1
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Sriramoju MK, Ko KT, Hsu STD. Tying a true topological protein knot by cyclization. Biochem Biophys Res Commun 2024; 696:149470. [PMID: 38244314 DOI: 10.1016/j.bbrc.2024.149470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024]
Abstract
Knotted proteins are fascinating to biophysicists because of their robust ability to fold into intricately defined three-dimensional structures with complex and topologically knotted arrangements. Exploring the biophysical properties of the knotted proteins is of significant interest, as they could offer enhanced chemical, thermal, and mechanostabilities. A true mathematical knot requires a closed path; in contrast, knotted protein structures have open N- and C-termini. To address the question of how a truly knotted protein differs from the naturally occurring counterpart, we enzymatically cyclized a 31 knotted YibK protein from Haemophilus influenza (HiYibK) to investigate the impact of path closure on its structure-function relationship and folding stability. Through the use of a multitude of structural and biophysical tools, including X-ray crystallography, NMR spectroscopy, small angle X-ray scattering, differential scanning calorimetry, and isothermal calorimetry, we showed that the path closure minimally perturbs the native structure and ligand binding of HiYibK. Nevertheless, the cyclization did alter the folding stability and mechanism according to chemical and thermal unfolding analysis. These molecular insights contribute to our fundamental understanding of protein folding and knotting that could have implications in the protein design with higher stabilities.
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Affiliation(s)
| | - Kuang-Ting Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (SKCM(2)), Hiroshima University, Higashihiroshima, 739-8527, Japan.
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2
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Noel JK, Haglund E. Topological Reaction Coordinate Captures the Folding Transition State Ensemble in a Pierced Lasso Protein. J Phys Chem B 2024; 128:117-124. [PMID: 38118146 DOI: 10.1021/acs.jpcb.3c06678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Proteins with a pierced lasso topology (PLT) have a covalent loop created by a disulfide bond, and the backbone circles back to thread the loop. This threaded topology has unique features compared to knotted topologies; notably, the topology is controlled by the chemical environment and the covalent loop remains intact even when denatured. In this work, we use the hormone leptin as our model PLT system and study its folding using molecular dynamics simulations that employ a structure-based (Go̅-like) model. We find that the reduced protein has a two-state folding mechanism with a transition state ensemble (TSE) that can be characterized by the reaction coordinate Q, the fraction of native contacts formed. In contrast, the oxidized protein, which must thread part of the polypeptide chain through a covalent loop, has a folding process that is poorly characterized by Q. Instead, we find that a topological coordinate that monitors the residue crossing the loop can identify the TSE of oxidized leptin. By precisely identifying the predicted TSE, one may now reliably calculate theoretical phi-values for the PLT protein, thereby enabling a comparison with experimental measurements. We find the loop-threading constraint leads to noncanonical phi-values that are uniformly small because this PLT protein has a flat energy landscape through the TSE.
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Affiliation(s)
- Jeffrey K Noel
- Structural Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii, Manoa, Honolulu, Hawaii 96822, United States
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3
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Hsu MF, Sriramoju MK, Lai CH, Chen YR, Huang JS, Ko TP, Huang KF, Hsu STD. Structure, dynamics, and stability of the smallest and most complex 7 1 protein knot. J Biol Chem 2024; 300:105553. [PMID: 38072060 PMCID: PMC10840475 DOI: 10.1016/j.jbc.2023.105553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins, but the predictions remain to be authenticated experimentally. Here, we showed by X-ray crystallography and solution-state NMR spectroscopy that Q9PR55, an 89-residue protein from Ureaplasma urealyticum, possesses a novel 71 knotted topology that is accurately predicted by AlphaFold 2, except for the flexible N terminus. Q9PR55 is monomeric in solution, making it the smallest and most complex knotted protein known to date. In addition to its exceptional chemical stability against urea-induced unfolding, Q9PR55 is remarkably robust to resist the mechanical unfolding-coupled proteolysis by a bacterial proteasome, ClpXP. Our results suggest that the mechanical resistance against pulling-induced unfolding is determined by the complexity of the knotted topology rather than the size of the molecule.
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Affiliation(s)
- Min-Feng Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Jing-Siou Huang
- Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Academia Sinica Protein Clinic, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashihiroshima, Japan.
