1
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Miller J, Urvoas A, Gigant B, Ouldali M, Arteni A, Mesneau A, Valerio-Lepiniec M, Artzner F, Dujardin E, Minard P. Engineering of brick and staple components for ordered assembly of synthetic repeat proteins. J Struct Biol 2023; 215:108012. [PMID: 37567372 DOI: 10.1016/j.jsb.2023.108012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Synthetic ɑRep repeat proteins are engineered as Brick and Staple protein pairs that together self-assemble into helical filaments. In most cases, the filaments spontaneously form supercrystals. Here, we describe an expanded series of ɑRep Bricks designed to stabilize the interaction between consecutive Bricks, to control the length of the assembled multimers, or to alter the spatial distribution of the Staple on the filaments. The effects of these Brick modifications on the assembly, on the final filament structure and on the crystal symmetry are analyzed by biochemical methods, electron microscopy and small angle X-ray scattering. We further extend the concept of Brick/Staple protein origami by designing a new type of "Janus"-like Brick protein that is equally assembled by orthogonal staples binding its inner or outer surfaces and thus ending inside or outside the filaments. The relative roles of longitudinal and lateral associations in the assembly process are discussed. This set of results demonstrates important proofs-of-principle for engineering these remarkably versatile proteins toward nanometer-to-micron scale constructions.
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Affiliation(s)
- Jessalyn Miller
- Emory University Department of Chemistry, 1515 Dickey Drive, Atlanta, GA 30322, USA(1); Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Benoit Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Ana Arteni
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Agnes Mesneau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France
| | - Franck Artzner
- Institut de Physique de Rennes (IPR), CNRS, UMR 6251, Université de Rennes 1, F-35042 Rennes, France
| | - Erik Dujardin
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS UMR 6303, Université de Bourgogne Franche-Comté, 21000 Dijon, France.
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette CEDEX, France.
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2
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Moreaud L, Viollet S, Urvoas A, Valerio-Lepiniec M, Mesneau A, Li de la Sierra-Gallay I, Miller J, Ouldali M, Marcelot C, Balor S, Soldan V, Meriadec C, Artzner F, Dujardin E, Minard P. Design, synthesis, and characterization of protein origami based on self-assembly of a brick and staple artificial protein pair. Proc Natl Acad Sci U S A 2023; 120:e2218428120. [PMID: 36893280 PMCID: PMC10089216 DOI: 10.1073/pnas.2218428120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/03/2023] [Indexed: 03/11/2023] Open
Abstract
A versatile strategy to create an inducible protein assembly with predefined geometry is demonstrated. The assembly is triggered by a binding protein that staples two identical protein bricks together in a predictable spatial conformation. The brick and staple proteins are designed for mutual directional affinity and engineered by directed evolution from a synthetic modular repeat protein library. As a proof of concept, this article reports on the spontaneous, extremely fast and quantitative self-assembly of two designed alpha-repeat (αRep) brick and staple proteins into macroscopic tubular superhelices at room temperature. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM with staining agent and cryoTEM) elucidate the resulting superhelical arrangement that precisely matches the a priori intended 3D assembly. The highly ordered, macroscopic biomolecular construction sustains temperatures as high as 75 °C thanks to the robust αRep building blocks. Since the α-helices of the brick and staple proteins are highly programmable, their design allows encoding the geometry and chemical surfaces of the final supramolecular protein architecture. This work opens routes toward the design and fabrication of multiscale protein origami with arbitrarily programmed shapes and chemical functions.
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Affiliation(s)
- Laureen Moreaud
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
| | - Sébastien Viollet
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Agathe Urvoas
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Marie Valerio-Lepiniec
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Agnès Mesneau
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Inès Li de la Sierra-Gallay
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Jessalyn Miller
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
- Department of Chemistry, Emory University, Atlanta, GA30322
| | - Malika Ouldali
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
| | - Cécile Marcelot
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
| | - Stéphanie Balor
- Microscopie Electronique Intégrative Toulouse, Centre de Biologie Intégrative, Université de Toulouse, CNRS, 31062, Toulouse, France
| | - Vanessa Soldan
- Microscopie Electronique Intégrative Toulouse, Centre de Biologie Intégrative, Université de Toulouse, CNRS, 31062, Toulouse, France
| | - Cristelle Meriadec
- Institut de Physique de Rennes, CNRS, UMR6251, Université de Rennes 1F-35042, Rennes, France
| | - Franck Artzner
- Institut de Physique de Rennes, CNRS, UMR6251, Université de Rennes 1F-35042, Rennes, France
| | - Erik Dujardin
- Centre d’Elaboration des Matériaux et d’Etudes Structurales, CNRS UPR8011F-31055, Toulouse, France
- Laboratoire Interdisciplinaire Carnot de Bourgogne, CNRS, UMR6303, Université de Bourgogne Franche-Comté21000, Dijon, France
| | - Philippe Minard
- CEA, CNRS, Institute for Integrative Biology of the Cell, Université Paris-Saclay91198, Gif-sur-Yvette, France
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3
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Think like a Virus: Toward Improving Nanovaccine Development against SARS-CoV-2. Viruses 2022; 14:v14071553. [PMID: 35891532 PMCID: PMC9318803 DOI: 10.3390/v14071553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
There is no doubt that infectious diseases present global impact on the economy, society, health, mental state, and even political aspects, causing a long-lasting dent, and the situation will surely worsen if and when the viral spread becomes out of control, as seen during the still ongoing coronavirus disease 2019 (COVID-19) pandemic. Despite the considerable achievements made in viral prevention and treatment, there are still significant challenges that can be overcome through careful understanding of the viral mechanism of action to establish common ground for innovating new preventative and treatment strategies. Viruses can be regarded as devil nanomachines, and one innovative approach to face and stop the spread of viral infections is the development of nanoparticles that can act similar to them as drug/vaccine carriers. Moreover, we can use the properties that different viruses have in designing nanoparticles that reassemble the virus conformational structures but that do not present the detrimental threats to human health that native viruses possess. This review discusses the current preventative strategies (i.e., vaccination) used in facing viral infections and the associated limitations, highlighting the importance of innovating new approaches to face viral infectious diseases and discussing the current nanoapplications in vaccine development and the challenges that still face the nanovaccine field.
