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Ferreira SGF, Sriramoju MK, Hsu STD, Faísca PFN, Machuqueiro M. Is There a Functional Role for the Knotted Topology in Protein UCH-L1? J Chem Inf Model 2024. [PMID: 39045738 DOI: 10.1021/acs.jcim.4c00880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Knotted proteins are present in nature, but there is still an open issue regarding the existence of a universal role for these remarkable structures. To address this question, we used classical molecular dynamics (MD) simulations combined with in vitro experiments to investigate the role of the Gordian knot in the catalytic activity of UCH-L1. To create an unknotted form of UCH-L1, we modified its amino acid sequence by truncating several residues from its N-terminus. Remarkably, we find that deleting the first two N-terminal residues leads to a partial loss of enzyme activity with conservation of secondary structural content and knotted topological state. This happens because the integrity of the N-terminus is critical to ensure the correct alignment of the catalytic triad. However, the removal of five residues from the N-terminus, which significantly disrupts the native structure and the topological state, leads to a complete loss of enzymatic activity. Overall, our findings indicate that UCH-L1's catalytic activity depends critically on the integrity of the N-terminus and the secondary structure content, with the latter being strongly coupled with the knotted topological state.
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Affiliation(s)
- Sara G F Ferreira
- BioISI - Instituto de Biossistemas e Ciências Integrativas, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manoj K Sriramoju
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 11529, Taiwan
| | - Patrícia F N Faísca
- BioISI - Instituto de Biossistemas e Ciências Integrativas, Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioISI - Instituto de Biossistemas e Ciências Integrativas, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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2
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Sikora M, Klimentova E, Uchal D, Sramkova D, Perlinska AP, Nguyen ML, Korpacz M, Malinowska R, Nowakowski S, Rubach P, Simecek P, Sulkowska JI. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model. Protein Sci 2024; 33:e4998. [PMID: 38888487 PMCID: PMC11184937 DOI: 10.1002/pro.4998] [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: 12/04/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
Abstract
Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (AF), this study computationally examines the entire UniProt database to create a robust dataset of knotted and unknotted proteins. Utilizing this dataset, we develop a machine learning (ML) model capable of accurately predicting the presence of knots in protein structures solely from their amino acid sequences. We tested the model's capabilities on 100 proteins whose structures had not yet been predicted by AF and found agreement with our local prediction in 92% cases. From the point of view of structural biology, we found that all potentially knotted proteins predicted by AF can be classified only into 17 families. This allows us to discover the presence of unknotted proteins in families with a highly conserved knot. We found only three new protein families: UCH, DUF4253, and DUF2254, that contain both knotted and unknotted proteins, and demonstrate that deletions within the knot core could potentially account for the observed unknotted (trivial) topology. Finally, we have shown that in the majority of knotted families (11 out of 15), the knotted topology is strictly conserved in functional proteins with very low sequence similarity. We have conclusively demonstrated that proteins AF predicts as unknotted are structurally accurate in their unknotted configurations. However, these proteins often represent nonfunctional fragments, lacking significant portions of the knot core (amino acid sequence).
