evolution suggests that the natural proteins are constrained by some functional prerequisites and should differ from randomly generated sequences. We have developed a protein sequence fitness scoring function that implements sequence and corresponding secondary structural information at tripeptide levels to differentiate natural and nonnatural proteins. The proposed fitness function is extensively validated on a dataset of about 210 000 natural and nonnatural protein sequences and benchmarked with existing methods for differentiating natural and nonnatural proteins. The high sensitivity, specificity, and percentage accuracy (0.81%, 0.95%, and 91% respectively) of the fitness function demonstrates its potential application for sampling the protein sequences with higher probability of mimicking natural proteins. Moreover, the four major classes of proteins (α proteins, β proteins, α/β proteins, and α + β proteins) are separately analyzed and β proteins are found to score slightly lower as compared to other classes. Further, an analysis of about 250 designed proteins (adopted from previously reported cases) helped to define the boundaries for sampling the ideal protein sequences. The protein sequence characterization aided by the proposed fitness function could facilitate the exploration of new perspectives in the design of novel functional proteins.
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Affiliation(s)
- Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
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12
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Mylemans B, Laier I, Kamata K, Akashi S, Noguchi H, Tame JRH, Voet ARD. Structural plasticity of a designer protein sheds light on β-propeller protein evolution. FEBS J 2020; 288:530-545. [PMID: 32343866 DOI: 10.1111/febs.15347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/07/2020] [Accepted: 04/23/2020] [Indexed: 11/26/2022]
Abstract
β-propeller proteins are common in nature, where they are observed to adopt 4- to 10-fold internal rotational pseudo-symmetry. This size diversity can be explained by the evolutionary process of gene duplication and fusion. In this study, we investigated a distorted β-propeller protein, an apparent intermediate between two symmetries. From this template, we created a perfectly symmetric 9-bladed β-propeller named Cake, using computational design and ancestral sequence reconstruction. The designed repeat sequence was found to be capable of generating both 8-fold and 9-fold propellers which are highly stable. Cake variants with 2-10 identical copies of the repeat sequence were characterised by X-ray crystallography and in solution. They were found to be highly stable, and to self-assemble into 8- or 9-fold symmetrical propellers. These findings show that the β-propeller fold allows sufficient structural plasticity to permit a given blade to assemble different forms, a transition from even to odd changes in blade number, and provide a potential explanation for the wide diversity of repeat numbers observed in natural propeller proteins. DATABASE: Structural data are available in Protein Data Bank database under the accession numbers 6TJB, 6TJC, 6TJD, 6TJE, 6TJF, 6TJG, 6TJH and 6TJI.
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Affiliation(s)
| | - Ina Laier
- Department of Chemistry, KU Leuven, Belgium
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13
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Vandebroek L, Noguchi H, Kamata K, Tame JRH, Van Meervelt L, Parac-Vogt TN, Voet ARD. Hybrid assemblies of a symmetric designer protein and polyoxometalates with matching symmetry. Chem Commun (Camb) 2020; 56:11601-11604. [DOI: 10.1039/d0cc05071g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A symmetric designer protein forms hybrid complexes with different polyoxometalates and may serve as a building block for porous frameworks.
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Affiliation(s)
- Laurens Vandebroek
- Laboratory for Bioinorganic Chemistry
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
- Biomolecular Architecture
| | - Hiroki Noguchi
- Laboratory for Biomolecular Modelling and Design
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
| | - Kenichi Kamata
- Drug Design Laboratory
- Yokohama City University 1-7-29
- Yokohama
- Japan
| | | | - Luc Van Meervelt
- Biomolecular Architecture
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
| | - Tatjana N. Parac-Vogt
- Laboratory for Bioinorganic Chemistry
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
| | - Arnout R. D. Voet
- Laboratory for Biomolecular Modelling and Design
- KU Leuven Department of Chemistry
- 3001 Leuven
- Belgium
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14
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Jeong WJ, Yu J, Song WJ. Proteins as diverse, efficient, and evolvable scaffolds for artificial metalloenzymes. Chem Commun (Camb) 2020; 56:9586-9599. [DOI: 10.1039/d0cc03137b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have extracted and categorized the desirable properties of proteins that are adapted as the scaffolds for artificial metalloenzymes.