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4
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Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
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Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
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5
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Liang S, Li Z, Zhan J, Zhou Y. De novo protein design by an energy function based on series expansion in distance and orientation dependence. Bioinformatics 2021; 38:86-93. [PMID: 34406339 DOI: 10.1093/bioinformatics/btab598] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Despite many successes, de novo protein design is not yet a solved problem as its success rate remains low. The low success rate is largely because we do not yet have an accurate energy function for describing the solvent-mediated interaction between amino acid residues in a protein chain. Previous studies showed that an energy function based on series expansions with its parameters optimized for side-chain and loop conformations can lead to one of the most accurate methods for side chain (OSCAR) and loop prediction (LEAP). Following the same strategy, we developed an energy function based on series expansions with the parameters optimized in four separate stages (recovering single-residue types without and with orientation dependence, selecting loop decoys and maintaining the composition of amino acids). We tested the energy function for de novo design by using Monte Carlo simulated annealing. RESULTS The method for protein design (OSCAR-Design) is found to be as accurate as OSCAR and LEAP for side-chain and loop prediction, respectively. In de novo design, it can recover native residue types ranging from 38% to 43% depending on test sets, conserve hydrophobic/hydrophilic residues at ∼75%, and yield the overall similarity in amino acid compositions at more than 90%. These performance measures are all statistically significantly better than several protein design programs compared. Moreover, the largest hydrophobic patch areas in designed proteins are near or smaller than those in native proteins. Thus, an energy function based on series expansion can be made useful for protein design. AVAILABILITY AND IMPLEMENTATION The Linux executable version is freely available for academic users at http://zhouyq-lab.szbl.ac.cn/resources/.
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Affiliation(s)
- Shide Liang
- Department of R & D, Bio-Thera Solutions, Guangzhou 510530, China
| | - Zhixiu Li
- Institute of Health and Biomedical Innovation, Queensland University of Technology at Translational Research Institute, Woolloongabba, QLD 3001, Australia
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast Campus, Southport, QLD 4222, Australia.,Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Yaoqi Zhou
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.,Peking University Shenzhen Graduate School, Shenzhen 518055, China
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6
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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7
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Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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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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9
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Circularly permuted LOV2 as a modular photoswitch for optogenetic engineering. Nat Chem Biol 2021; 17:915-923. [PMID: 33958793 DOI: 10.1038/s41589-021-00792-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/02/2021] [Indexed: 02/02/2023]
Abstract
Plant-based photosensors, such as the light-oxygen-voltage sensing domain 2 (LOV2) from oat phototropin 1, can be modularly wired into cell signaling networks to remotely control protein activity and physiological processes. However, the applicability of LOV2 is hampered by the limited choice of available caging surfaces and its preference to accommodate the effector domains downstream of the C-terminal Jα helix. Here, we engineered a set of LOV2 circular permutants (cpLOV2) with additional caging capabilities, thereby expanding the repertoire of genetically encoded photoswitches to accelerate the design of optogenetic devices. We demonstrate the use of cpLOV2-based optogenetic tools to reversibly gate ion channels, antagonize CRISPR-Cas9-mediated genome engineering, control protein subcellular localization, reprogram transcriptional outputs, elicit cell suicide and generate photoactivatable chimeric antigen receptor T cells for inducible tumor cell killing. Our approach is widely applicable for engineering other photoreceptors to meet the growing need of optogenetic tools tailored for biomedical and biotechnological applications.
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10
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Gidley F, Parmeggiani F. Repeat proteins: designing new shapes and functions for solenoid folds. Curr Opin Struct Biol 2021; 68:208-214. [PMID: 33721772 DOI: 10.1016/j.sbi.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 10/21/2022]
Abstract
The modular nature of repeat proteins has inspired the design of regular and completely novel sequences and structures. Research in the past years has provided a broad set of design approaches and new repeat proteins that have found applications in molecular recognition, taking advantage of the natural ability of some of these families to bind proteins, peptides and nucleic acids. Here, we provide an overview on the recent trends in design of repeat proteins, particularly solenoid folds, and their applications. By exploiting the intrinsic modularity of repeats, new architectures have been designed that combine different types of repeat, are easily scalable by changing the number of repeats and can be quickly generated by using existing modular building blocks.
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Affiliation(s)
- Frances Gidley
- School of Chemistry, School of Biochemistry, Bristol Biodesign Institute, University of Bristol, United Kingdom
| | - Fabio Parmeggiani
- School of Chemistry, School of Biochemistry, Bristol Biodesign Institute, University of Bristol, United Kingdom.