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Affiliation(s)
- Maciej Sikora
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
| | - Eva Klimentova
- Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrnoCzech Republic
| | - Dawid Uchal
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Physics, University of WarsawWarsawPoland
| | - Denisa Sramkova
- Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrnoCzech Republic
| | | | - Mai Lan Nguyen
- Centre of New Technologies, University of WarsawWarsawPoland
| | - Marta Korpacz
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
| | - Roksana Malinowska
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
| | - Szymon Nowakowski
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
- Faculty of Physics, University of WarsawWarsawPoland
| | - Pawel Rubach
- Centre of New Technologies, University of WarsawWarsawPoland
- Warsaw School of EconomicsWarsawPoland
| | - Petr Simecek
- Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
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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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Salicari L, Baiesi M, Orlandini E, Trovato A. Folding kinetics of an entangled protein. PLoS Comput Biol 2023; 19:e1011107. [PMID: 37956216 PMCID: PMC10681328 DOI: 10.1371/journal.pcbi.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
The possibility of the protein backbone adopting lasso-like entangled motifs has attracted increasing attention. After discovering the surprising abundance of natively entangled protein domain structures, it was shown that misfolded entangled subpopulations might become thermosensitive or escape the homeostasis network just after translation. To investigate the role of entanglement in shaping folding kinetics, we introduce a novel indicator and analyze simulations of a coarse-grained, structure-based model for two small single-domain proteins. The model recapitulates the well-known two-state folding mechanism of a non-entangled SH3 domain. However, despite its small size, a natively entangled antifreeze RD1 protein displays a rich refolding behavior, populating two distinct kinetic intermediates: a short-lived, entangled, near-unfolded state and a longer-lived, non-entangled, near-native state. The former directs refolding along a fast pathway, whereas the latter is a kinetic trap, consistently with known experimental evidence of two different characteristic times. Upon trapping, the natively entangled loop folds without being threaded by the N-terminal residues. After trapping, the native entangled structure emerges by either backtracking to the unfolded state or threading through the already formed but not yet entangled loop. Along the fast pathway, trapping does not occur because the native contacts at the closure of the lasso-like loop fold after those involved in the N-terminal thread, confirming previous predictions. Despite this, entanglement may appear already in unfolded configurations. Remarkably, a longer-lived, near-native intermediate, with non-native entanglement properties, recalls what was observed in cotranslational folding.
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Affiliation(s)
- Leonardo Salicari
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Marco Baiesi
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
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6
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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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7
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Rivera M, Burgos‐Bravo F, Engelberger F, Asor R, Lagos‐Espinoza MIA, Figueroa M, Kukura P, Ramírez‐Sarmiento CA, Baez M, Smith SB, Wilson CAM. Effect of temperature and nucleotide on the binding of BiP chaperone to a protein substrate. Protein Sci 2023; 32:e4706. [PMID: 37323096 PMCID: PMC10303699 DOI: 10.1002/pro.4706] [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: 12/18/2022] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
BiP (immunoglobulin heavy-chain binding protein) is a Hsp70 monomeric ATPase motor that plays broad and crucial roles in maintaining proteostasis inside the cell. Structurally, BiP is formed by two domains, a nucleotide-binding domain (NBD) with ATPase activity connected by a flexible hydrophobic linker to the substrate-binding domain. While the ATPase and substrate binding activities of BiP are allosterically coupled, the latter is also dependent on nucleotide binding. Recent structural studies have provided new insights into BiP's allostery; however, the influence of temperature on the coupling between substrate and nucleotide binding to BiP remains unexplored. Here, we study BiP's binding to its substrate at the single molecule level using thermo-regulated optical tweezers which allows us to mechanically unfold the client protein and explore the effect of temperature and different nucleotides on BiP binding. Our results confirm that the affinity of BiP for its protein substrate relies on nucleotide binding, by mainly regulating the binding kinetics between BiP and its substrate. Interestingly, our findings also showed that the apparent affinity of BiP for its protein substrate in the presence of nucleotides remains invariable over a wide range of temperatures, suggesting that BiP may interact with its client proteins with similar affinities even when the temperature is not optimal. Thus, BiP could play a role as a "thermal buffer" in proteostasis.
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Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBio)SantiagoChile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Francesca Burgos‐Bravo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
- Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Felipe Engelberger
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | - Roi Asor
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
- The Kavli Institute for Nanoscience DiscoveryOxfordUK
| | - Miguel I. A. Lagos‐Espinoza
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | - Maximiliano Figueroa
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias BiológicasUniversidad de ConcepciónConcepciónChile
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK
- The Kavli Institute for Nanoscience DiscoveryOxfordUK
| | - César A. Ramírez‐Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiagoChile
- ANID–Millennium Science Initiative Program–Millennium Institute for Integrative Biology (iBio)SantiagoChile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
| | | | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y FarmacéuticasUniversidad de ChileSantiagoChile
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8
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Rivera M, Mjaavatten A, Smith SB, Baez M, Wilson CAM. Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers. Biophys J 2023; 122:513-521. [PMID: 36587240 PMCID: PMC9941719 DOI: 10.1016/j.bpj.2022.12.034] [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: 02/07/2022] [Revised: 06/15/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Temperature is a useful system variable to gather kinetic and thermodynamic information from proteins. Usually, free energy and the associated entropic and enthalpic contributions are obtained by quantifying the conformational equilibrium based on melting experiments performed in bulk conditions. Such experiments are suitable only for those small single-domain proteins whose side reactions of irreversible aggregation are unlikely to occur. Here, we avoid aggregation by pulling single-protein molecules in a thermo-regulated optical tweezers. Thus, we are able to explore the temperature dependence of the thermodynamic and kinetic parameters of MJ0366 from Methanocaldococcus jannaschii at the single-molecule level. By performing force-ramp experiments between 2°C and 40°C, we found that MJ0366 has a nonlinear dependence of free energy with temperature and a specific heat change of 2.3 ± 1.2 kcal/mol∗K. These thermodynamic parameters are compatible with a two-state unfolding/refolding mechanism for MJ0366. However, the kinetics measured as a function of the temperature show a complex behavior, suggesting a three-state folding mechanism comprising a high-energy intermediate state. The combination of two perturbations, temperature and force, reveals a high-energy species in the folding mechanism of MJ0366 not detected in force-ramp experiments at constant temperature.