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Affiliation(s)
- Woo Jae Jeong
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jaeseung Yu
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Woon Ju Song
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
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15
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Grayson KJ, Anderson JLR. Designed for life: biocompatible de novo designed proteins and components. J R Soc Interface 2019; 15:rsif.2018.0472. [PMID: 30158186 PMCID: PMC6127164 DOI: 10.1098/rsif.2018.0472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo. Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.
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Affiliation(s)
- Katie J Grayson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK .,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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16
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Lin YW. Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters. Molecules 2019; 24:E2743. [PMID: 31362341 PMCID: PMC6696605 DOI: 10.3390/molecules24152743] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 01/22/2023] Open
Abstract
Metalloproteins and metalloenzymes play important roles in biological systems by using the limited metal ions, complexes, and clusters that are associated with the protein matrix. The design of artificial metalloproteins and metalloenzymes not only reveals the structure and function relationship of natural proteins, but also enables the synthesis of artificial proteins and enzymes with improved properties and functions. Acknowledging the progress in rational design from single to multiple active sites, this review focuses on recent achievements in the design of artificial metalloproteins and metalloenzymes with metal clusters, including zinc clusters, cadmium clusters, iron-sulfur clusters, and copper-sulfur clusters, as well as noble metal clusters and others. These metal clusters were designed in both native and de novo protein scaffolds for structural roles, electron transfer, or catalysis. Some synthetic metal clusters as functional models of native enzymes are also discussed. These achievements provide valuable insights for deep understanding of the natural proteins and enzymes, and practical clues for the further design of artificial enzymes with functions comparable or even beyond those of natural counterparts.
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Affiliation(s)
- Ying-Wu Lin
- School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.
- Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.
- Hunan Key Laboratory for the Design and Application of Actinide Complexes, University of South China, Hengyang 421001, China.
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17
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Noguchi H, Addy C, Simoncini D, Wouters S, Mylemans B, Van Meervelt L, Schiex T, Zhang KYJ, Tame JRH, Voet ARD. Computational design of symmetrical eight-bladed β-propeller proteins. IUCRJ 2019; 6:46-55. [PMID: 30713702 PMCID: PMC6327176 DOI: 10.1107/s205225251801480x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/19/2018] [Indexed: 05/04/2023]
Abstract
β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.
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Affiliation(s)
- Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Christine Addy
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - David Simoncini
- MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France
| | - Staf Wouters
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - Luc Van Meervelt
- Laboratory of Biomolecular Architecture, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Thomas Schiex
- MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Jeremy R. H. Tame
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Arnout R. D. Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
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Clarke DE, Noguchi H, Gryspeerdt JLAG, De Feyter S, Voet ARD. Artificial β-propeller protein-based hydrolases. Chem Commun (Camb) 2019; 55:8880-8883. [DOI: 10.1039/c9cc04388h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We investigated symmetrical β-propeller protein scaffolds as artificial hydrolases and discovered their catalytic mechanism to be centred around a threonine–histidine dyad.