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11
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Vrancken JPM, Tame JRH, Voet ARD. Development and applications of artificial symmetrical proteins. Comput Struct Biotechnol J 2020; 18:3959-3968. [PMID: 33335692 PMCID: PMC7734218 DOI: 10.1016/j.csbj.2020.10.040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 12/28/2022] Open
Abstract
Since the determination of the first molecular models of proteins there has been interest in creating proteins artificially, but such methods have only become widely successful in the last decade. Gradual improvements over a long period of time have now yielded numerous examples of non-natural proteins, many of which are built from repeated elements. In this review we discuss the design of such symmetrical proteins and their various applications in chemistry and medicine.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
| | - 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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12
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Öhlknecht C, Petrov D, Engele P, Kröß C, Sprenger B, Fischer A, Lingg N, Schneider R, Oostenbrink C. Enhancing the promiscuity of a member of the Caspase protease family by rational design. Proteins 2020; 88:1303-1318. [PMID: 32432825 PMCID: PMC7497161 DOI: 10.1002/prot.25950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/19/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
The N-terminal cleavage of fusion tags to restore the native N-terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in-silico to yield enhanced promiscuity toward different N-terminal amino acids. Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease. These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations. The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results. Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids. We believe that the created mutants constitute an important step toward generalized procedures to restore original N-termini of recombinant fusion proteins.
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Affiliation(s)
- Christoph Öhlknecht
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Drazen Petrov
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
| | - Petra Engele
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Christina Kröß
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Bernhard Sprenger
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | | | - Nico Lingg
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Rainer Schneider
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
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13
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Broom A, Trainor K, Jacobi Z, Meiering EM. Computational Modeling of Protein Stability: Quantitative Analysis Reveals Solutions to Pervasive Problems. Structure 2020; 28:717-726.e3. [DOI: 10.1016/j.str.2020.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/26/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
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14
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Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design. J Mol Biol 2020; 432:3898-3914. [PMID: 32330481 PMCID: PMC7322520 DOI: 10.1016/j.jmb.2020.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Natural evolution has generated an impressively diverse protein universe via duplication and recombination from a set of protein fragments that served as building blocks. The application of these concepts to the design of new proteins using subdomain-sized fragments from different folds has proven to be experimentally successful. To better understand how evolution has shaped our protein universe, we performed an all-against-all comparison of protein domains representing all naturally existing folds and identified conserved homologous protein fragments. Overall, we found more than 1000 protein fragments of various lengths among different folds through similarity network analysis. These fragments are present in very different protein environments and represent versatile building blocks for protein design. These data are available in our web server called F(old P)uzzle (fuzzle.uni-bayreuth.de), which allows to individually filter the dataset and create customized networks for folds of interest. We believe that our results serve as an invaluable resource for structural and evolutionary biologists and as raw material for the design of custom-made proteins.
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Affiliation(s)
- Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Francisco Lobos
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dominik Lemm
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Saacnicteh Toledo-Patino
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Steffen Schmidt
- Max Planck Institute for Developmental Biology, Tübingen, Germany; Computational Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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15
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Brunette TJ, Bick MJ, Hansen JM, Chow CM, Kollman JM, Baker D. Modular repeat protein sculpting using rigid helical junctions. Proc Natl Acad Sci U S A 2020; 117:8870-8875. [PMID: 32245816 PMCID: PMC7183188 DOI: 10.1073/pnas.1908768117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ∼10-nm-diameter "L" and "V" shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.
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Affiliation(s)
- T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA 98195;
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Jesse M Hansen
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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16
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Ouyang M, Li X, Zhang J, Feng P, Pu H, Kong L, Bai Z, Rong L, Xu X, Chi W, Wang Q, Chen F, Lu C, Shen J, Zhang L. Liquid-Liquid Phase Transition Drives Intra-chloroplast Cargo Sorting. Cell 2020; 180:1144-1159.e20. [PMID: 32169217 DOI: 10.1016/j.cell.2020.02.045] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/14/2020] [Accepted: 02/20/2020] [Indexed: 12/21/2022]
Abstract
In eukaryotic cells, organelle biogenesis is pivotal for cellular function and cell survival. Chloroplasts are unique organelles with a complex internal membrane network. The mechanisms of the migration of imported nuclear-encoded chloroplast proteins across the crowded stroma to thylakoid membranes are less understood. Here, we identified two Arabidopsis ankyrin-repeat proteins, STT1 and STT2, that specifically mediate sorting of chloroplast twin arginine translocation (cpTat) pathway proteins to thylakoid membranes. STT1 and STT2 form a unique hetero-dimer through interaction of their C-terminal ankyrin domains. Binding of cpTat substrate by N-terminal intrinsically disordered regions of STT complex induces liquid-liquid phase separation. The multivalent nature of STT oligomer is critical for phase separation. STT-Hcf106 interactions reverse phase separation and facilitate cargo targeting and translocation across thylakoid membranes. Thus, the formation of phase-separated droplets emerges as a novel mechanism of intra-chloroplast cargo sorting. Our findings highlight a conserved mechanism of phase separation in regulating organelle biogenesis.
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Affiliation(s)
- Min Ouyang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoyi Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jing Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peiqiang Feng
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hua Pu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lingxi Kong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zechen Bai
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Rong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiumei Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Chinese Academy of Sciences, Beijing 100086, China
| | - Congming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jianren Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Lixin Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng 475001, China.