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Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | | | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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9
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Yang TJ, Li TN, Huang RS, Pan MYC, Lin SY, Lin S, Wu KP, Wang LHC, Hsu STD. Tumor suppressor BAP1 nuclear import is governed by transportin-1. J Cell Biol 2022; 221:213174. [PMID: 35446349 DOI: 10.1083/jcb.202201094] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/16/2022] [Accepted: 03/31/2022] [Indexed: 12/30/2022] Open
Abstract
Subcellular localization of the deubiquitinating enzyme BAP1 is deterministic for its tumor suppressor activity. While the monoubiquitination of BAP1 by an atypical E2/E3-conjugated enzyme UBE2O and BAP1 auto-deubiquitination are known to regulate its nuclear localization, the molecular mechanism by which BAP1 is imported into the nucleus has remained elusive. Here, we demonstrated that transportin-1 (TNPO1, also known as Karyopherin β2 or Kapβ2) targets an atypical C-terminal proline-tyrosine nuclear localization signal (PY-NLS) motif of BAP1 and serves as the primary nuclear transporter of BAP1 to achieve its nuclear import. TNPO1 binding dissociates dimeric BAP1 and sequesters the monoubiquitination sites flanking the PY-NLS of BAP1 to counteract the function of UBE2O that retains BAP1 in the cytosol. Our findings shed light on how TNPO1 regulates the nuclear import, self-association, and monoubiquitination of BAP1 pertinent to oncogenesis.
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Affiliation(s)
- Tzu-Jing Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Tian-Neng Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Rih-Sheng Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Max Yu-Chen Pan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Academia Sinica Common Mass Spectrometry Facilities for Proteomics and Protein Modification Analysis, Academia Sinica, Taipei, Taiwan
| | - Steven Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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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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12
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Paissoni C, Puri S, Wang I, Chen SY, Camilloni C, Hsu STD. Converging experimental and computational views of the knotting mechanism of a small knotted protein. Biophys J 2021; 120:2276-2286. [PMID: 33812848 PMCID: PMC8390826 DOI: 10.1016/j.bpj.2021.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 01/18/2023] Open
Abstract
MJ0366 from Methanocaldococcus jannaschii is the smallest topologically knotted protein known to date. 92 residues in length, MJ0366 ties a trefoil (31) knot by threading its C-terminal helix through a buttonhole formed by the remainder of the secondary structure elements. By generating a library of point mutations at positions pertinent to the knot formation, we systematically evaluated the contributions of individual residues to the folding stability and kinetics of MJ0366. The experimental Φ-values were used as restraints to computationally generate an ensemble of conformations that correspond to the transition state of MJ0366, which revealed several nonnative contacts. The importance of these nonnative contacts in stabilizing the transition state of MJ0366 was confirmed by a second round of mutagenesis, which also established the pivotal role of F15 in stapling the network of hydrophobic interactions around the threading C-terminal helix. Our converging experimental and computational results show that, despite the small size, the transition state of MJ0366 is formed at a very late stage of the folding reaction coordinate, following a polarized pathway. Eventually, the formation of extensive native contacts, as well as a number of nonnative ones, leads to the threading of the C-terminal helix that defines the topological knot.