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Affiliation(s)
- David E. Clarke
- Division of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- Leuven
- Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | | | - Steven De Feyter
- Division of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- Leuven
- Belgium
| | - Arnout R. D. Voet
- Laboratory of Biomolecular Modelling and Design
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
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19
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Kobayashi N, Inano K, Sasahara K, Sato T, Miyazawa K, Fukuma T, Hecht MH, Song C, Murata K, Arai R. Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks. ACS Synth Biol 2018; 7:1381-1394. [PMID: 29690759 DOI: 10.1021/acssynbio.8b00007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design of novel proteins that self-assemble into supramolecular complexes is important for development in nanobiotechnology and synthetic biology. Recently, we designed and created a protein nanobuilding block (PN-Block), WA20-foldon, by fusing an intermolecularly folded dimeric de novo WA20 protein and a trimeric foldon domain of T4 phage fibritin (Kobayashi et al., J. Am. Chem. Soc. 2015, 137, 11285). WA20-foldon formed several types of self-assembling nanoarchitectures in multiples of 6-mers, including a barrel-like hexamer and a tetrahedron-like dodecamer. In this study, to construct chain-like polymeric nanostructures, we designed de novo extender protein nanobuilding blocks (ePN-Blocks) by tandemly fusing two de novo binary-patterned WA20 proteins with various linkers. The ePN-Blocks with long helical linkers or flexible linkers were expressed in soluble fractions of Escherichia coli, and the purified ePN-Blocks were analyzed by native PAGE, size exclusion chromatography-multiangle light scattering (SEC-MALS), small-angle X-ray scattering (SAXS), and transmission electron microscopy. These results suggest formation of various structural homo-oligomers. Subsequently, we reconstructed hetero-oligomeric complexes from extender and stopper PN-Blocks by denaturation and refolding. The present SEC-MALS and SAXS analyses show that extender and stopper PN-Block (esPN-Block) heterocomplexes formed different types of extended chain-like conformations depending on their linker types. Moreover, atomic force microscopy imaging in liquid suggests that the esPN-Block heterocomplexes with metal ions further self-assembled into supramolecular nanostructures on mica surfaces. Taken together, the present data demonstrate that the design and construction of self-assembling PN-Blocks using de novo proteins is a useful strategy for building polymeric nanoarchitectures of supramolecular protein complexes.
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Affiliation(s)
- Naoya Kobayashi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | | | | | - Takaaki Sato
- Center for Energy and Environmental Science, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Nagano, Nagano 380-8553, Japan
| | - Keisuke Miyazawa
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Fukuma
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Michael H Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Ryoichi Arai
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama 230-0045, Japan
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan
- Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
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20
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Noguchi H, Mylemans B, De Zitter E, Van Meervelt L, Tame JRH, Voet A. Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies. Biochem Biophys Res Commun 2018; 497:1038-1042. [PMID: 29481797 DOI: 10.1016/j.bbrc.2018.02.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 01/29/2023]
Abstract
β-propeller proteins are highly symmetrical, being composed of a repeated motif with four anti-parallel β-sheets arranged around a central axis. Recently we designed the first completely symmetrical β-propeller protein, Pizza6, consisting of six identical tandem repeats. Pizza6 is expected to prove a useful building block for bionanotechnology, and also a tool to investigate the folding and evolution of β-propeller proteins. Folding studies are made difficult by the high stability and the lack of buried Trp residues to act as monitor fluorophores, so we have designed and characterized several Trp-containing Pizza6 derivatives. In total four proteins were designed, of which three could be purified and characterized. Crystal structures confirm these mutant proteins maintain the expected structure, and a clear redshift of Trp fluorescence emission could be observed upon denaturation. Among the derivative proteins, Pizza6-AYW appears to be the most suitable model protein for future folding/unfolding kinetics studies as it has a comparable stability as natural β-propeller proteins.
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Affiliation(s)
- Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Elke De Zitter
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Luc Van Meervelt
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium.
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21
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Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
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Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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22
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Functionalization of protein crystals with metal ions, complexes and nanoparticles. Curr Opin Chem Biol 2017; 43:68-76. [PMID: 29245143 DOI: 10.1016/j.cbpa.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/09/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects.
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23
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Freeman A. Protein-Mediated Biotemplating on the Nanoscale. Biomimetics (Basel) 2017; 2:E14. [PMID: 31105177 PMCID: PMC6352702 DOI: 10.3390/biomimetics2030014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/18/2017] [Accepted: 08/01/2017] [Indexed: 12/26/2022] Open
Abstract
Purified proteins offer a homogeneous population of biological nanoparticles, equipped in many cases with specific binding sites enabling the directed self-assembly of envisaged one-, two- or three-dimensional arrays. These arrays may serve as nanoscale biotemplates for the preparation of novel functional composite materials, which exhibit potential applications, especially in the fields of nanoelectronics and optical devices. This review provides an overview of the field of protein-mediated biotemplating, focussing on achievements made throughout the past decade. It is comprised of seven sections designed according to the size and configuration of the protein-made biotemplate. Each section describes the design and size of the biotemplate, the resulting hybrid structures, the fabrication methodology, the analytical tools employed for the structural analysis of the hybrids obtained, and, finally, their claimed/intended applications and a feasibility demonstration (whenever available). In conclusion, a short assessment of the overall status of the achievements already made vs. the future challenges of this field is provided.