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17
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Chen T, Wang B, Wang F, Niu G, Zhang S, Li J, Hong Z. The Evolutionarily Conserved Serine Residues in BRI1 LRR Motifs Are Critical for Protein Secretion. FRONTIERS IN PLANT SCIENCE 2020; 11:32. [PMID: 32117374 PMCID: PMC7016217 DOI: 10.3389/fpls.2020.00032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
As a well-studied leucine-rich-repeat receptor-like kinases (LRR-RLKs) in Arabidopsis (Arabidopsis thaliana), BRI1 functions as a cell surface receptor for sensing the smallest ligand molecule identified thus far. The weak allele bri1-9 (S662F) harbors a mutation at the conserved serine (Ser*) residue among 25 LRRs, which leads to the protein retention in the ER. However, very little is known about the importance of these residues. Through site-directed mutagenesis and a phenotypic complementation test, we examined the effects of these conserved serine residues (S*-chain) on protein secretion and functions. The results showed that the replacements of these serine residues significantly changed the sub-localization of BRI1-GFPs to the ER and that rigid space constraints, as well as the requirement of successive inner polar contacts, affect these sites. In addition, the continuous presence of Ser* is mainly disrupted at the LRR-island domain interface, and the changes of these four nonserine residues to serine greatly decreased the protein ability to complement bri1-301 compact phenotype and the BR signaling activation. The sequence alignment revealed that other known LRR-RLK also harbors the S*-chain and the non-Ser* residues at the ligand-binding region along the S*-chain, which confirms the evolutionary significance of residues at these sites in plant LRR-RLKs.
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Affiliation(s)
- Tianshu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Fangfang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guanting Niu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shuo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jianming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zhi Hong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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18
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Ueda G, Antanasijevic A, Fallas JA, Sheffler W, Copps J, Ellis D, Hutchinson GB, Moyer A, Yasmeen A, Tsybovsky Y, Park YJ, Bick MJ, Sankaran B, Gillespie RA, Brouwer PJM, Zwart PH, Veesler D, Kanekiyo M, Graham BS, Sanders RW, Moore JP, Klasse PJ, Ward AB, King NP, Baker D. Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens. eLife 2020; 9:57659. [PMID: 32748788 PMCID: PMC7402677 DOI: 10.7554/elife.57659] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/02/2020] [Indexed: 02/06/2023] Open
Abstract
Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first de novo designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.
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Affiliation(s)
- George Ueda
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States,International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research InstituteLa JollaUnited States
| | - Jorge A Fallas
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - William Sheffler
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States,International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research InstituteLa JollaUnited States
| | - Daniel Ellis
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Adam Moyer
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell UniversityNew YorkUnited States
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer InstituteFrederickUnited States
| | - Young-Jun Park
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Matthew J Bick
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley LaboratoryBerkeleyUnited States
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Philip JM Brouwer
- Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of AmsterdamAmsterdamNetherlands
| | - Peter H Zwart
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley LaboratoryBerkeleyUnited States,Center for Advanced Mathematics in Energy Research Applications, Computational Research Division, Lawrence Berkeley LaboratoryBerkeleyUnited States
| | - David Veesler
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Rogier W Sanders
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell UniversityNew YorkUnited States,Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of AmsterdamAmsterdamNetherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell UniversityNew YorkUnited States
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell UniversityNew YorkUnited States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States,International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research InstituteLa JollaUnited States
| | - Neil P King
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States
| | - David Baker
- Department of Biochemistry, University of WashingtonSeattleUnited States,Institute for Protein Design, University of WashingtonSeattleUnited States,Howard Hughes Medical Institute, University of WashingtonSeattleUnited States
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19
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Heal JW, Bartlett GJ, Wood CW, Thomson AR, Woolfson DN. Applying graph theory to protein structures: an Atlas of coiled coils. Bioinformatics 2019; 34:3316-3323. [PMID: 29722888 PMCID: PMC6157074 DOI: 10.1093/bioinformatics/bty347] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Motivation To understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterized experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analyzing this resource. Here, we use tools from graph theory to define an Atlas classification scheme for automatically categorizing certain protein substructures. Results Focusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein-protein interaction motifs, we present a suite of computational resources designed for analyzing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based Atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the 'dark matter' of coiled-coil structures; i.e. those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design. Availability and implementation iSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.