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Affiliation(s)
- Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Sarita Puri
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Iren Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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13
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Cross-over Loop Cysteine C152 Acts as an Antioxidant to Maintain the Folding Stability and Deubiquitinase Activity of UCH-L1 Under Oxidative Stress. J Mol Biol 2021; 433:166879. [PMID: 33617897 DOI: 10.1016/j.jmb.2021.166879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 02/12/2021] [Indexed: 11/20/2022]
Abstract
Redox-dependent inactivation of deubiquitinases (DUBs) is a critical factor for attenuating their DUB activity in response to cellular oxidative stress. Ubiquitin C-terminal hydrolase isoform (UCH-L1) is an important DUB that is highly expressed in human neuronal cells and is implicated in a myriad of human diseases such as neurodegenerative diseases and cancer. Increasing evidence suggests an important role of UCH-L1 in redox regulation and the protection of neuronal cells from oxidative stress. In this study, we examined the molecular basis of how UCH-L1 responds to oxidation in a reversible manner. Using H2O2 as a model oxidant, we showed by mass spectrometry that a subset of methionine and cysteine residues, namely (M1, M6, M12, C90, and C152) were more susceptible to oxidation. Spectroscopic analysis showed that oxidation of C90 can lead to profound structural changes in addition to the loss of function. Importantly, we further demonstrated that C152, which is located at the substrate recognition cross-over loop, serves as a reactive oxygen species (ROS) scavenger to protect catalytic C90 from oxidation under moderate oxidative conditions. Hydrogen-deuterium exchange mass spectrometry analysis provided detailed structural mapping of the destabilizing effect of H2O2-mediated oxidation, which resulted in global destabilization far beyond the oxidation sites. These perturbations may be responsible for irreversible aggregation when subject to prolonged oxidative stress.
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14
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Piejko M, Niewieczerzal S, Sulkowska JI. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots. Isr J Chem 2020. [DOI: 10.1002/ijch.202000036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maciej Piejko
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
| | | | - Joanna I. Sulkowska
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
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15
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Rivera M, Hao Y, Maillard RA, Baez M. Mechanical unfolding of a knotted protein unveils the kinetic and thermodynamic consequences of threading a polypeptide chain. Sci Rep 2020; 10:9562. [PMID: 32533020 PMCID: PMC7292828 DOI: 10.1038/s41598-020-66258-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
Knots are remarkable topological features in nature. The presence of knots in crystallographic structures of proteins have stimulated considerable research to determine the kinetic and thermodynamic consequences of threading a polypeptide chain. By mechanically manipulating MJ0366, a small single domain protein harboring a shallow trefoil knot, we allow the protein to refold from either the knotted or the unknotted denatured state to characterize the free energy profile associated to both folding pathways. By comparing the stability of the native state with reference to the knotted and unknotted denatured state we find that knotting the polypeptide chain of MJ0366 increase the folding energy barrier in a magnitude close to the energy cost of forming a knot randomly in the denatured state. These results support that a protein knot can be formed during a single cooperative step of folding but occurs at the expenses of a large increment on the free energy barrier.
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Affiliation(s)
- Maira Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Yuxin Hao
- Department of Chemistry, Georgetown University, Washington, DC, 20057, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, DC, 20057, USA.
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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16
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Sulkowska JI. On folding of entangled proteins: knots, lassos, links and θ-curves. Curr Opin Struct Biol 2020; 60:131-141. [PMID: 32062143 DOI: 10.1016/j.sbi.2020.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/15/2022]
Abstract
Around 6% of protein structures deposited in the PDB are entangled, forming knots, slipknots, lassos, links, and θ-curves. In each of these cases, the protein backbone weaves through itself in a complex way, and at some point passes through a closed loop, formed by other regions of the protein structure. Such a passing can be interpreted as crossing a topological barrier. How proteins overcome such barriers, and therefore different degrees of frustration, challenged scientists and has shed new light on the field of protein folding. In this review, we summarize the current knowledge about the free energy landscape of proteins with non-trivial topology. We describe identified mechanisms which lead proteins to self-tying. We discuss the influence of excluded volume, such as crowding and chaperones, on tying, based on available data. We briefly discuss the diversity of topological complexity of proteins and their evolution. We also list available tools to investigate non-trivial topology. Finally, we formulate intriguing and challenging questions at the boundary of biophysics, bioinformatics, biology, and mathematics, which arise from the discovery of entangled proteins.