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4
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Hsu STD. Folding and functions of knotted proteins. Curr Opin Struct Biol 2023; 83:102709. [PMID: 37778185 DOI: 10.1016/j.sbi.2023.102709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Topologically knotted proteins have entangled structural elements within their native structures that cannot be disentangled simply by pulling from the N- and C-termini. Systematic surveys have identified different types of knotted protein structures, constituting as much as 1% of the total entries within the Protein Data Bank. Many knotted proteins rely on their knotted structural elements to carry out evolutionarily conserved biological functions. Being knotted may also provide mechanical stability to withstand unfolding-coupled proteolysis. Reconfiguring a knotted protein topology by circular permutation or cyclization provides insights into the importance of being knotted in the context of folding and functions. With the explosion of predicted protein structures by artificial intelligence, we are now entering a new era of exploring the entangled protein universe.
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Affiliation(s)
- Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
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5
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Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. De novo design of knotted tandem repeat proteins. Nat Commun 2023; 14:6746. [PMID: 37875492 PMCID: PMC10598012 DOI: 10.1038/s41467-023-42388-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (31) and pentafoil (51) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein's structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.
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Affiliation(s)
- Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Carolina T Orozco
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jonathan D Jones
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
- Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N, Seattle, WA, 98009, USA.
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Especial JNC, Faísca PFN. Effects of sequence-dependent non-native interactions in equilibrium and kinetic folding properties of knotted proteins. J Chem Phys 2023; 159:065101. [PMID: 37551809 DOI: 10.1063/5.0160886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
Determining the role of non-native interactions in folding dynamics, kinetics, and mechanisms is a classic problem in protein folding. More recently, this question has witnessed a renewed interest in light of the hypothesis that knotted proteins require the assistance of non-native interactions to fold efficiently. Here, we conduct extensive equilibrium and kinetic Monte Carlo simulations of a simple off-lattice C-alpha model to explore the role of non-native interactions in the thermodynamics and kinetics of three proteins embedding a trefoil knot in their native structure. We find that equilibrium knotted conformations are stabilized by non-native interactions that are non-local, and proximal to native ones, thus enhancing them. Additionally, non-native interactions increase the knotting frequency at high temperatures, and in partially folded conformations below the transition temperatures. Although non-native interactions clearly enhance the efficiency of transition from an unfolded conformation to a partially folded knotted one, they are not required to efficiently fold a knotted protein. Indeed, a native-centric interaction potential drives the most efficient folding transition, provided that the simulation temperature is well below the transition temperature of the considered model system.
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Affiliation(s)
- João N C Especial
- Departamento de Física, Faculdade de Ciências, Ed. C8, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física, Faculdade de Ciências, Ed. C8, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
- BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
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Ozmaian M, Makarov DE. Long-lived metastable knots in polyampholyte chains. PLoS One 2023; 18:e0287200. [PMID: 37315055 PMCID: PMC10266668 DOI: 10.1371/journal.pone.0287200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
Knots in proteins and DNA are known to have significant effect on their equilibrium and dynamic properties as well as on their function. While knot dynamics and thermodynamics in electrically neutral and uniformly charged polymer chains are relatively well understood, proteins are generally polyampholytes, with varied charge distributions along their backbones. Here we use simulations of knotted polymer chains to show that variation in the charge distribution on a polyampholyte chain with zero net charge leads to significant variation in the resulting knot dynamics, with some charge distributions resulting in long-lived metastable knots that escape the (open-ended) chain on a timescale that is much longer than that for knots in electrically neutral chains. The knot dynamics in such systems can be described, quantitatively, using a simple one-dimensional model where the knot undergoes biased Brownian motion along a "reaction coordinate", equal to the knot size, in the presence of a potential of mean force. In this picture, long-lived knots result from charge sequences that create large electrostatic barriers to knot escape. This model allows us to predict knot lifetimes even when those times are not directly accessible by simulations.