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Affiliation(s)
- Jack W Heal
- School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Andrew R Thomson
- School of Chemistry, University of Bristol, Bristol, UK.,School of Chemistry, University of Glasgow, Glasgow, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Life Sciences Building, Bristol, UK
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20
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Du Y, Chen F, Zhang J, Lin Z, Ma Q, Xu G, Xiao D, Gui Y, Yang J, Wan S. A rare TTC30B variant is identified as a candidate for synpolydactyly in a Chinese pedigree. Bone 2019; 127:503-509. [PMID: 31306809 DOI: 10.1016/j.bone.2019.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 01/20/2023]
Abstract
BACKGROUND Syndactyly type II (synpolydactyly, SPD) is a rare autosomal dominant inherited disease with higher incomplete penetrance. Currently, several variants in HOXD13 and one deletion in FBLN1 have been associated with SPD. However, the causative variants in several SPD families and their etiological mechanism are still largely unknown. METHODS Whole exome and PCR-sanger sequencing followed by two-point linkage analysis were performed to identify the pathogenic variant in a six-generation Chinese pedigree. Homology modeling in combination with the RNAi and qRT-PCR experiments was used for revealing the pathogenic mechanism of the TTC30B variant. RESULTS A six-generation SPD family was reported. The affected subjects in this family had no other clinical malformation beyond SPD. A rare missense variant c.1157C>T [p.Ala375Val] (chr2:178416368, hg19) in TTC30B was demonstrated to be responsible for this SPD family. The modeling structure indicated that the Ala375 was evolutionarily and structurally conserved. The variant p.Ala375Val was predicted to be deleterious for protein structure and/or stability. Two-point linkage analysis resulted in a maximum LOD score of 3.1444 (P = 0.000071). Furthermore, we found that TTC30B was regulated by the Shh signaling pathway and the abnormal expression of TTC30B will affect the activation of the Shh signaling pathway in human retinal pigment epithelial cells. CONCLUSIONS This study demonstrates for the first time that an IFT (intraflagellar transport) - related gene TTC30B is implicated with SPD.
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Affiliation(s)
- Ye Du
- Medical Research Center, The People's Hospital of Longhua, Shenzhen 518109, China; Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Fangfang Chen
- Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jian Zhang
- Department of Hand Microsurgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Zheguang Lin
- Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Qian Ma
- Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Guisheng Xu
- Department of Hand Microsurgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Deming Xiao
- Department of Hand Microsurgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Yaoting Gui
- Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Jun Yang
- Department of Radiology, Peking University Shenzhen Hospital, Shenzhen 518036, China.
| | - Shengxiang Wan
- Department of Hand Microsurgery, Peking University Shenzhen Hospital, Shenzhen 518036, China.
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21
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Hughes SA, Wang F, Wang S, Kreutzberger MAB, Osinski T, Orlova A, Wall JS, Zuo X, Egelman EH, Conticello VP. Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Proc Natl Acad Sci U S A 2019; 116:14456-14464. [PMID: 31262809 PMCID: PMC6642399 DOI: 10.1073/pnas.1903910116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
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Affiliation(s)
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Albina Orlova
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
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22
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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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23
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ElGamacy M, Coles M, Lupas A. Asymmetric protein design from conserved supersecondary structures. J Struct Biol 2018; 204:380-387. [DOI: 10.1016/j.jsb.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
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24
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ElGamacy M, Coles M, Ernst P, Zhu H, Hartmann MD, Plückthun A, Lupas AN. An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture. ACS Synth Biol 2018; 7:2226-2235. [PMID: 30148951 DOI: 10.1021/acssynbio.8b00224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Designing proteins with novel folds remains a major challenge, as the biophysical properties of the target fold are not known a priori and no sequence profile exists to describe its features. Therefore, most computational design efforts so far have been directed toward creating proteins that recapitulate existing folds. Here we present a strategy centered upon the design of novel intramolecular interfaces that enables the construction of a target fold from a set of starting fragments. This strategy effectively reduces the amount of computational sampling necessary to achieve an optimal sequence, without compromising the level of topological control. The solenoid architecture has been a target of extensive protein design efforts, as it provides a highly modular platform of low topological complexity. However, none of the previous efforts have attempted to depart from the natural form, which is characterized by a uniformly handed superhelical architecture. Here we aimed to design a more complex platform, abolishing the superhelicity by introducing internally alternating handedness, resulting in a novel, corrugated architecture. We employed our interface-driven strategy, designing three proteins and confirming the design by solving the structure of two examples.
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Affiliation(s)
- Mohammad ElGamacy
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Hongbo Zhu
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrei N. Lupas
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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25
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Almhjell PJ, Mills JH. Metal-chelating non-canonical amino acids in metalloprotein engineering and design. Curr Opin Struct Biol 2018; 51:170-176. [DOI: 10.1016/j.sbi.2018.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/12/2018] [Indexed: 11/26/2022]
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26
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Waters EA, Shusta EV. The variable lymphocyte receptor as an antibody alternative. Curr Opin Biotechnol 2018; 52:74-79. [PMID: 29597074 PMCID: PMC6082701 DOI: 10.1016/j.copbio.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 01/21/2023]
Abstract
Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins in jawless vertebrates that function similarly to Ig antibodies. However, VLRs possess a distinct crescent-shaped structure and modularity that results in a concave binding interface that contrasts significantly with Ig antibodies. Antigen binding interactions result in specific, high affinity VLR binding interactions with both proteins and glycans. The natural sourcing of VLRs allows for immunization strategies, while the modularity enables a whole host of protein engineering approaches including consensus scaffolds, designed libraries and directed evolution with display technologies. VLR technologies have been recently deployed for applications in cell-specific targeting, drug delivery, tumor diagnostics and even protein stabilization. It is anticipated that the VLR field will continue to emerge to provide unique solutions for targeting glycans, evolutionarily conserved proteins and cellular specificity.
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Affiliation(s)
- Elizabeth A Waters
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Eric V Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI 53706, USA.