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Affiliation(s)
- Joanna Ida Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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17
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Perego C, Potestio R. Computational methods in the study of self-entangled proteins: a critical appraisal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:443001. [PMID: 31269476 DOI: 10.1088/1361-648x/ab2f19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The existence of self-entangled proteins, the native structure of which features a complex topology, unveils puzzling, and thus fascinating, aspects of protein biology and evolution. The discovery that a polypeptide chain can encode the capability to self-entangle in an efficient and reproducible way during folding, has raised many questions, regarding the possible function of these knots, their conservation along evolution, and their role in the folding paradigm. Understanding the function and origin of these entanglements would lead to deep implications in protein science, and this has stimulated the scientific community to investigate self-entangled proteins for decades by now. In this endeavour, advanced experimental techniques are more and more supported by computational approaches, that can provide theoretical guidelines for the interpretation of experimental results, and for the effective design of new experiments. In this review we provide an introduction to the computational study of self-entangled proteins, focusing in particular on the methodological developments related to this research field. A comprehensive collection of techniques is gathered, ranging from knot theory algorithms, that allow detection and classification of protein topology, to Monte Carlo or molecular dynamics strategies, that constitute crucial instruments for investigating thermodynamics and kinetics of this class of proteins.
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Affiliation(s)
- Claudio Perego
- Max Panck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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18
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Ko KT, Hu IC, Huang KF, Lyu PC, Hsu STD. Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer. Structure 2019; 27:1224-1233.e4. [DOI: 10.1016/j.str.2019.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/01/2019] [Accepted: 04/05/2019] [Indexed: 11/28/2022]
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19
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Perego C, Potestio R. Searching the Optimal Folding Routes of a Complex Lasso Protein. Biophys J 2019; 117:214-228. [PMID: 31235180 PMCID: PMC6700606 DOI: 10.1016/j.bpj.2019.05.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/29/2019] [Accepted: 05/30/2019] [Indexed: 10/27/2022] Open
Abstract
Understanding how polypeptides can efficiently and reproducibly attain a self-entangled conformation is a compelling biophysical challenge that might shed new light on our general knowledge of protein folding. Complex lassos, namely self-entangled protein structures characterized by a covalent loop sealed by a cysteine bridge, represent an ideal test system in the framework of entangled folding. Indeed, because cysteine bridges form in oxidizing conditions, they can be used as on/off switches of the structure topology to investigate the role played by the backbone entanglement in the process. In this work, we have used molecular dynamics to simulate the folding of a complex lasso glycoprotein, granulocyte-macrophage colony-stimulating factor, modeling both reducing and oxidizing conditions. Together with a well-established Gō-like description, we have employed the elastic folder model, a coarse-grained, minimalistic representation of the polypeptide chain driven by a structure-based angular potential. The purpose of this study is to assess the kinetically optimal pathways in relation to the formation of the native topology. To this end, we have implemented an evolutionary strategy that tunes the elastic folder model potentials to maximize the folding probability within the early stages of the dynamics. The resulting protein model is capable of folding with high success rate, avoiding the kinetic traps that hamper the efficient folding in the other tested models. Employing specifically designed topological descriptors, we could observe that the selected folding routes avoid the topological bottleneck by locking the cysteine bridge after the topology is formed. These results provide valuable insights on the selection of mechanisms in self-entangled protein folding while, at the same time, the proposed methodology can complement the usage of established minimalistic models and draw useful guidelines for more detailed simulations.