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Affiliation(s)
- Masoumeh Ozmaian
- College of Engineering, West Texas A&M University, Canyon, Texas, United States of America
| | - Dmitrii E. Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States of America
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, United States of America
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8
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Zhu H, Tian F, Sun L, Zhu Y, Qiu Q, Dai L. Computational Design of Extraordinarily Stable Peptide Structures through Side-Chain-Locked Knots. J Phys Chem Lett 2022; 13:7741-7748. [PMID: 35969173 DOI: 10.1021/acs.jpclett.2c02385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Extraordinarily stable protein and peptide structures are critically demanded in many applications. Typical approaches to enhance protein and peptide stability are strengthening certain interactions. Here, we develop a very different approach: stabilizing peptide structures through side-chain-locked knots. More specifically, a peptide core consists of a knot, which is prevented from unknotting and unfolding by large side chains of amino acids at knot boundaries. These side chains impose free energy barriers for unknotting. The free energy barriers are quantified using all-atom and coarse-grained simulations. The barriers become infinitely high for large side chains and tight knot cores, resulting in stable peptide structures, which never unfold unless one chemical bond is broken. The extraordinary stability is essentially kinetic stability. Our new approach lifts the thermodynamic restriction in designing peptide structures, provides extra freedom in selecting sequence and structural motifs that are thermodynamically unstable, and should expand the functionality of peptides. This work also provides a bottom-up understanding of how knotting enhances protein stability.
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Affiliation(s)
- Haoqi Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Fujia Tian
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Sun
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yongjian Zhu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Qiyuan Qiu
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Kowloon 999077, Hong Kong Special Administrative Region of the People's Republic of China
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9
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Wang J, Peng X. In silico method for identifying the key residues in a knotted protein: with MJ0366 as an example. Phys Chem Chem Phys 2022; 24:27495-27504. [DOI: 10.1039/d2cp03589h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A simple in silico method for predicting the key residues for knotting and unknotting a knotted protein is put forward, with the residues ranked by the relevance to knotting and unknotting in the annealing molecular dynamics simulations.
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Affiliation(s)
- Jianmei Wang
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
- Beijing Academy of Quantum Information Sciences, Beijing 100193, China
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10
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Puri S, Hsu STD. Elucidation of folding pathways of knotted proteins. Methods Enzymol 2022; 675:275-297. [DOI: 10.1016/bs.mie.2022.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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11
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Hsu STD, Lee YTC, Mikula KM, Backlund SM, Tascón I, Goldman A, Iwaï H. Tying up the Loose Ends: A Mathematically Knotted Protein. Front Chem 2021; 9:663241. [PMID: 34109153 PMCID: PMC8182377 DOI: 10.3389/fchem.2021.663241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Knots have attracted scientists in mathematics, physics, biology, and engineering. Long flexible thin strings easily knot and tangle as experienced in our daily life. Similarly, long polymer chains inevitably tend to get trapped into knots. Little is known about their formation or function in proteins despite >1,000 knotted proteins identified in nature. However, these protein knots are not mathematical knots with their backbone polypeptide chains because of their open termini, and the presence of a “knot” depends on the algorithm used to create path closure. Furthermore, it is generally not possible to control the topology of the unfolded states of proteins, therefore making it challenging to characterize functional and physicochemical properties of knotting in any polymer. Covalently linking the amino and carboxyl termini of the deeply trefoil-knotted YibK from Pseudomonas aeruginosa allowed us to create the truly backbone knotted protein by enzymatic peptide ligation. Moreover, we produced and investigated backbone cyclized YibK without any knotted structure. Thus, we could directly probe the effect of the backbone knot and the decrease in conformational entropy on protein folding. The backbone cyclization did not perturb the native structure and its cofactor binding affinity, but it substantially increased the thermal stability and reduced the aggregation propensity. The enhanced stability of a backbone knotted YibK could be mainly originated from an increased ruggedness of its free energy landscape and the destabilization of the denatured state by backbone cyclization with little contribution from a knot structure. Despite the heterogeneity in the side-chain compositions, the chemically unfolded cyclized YibK exhibited several macroscopic physico-chemical attributes that agree with theoretical predictions derived from polymer physics.
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Affiliation(s)
- Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kornelia M Mikula
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sofia M Backlund
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Igor Tascón
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Adrian Goldman
- Division of Biochemistry, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, West Yorkshire, United Kingdom
| | - Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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