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27
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Wood CW, Heal JW, Thomson AR, Bartlett GJ, Ibarra AÁ, Brady RL, Sessions RB, Woolfson DN. ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. Bioinformatics 2018; 33:3043-3050. [PMID: 28582565 PMCID: PMC5870769 DOI: 10.1093/bioinformatics/btx352] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/31/2017] [Indexed: 12/03/2022] Open
Abstract
Motivation The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Results Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the ‘dark matter of protein-fold space’. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. Availability and implementation A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christopher W Wood
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.,School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Jack W Heal
- School of Chemistry, University of Bristol, Bristol BS8?1TS, UK
| | - Andrew R Thomson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Gail J Bartlett
- School of Chemistry, University of Bristol, Bristol BS8?1TS, UK
| | - Amaurys Á Ibarra
- School of Biochemistry, University of Bristol, Bristol BS8?1TD, UK
| | - R Leo Brady
- School of Biochemistry, University of Bristol, Bristol BS8?1TD, UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, University of Bristol, Bristol BS8 1TQ, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.,School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, University of Bristol, Bristol BS8 1TQ, UK
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28
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Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. J Struct Biol 2018; 201:100-107. [DOI: 10.1016/j.jsb.2017.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/11/2017] [Accepted: 09/02/2017] [Indexed: 11/17/2022]
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29
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Lapenta F, Aupič J, Strmšek Ž, Jerala R. Coiled coil protein origami: from modular design principles towards biotechnological applications. Chem Soc Rev 2018; 47:3530-3542. [DOI: 10.1039/c7cs00822h] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
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30
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Collins BC, Gunn RJ, McKitrick TR, Cummings RD, Cooper MD, Herrin BR, Wilson IA. Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates. Structure 2017; 25:1667-1678.e4. [PMID: 28988747 PMCID: PMC5677568 DOI: 10.1016/j.str.2017.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/16/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Abstract
High-quality reagents to study and detect glycans with high specificity for research and clinical applications are severely lacking. Here, we structurally and functionally characterize several variable lymphocyte receptor (VLR)-based antibodies from lampreys immunized with O erythrocytes that specifically recognize the blood group H-trisaccharide type II antigen. Glycan microarray analysis and biophysical data reveal that these VLRs exhibit greater specificity for H-trisaccharide compared with the plant lectin UEA-1, which is widely used in blood typing. Among these antibodies, O13 exhibits superior specificity for H-trisaccharide, the basis for which is revealed by comparative analysis of high-resolution VLR:glycan crystal structures. Using a structure-guided approach, we designed an O13 mutant with further enhanced specificity for H-trisaccharide. These insights into glycan recognition by VLRs suggest that lampreys can produce highly specific glycan antibodies, and are a valuable resource for the production of next-generation glycan reagents for biological and biomedical research and as diagnostics and therapeutics.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/biosynthesis
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/isolation & purification
- Antibody Specificity
- Binding Sites
- Blood Group Antigens/analysis
- Blood Group Antigens/immunology
- Blood Grouping and Crossmatching/methods
- Crystallography, X-Ray
- Erythrocytes/chemistry
- Erythrocytes/immunology
- Humans
- Immunization
- Lampreys/immunology
- Models, Molecular
- Plant Lectins/chemistry
- Plant Lectins/immunology
- Polysaccharides/chemistry
- Polysaccharides/immunology
- Polysaccharides/metabolism
- Protein Binding
- Protein Conformation
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Trisaccharides/chemistry
- Trisaccharides/immunology
- Trisaccharides/metabolism
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Affiliation(s)
- Bernard C Collins
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin J Gunn
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanya R McKitrick
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Richard D Cummings
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Brantley R Herrin
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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31
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Ferreiro DU, Komives EA, Wolynes PG. Frustration, function and folding. Curr Opin Struct Biol 2017; 48:68-73. [PMID: 29101782 DOI: 10.1016/j.sbi.2017.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 01/08/2023]
Abstract
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful catalysis, are examples of basic chemical activities that the great majority of polypeptides do not display, and are thought to be the outcome of the natural history of proteins. Function, a concept genuine to Biology, is at the core of evolution and often conflicts with the physical constraints. Locating the frustration between discrepant goals in a recurrent system leads to fundamental insights about the chances and necessities that shape the encoding of biological information.
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Affiliation(s)
- Diego U Ferreiro
- Protein Physiology Lab, FCEyN-Universidad de Buenos Aires, IQUIBICEN/CONICET, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA Buenos Aires, Argentina
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA; Department of Chemistry, Rice University, Houston, TX, USA; Department of Physics, Rice University, Houston, TX, USA; Department of Biosciences, Rice University, Houston, TX, USA
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32
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Drobnak I, Ljubetič A, Gradišar H, Pisanski T, Jerala R. Designed Protein Origami. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 940:7-27. [PMID: 27677507 DOI: 10.1007/978-3-319-39196-0_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Proteins are highly perfected natural molecular machines, owing their properties to the complex tertiary structures with precise spatial positioning of different functional groups that have been honed through millennia of evolutionary selection. The prospects of designing new molecular machines and structural scaffolds beyond the limits of natural proteins make design of new protein folds a very attractive prospect. However, de novo design of new protein folds based on optimization of multiple cooperative interactions is very demanding. As a new alternative approach to design new protein folds unseen in nature, folds can be designed as a mathematical graph, by the self-assembly of interacting polypeptide modules within the single chain. Orthogonal coiled-coil dimers seem like an ideal building module due to their shape, adjustable length, and above all their designability. Similar to the approach of DNA nanotechnology, where complex tertiary structures are designed from complementary nucleotide segments, a polypeptide chain composed of a precisely specified sequence of coiled-coil forming segments can be designed to self-assemble into polyhedral scaffolds. This modular approach encompasses long-range interactions that define complex tertiary structures. We envision that by expansion of the toolkit of building blocks and design strategies of the folding pathways protein origami technology will be able to construct diverse molecular machines.