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Affiliation(s)
- Amihay Freeman
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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24
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Voet ARD, Tame JRH. Protein-templated synthesis of metal-based nanomaterials. Curr Opin Biotechnol 2017; 46:14-19. [DOI: 10.1016/j.copbio.2016.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/24/2016] [Indexed: 01/07/2023]
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25
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Kobayashi N, Arai R. Design and construction of self-assembling supramolecular protein complexes using artificial and fusion proteins as nanoscale building blocks. Curr Opin Biotechnol 2017; 46:57-65. [DOI: 10.1016/j.copbio.2017.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/09/2016] [Accepted: 01/04/2017] [Indexed: 01/03/2023]
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26
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Zaucha J, Heddle JG. Resurrecting the Dead (Molecules). Comput Struct Biotechnol J 2017; 15:351-358. [PMID: 28652896 PMCID: PMC5472138 DOI: 10.1016/j.csbj.2017.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/11/2017] [Accepted: 05/21/2017] [Indexed: 12/15/2022] Open
Abstract
Biological molecules, like organisms themselves, are subject to genetic drift and may even become "extinct". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of "molecular resurrection" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began.
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Affiliation(s)
- Jan Zaucha
- Departament of Computer Science, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Jonathan G. Heddle
- Bionanoscience and Biochemistry Laboratory, Jagiellonian University, Malopolska Centre of Biotechnology, Gronstajowa 7A, 30-387 Kraków, Poland
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27
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Observation of gold sub-nanocluster nucleation within a crystalline protein cage. Nat Commun 2017; 8:14820. [PMID: 28300064 PMCID: PMC5357307 DOI: 10.1038/ncomms14820] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 02/06/2017] [Indexed: 01/18/2023] Open
Abstract
Protein scaffolds provide unique metal coordination environments that promote biomineralization processes. It is expected that protein scaffolds can be developed to prepare inorganic nanomaterials with important biomedical and material applications. Despite many promising applications, it remains challenging to elucidate the detailed mechanisms of formation of metal nanoparticles in protein environments. In the present work, we describe a crystalline protein cage constructed by crosslinking treatment of a single crystal of apo-ferritin for structural characterization of the formation of sub-nanocluster with reduction reaction. The crystal structure analysis shows the gradual movement of the Au ions towards the centre of the three-fold symmetric channels of the protein cage to form a sub-nanocluster with accompanying significant conformational changes of the amino-acid residues bound to Au ions during the process. These results contribute to our understanding of metal core formation as well as interactions of the metal core with the protein environment. Proteins can template the synthesis of inorganic nanoparticles, but the formation mechanisms remain vague. Here, the authors directly observe, through a sequence of X-ray crystal structures, the stages of gold sub-nanocluster growth within the confined environment of a ferritin cage.
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28
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Norn CH, André I. Computational design of protein self-assembly. Curr Opin Struct Biol 2016; 39:39-45. [DOI: 10.1016/j.sbi.2016.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/07/2016] [Accepted: 04/07/2016] [Indexed: 01/29/2023]
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29
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Using natural sequences and modularity to design common and novel protein topologies. Curr Opin Struct Biol 2016; 38:26-36. [PMID: 27270240 DOI: 10.1016/j.sbi.2016.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 02/07/2023]
Abstract
Protein design is still a challenging undertaking, often requiring multiple attempts or iterations for success. Typically, the source of failure is unclear, and scoring metrics appear similar between successful and failed cases. Nevertheless, the use of sequence statistics, modularity and symmetry from natural proteins, combined with computational design both at the coarse-grained and atomistic levels is propelling a new wave of design efforts to success. Here we highlight recent examples of design, showing how the wealth of natural protein sequence and topology data may be leveraged to reduce the search space and increase the likelihood of achieving desired outcomes.
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30
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Affiliation(s)
- Li Shang
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, D-76131 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Strasse 1, D-76131 Karlsruhe, Germany
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