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Affiliation(s)
- Igor Drobnak
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Helena Gradišar
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Tomaž Pisanski
- Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.,University of Primorska, Koper, Slovenia
| | - Roman Jerala
- Laboratory of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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33
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Advances in design of protein folds and assemblies. Curr Opin Chem Biol 2017; 40:65-71. [DOI: 10.1016/j.cbpa.2017.06.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/29/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022]
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34
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De S, Chi B, Granier T, Qi T, Maurizot V, Huc I. Designing cooperatively folded abiotic uni- and multimolecular helix bundles. Nat Chem 2017; 10:51-57. [PMID: 29256508 DOI: 10.1038/nchem.2854] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023]
Abstract
Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.
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Affiliation(s)
- Soumen De
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Bo Chi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Thierry Granier
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ting Qi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Victor Maurizot
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ivan Huc
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
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35
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Bulutoglu B, Banta S. Block V RTX Domain of Adenylate Cyclase from Bordetella pertussis: A Conformationally Dynamic Scaffold for Protein Engineering Applications. Toxins (Basel) 2017; 9:E289. [PMID: 28926974 PMCID: PMC5618222 DOI: 10.3390/toxins9090289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 01/27/2023] Open
Abstract
The isolated Block V repeats-in-toxin (RTX) peptide domain of adenylate cyclase (CyaA) from Bordetella pertussis reversibly folds into a β-roll secondary structure upon calcium binding. In this review, we discuss how the conformationally dynamic nature of the peptide is being engineered and employed as a switching mechanism to mediate different protein functions and protein-protein interactions. The peptide has been used as a scaffold for diverse applications including: a precipitation tag for bioseparations, a cross-linking domain for protein hydrogel formation and as an alternative scaffold for biomolecular recognition applications. Proteins and peptides such as the RTX domains that exhibit natural stimulus-responsive behavior are valuable building blocks for emerging synthetic biology applications.
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Affiliation(s)
- Beyza Bulutoglu
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA.
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36
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Designing repeat proteins: a modular approach to protein design. Curr Opin Struct Biol 2017; 45:116-123. [DOI: 10.1016/j.sbi.2017.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 01/01/2023]
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37
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Towards designing new nano-scale protein architectures. Essays Biochem 2017; 60:315-324. [PMID: 27903819 DOI: 10.1042/ebc20160018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 08/11/2016] [Accepted: 08/18/2016] [Indexed: 11/17/2022]
Abstract
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design. This review offers an overview on rational and computational design approaches focusing on the main achievements of novel protein nanostructure design.
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38
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Voet ARD, Simoncini D, Tame JRH, Zhang KYJ. Evolution-Inspired Computational Design of Symmetric Proteins. Methods Mol Biol 2017; 1529:309-322. [PMID: 27914059 DOI: 10.1007/978-1-4939-6637-0_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Monomeric proteins with a number of identical repeats creating symmetrical structures are potentially very valuable building blocks with a variety of bionanotechnological applications. As such proteins do not occur naturally, the emerging field of computational protein design serves as an excellent tool to create them from nonsymmetrical templates. Existing pseudo-symmetrical proteins are believed to have evolved from oligomeric precursors by duplication and fusion of identical repeats. Here we describe a computational workflow to reverse-engineer this evolutionary process in order to create stable proteins consisting of identical sequence repeats.
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Affiliation(s)
- Arnout R D Voet
- Laboratory for Biomolecular Modelling and Design, KU Leuven, Celestijnenlaan 200G, Leuven, 3000, Belgium.
| | - David Simoncini
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
- MIAT, UR-875, INRA, F-31320, Castanet Tolosan, France
| | - 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
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, 1-7-22 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
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39
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Ernst P, Plückthun A. Advances in the design and engineering of peptide-binding repeat proteins. Biol Chem 2017; 398:23-29. [DOI: 10.1515/hsz-2016-0233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 08/23/2016] [Indexed: 11/15/2022]
Abstract
Abstract
The specific recognition of peptides, which we define to include unstructured regions or denatured forms of proteins, is an intrinsic part of a multitude of biochemical assays and procedures. Many cellular interactions are also based on this principle as well. While it would be highly desirable to have a stockpile of sequence-specific binders for essentially any sequence, a de novo selection of individual binders against every possible target peptide sequence would be rather difficult to reduce to practice. Modular peptide binders could overcome this problem, as preselected and/or predesigned modules could be reused for the generation of new binders and thereby revolutionize the generation of binding proteins. This minireview summarizes advances in the development of peptide binders and possible scaffolds for their design.
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40
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Rämisch S, Pramhed A, Tillgren V, Aspberg A, Logan DT. Crystal structure of human chondroadherin: solving a difficult molecular-replacement problem usingde novomodels. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:53-63. [DOI: 10.1107/s205979831601980x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/12/2016] [Indexed: 02/08/2023]
Abstract
Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing withde novomodels, the first of a β-rich protein. Structure determination of hCHAD using traditional, though nonsystematic, molecular replacement was unsuccessful in the hands of the authors, possibly owing to a combination of low sequence identity to other LRR proteins, four copies in the asymmetric unit and weak translational pseudosymmetry. However, it was possible to solve the structure by generating a large number ofde novomodels for the central LRR domain usingRosettaand multiple parallel molecular-replacement attempts usingAMPLE. The hCHAD structure reveals an ordered C-terminal domain belonging to the LRRCT fold, with the integrin-binding motif (WLEAK) being part of a regular α-helix, and suggests ways in which experimental therapeutic peptides can be improved. The crystal structure itself and docking simulations further support that hCHAD dimers form in a similar manner to other matrix LRR proteins.
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41
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Computational design of a homotrimeric metalloprotein with a trisbipyridyl core. Proc Natl Acad Sci U S A 2016; 113:15012-15017. [PMID: 27940918 DOI: 10.1073/pnas.1600188113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2'-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3]2+ complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystal structure for the residues at the protein interface is ∼1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.
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Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D. Computational design of self-assembling cyclic protein homo-oligomers. Nat Chem 2016; 9:353-360. [PMID: 28338692 PMCID: PMC5367466 DOI: 10.1038/nchem.2673] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022]
Abstract
Self-assembling cyclic protein homo-oligomers play important roles in biology and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue pair transform method for assessing the design ability of a protein-protein interface. This method is sufficiently rapid to enable systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were experimentally characterized, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (4 homodimers, 6 homotrimers, 6 homotetramers and 1 homopentamer) had solution small angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each of these were shown to be very close to their design model.
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Affiliation(s)
- Jorge A Fallas
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Vanessa Nguyen
- Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Dan E McNamara
- Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, California 90095, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA
| | - Jose Henrique Pereira
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA.,Joint BioEnergy Institute, Emeryville, California 94608, USA
| | - Fabio Parmeggiani
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, California 90095, USA
| | - Todd R Yeates
- Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, California 90095, USA
| | - Peter Zwart
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PR, Zerbe O, Baker D, Caflisch A, Plückthun A. Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition. J Mol Biol 2016; 428:4467-4489. [DOI: 10.1016/j.jmb.2016.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 10/21/2022]
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44
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Zhu H, Sepulveda E, Hartmann MD, Kogenaru M, Ursinus A, Sulz E, Albrecht R, Coles M, Martin J, Lupas AN. Origin of a folded repeat protein from an intrinsically disordered ancestor. eLife 2016; 5:e16761. [PMID: 27623012 PMCID: PMC5074805 DOI: 10.7554/elife.16761] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/09/2016] [Indexed: 01/03/2023] Open
Abstract
Repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. Many of these originated in a non-repetitive context as cofactors of RNA-based replication and catalysis, and required the RNA to assume their active conformation. In search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (TPR), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the putatively ancient ribosomal protein S20 (RPS20), which only becomes structured in the context of the ribosome. We evaluated the ability of the RPS20 hairpin to form a TPR fold by amplification and obtained structures identical to natural TPRs for variants with 2-5 point mutations per repeat. The mutations were neutral in the parent organism, suggesting that they could have been sampled in the course of evolution. TPRs could thus have plausibly arisen by amplification from an ancestral helical hairpin.
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Affiliation(s)
- Hongbo Zhu
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Edgardo Sepulveda
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Manjunatha Kogenaru
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Astrid Ursinus
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eva Sulz
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Luo Q, Hou C, Bai Y, Wang R, Liu J. Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures. Chem Rev 2016; 116:13571-13632. [PMID: 27587089 DOI: 10.1021/acs.chemrev.6b00228] [Citation(s) in RCA: 357] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.
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Affiliation(s)
- Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yushi Bai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Taipa, Macau SAR 999078, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
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Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension. Proc Natl Acad Sci U S A 2016; 113:10346-51. [PMID: 27573845 DOI: 10.1073/pnas.1525308113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops.
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Abstract
Advances in protein engineering tools, both computational and experimental, has afforded many new protein structures and functions. Here, we present a snapshot of repeat-protein engineering efforts towards new, versatile, alternative binding scaffolds for use in analytical sensors and as imaging agents. Analytical assays, sensors and imaging agents based on the direct binding of analyte are increasingly important for research and diagnostics in medicine, food safety, and national security.
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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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49
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Liu H, Chen Q. Computational protein design for given backbone: recent progresses in general method-related aspects. Curr Opin Struct Biol 2016; 39:89-95. [PMID: 27348345 DOI: 10.1016/j.sbi.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/18/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
Abstract
To achieve high success rate in protein design requires a reliable sequence design method to find amino acid sequences that stably fold into a desired backbone structure. This problem is addressed by computational protein design through the approach of energy minimization. Here we review recent method progresses related to improving the accuracy of this approach. First, the quality of the energy model is a key factor. Second, with structure sensitive energy functions, whether and how backbone flexibility is considered can have large effects on design accuracy, although usually only small adjustments of the backbone structure itself are involved. Third, the effective accuracy of design results can be boosted by post-processing a small number of designed sequences with complementary models that may not be efficient enough for full sequence optimization. Finally, computational method development will benefit greatly from increasingly efficient experimental approaches that can be applied to obtain extensive feedbacks.
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Affiliation(s)
- Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, China; Hefei National Laboratory for Physical Sciences at the Microscales, China; Collaborative Innovation Center of Chemistry for Life Sciences, Hefei, Anhui 230027, China; Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.
| | - Quan Chen
- School of Life Sciences, University of Science and Technology of China, China
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50
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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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