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Affiliation(s)
- Claudio Perego
- Polymer Theory Department, Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Raffaello Potestio
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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20
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He C, Li S, Gao X, Xiao A, Hu C, Hu X, Hu X, Li H. Direct observation of the fast and robust folding of a slipknotted protein by optical tweezers. NANOSCALE 2019; 11:3945-3951. [PMID: 30762052 DOI: 10.1039/c8nr10070e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding the folding mechanism of knotted and slipknotted proteins has attracted considerable interest. Due to their topological complexity, knotted and slipknotted proteins are predicted to fold slowly and involve large topological barriers. Molecular dynamics simulation studies suggest that a slipknotted conformation can serve as an important intermediate to help greatly reduce the topological difficulty during the folding of some knotted proteins. Here we use a single molecule optical tweezers technique to directly probe the folding of a small slipknotted protein AFV3-109. We found that stretching AFV3-109 can lead to the untying of the slipknot and complete unfolding of AFV3-109. Upon relaxation, AFV3-109 can readily refold back to its native slipknot conformation with high fidelity when the stretching force is lower than 6 pN. The refolding of AFV3-109 occurs in a sharp two-state like transition. Our results indicate that, different from knotted proteins, the folding of a slipknotted protein like AFV3-109 can be fast, and may not necessarily involve a high topological barrier.
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Affiliation(s)
- Chengzhi He
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Shuai Li
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Xiaoqing Gao
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Adam Xiao
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Chunguang Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Xiaodong Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Hongbin Li
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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21
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Sivertsson EM, Jackson SE, Itzhaki LS. The AAA+ protease ClpXP can easily degrade a 3 1 and a 5 2-knotted protein. Sci Rep 2019; 9:2421. [PMID: 30787316 PMCID: PMC6382783 DOI: 10.1038/s41598-018-38173-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Knots in proteins are hypothesized to make them resistant to enzymatic degradation by ATP-dependent proteases and recent studies have shown that whereas ClpXP can easily degrade a protein with a shallow 31 knot, it cannot degrade 52-knotted proteins if degradation is initiated at the C-terminus. Here, we present detailed studies of the degradation of both 31- and 52-knotted proteins by ClpXP using numerous constructs where proteins are tagged for degradation at both N- and C-termini. Our results confirm and extend earlier work and show that ClpXP can easily degrade a deeply 31-knotted protein. In contrast to recently published work on the degradation of 52-knotted proteins, our results show that the ClpXP machinery can also easily degrade these proteins. However, the degradation depends critically on the location of the degradation tag and the local stability near the tag. Our results are consistent with mechanisms in which either the knot simply slips along the polypeptide chain and falls off the free terminus, or one in which the tightened knot enters the translocation pore of ClpXP. Results of experiments on knotted protein fusions with a highly stable domain show partial degradation and the formation of degradation intermediates.
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Affiliation(s)
- Elin M Sivertsson
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Sophie E Jackson
- Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Laura S Itzhaki
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK.
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22
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Untying a Protein Knot by Circular Permutation. J Mol Biol 2019; 431:857-863. [DOI: 10.1016/j.jmb.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 01/13/2023]
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23
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Jarmolinska AI, Perlinska AP, Runkel R, Trefz B, Ginn HM, Virnau P, Sulkowska JI. Proteins' Knotty Problems. J Mol Biol 2018; 431:244-257. [PMID: 30391297 DOI: 10.1016/j.jmb.2018.10.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022]
Abstract
Knots in proteins are increasingly being recognized as an important structural concept, and the folding of these peculiar structures still poses considerable challenges. From a functional point of view, most protein knots discovered so far are either enzymes or DNA-binding proteins. Our comprehensive topological analysis of the Protein Data Bank reveals several novel structures including knotted mitochondrial proteins and the most deeply embedded protein knot discovered so far. For the latter, we propose a novel folding pathway based on the idea that a loose knot forms at a terminus and slides to its native position. For the mitochondrial proteins, we discuss the folding problem from the perspective of transport and suggest that they fold inside the mitochondria. We also discuss the evolutionary origin of a novel class of knotted membrane proteins and argue that a novel knotted DNA-binding protein constitutes a new fold. Finally, we have also discovered a knot in an artificially designed protein structure.
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Affiliation(s)
- Aleksandra I Jarmolinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland
| | - Agata P Perlinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Banacha 2c, 02-097 Warsaw, Poland
| | - Robert Runkel
- Department of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Benjamin Trefz
- Department of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany; Graduate School Material Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Helen M Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Virnau
- Department of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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24
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Comparative folding analyses of unknotted versus trefoil-knotted ornithine transcarbamylases suggest stabilizing effects of protein knots. Biochem Biophys Res Commun 2018; 503:822-829. [DOI: 10.1016/j.bbrc.2018.06.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/16/2022]
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25
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Sriramoju MK, Chen Y, Lee YTC, Hsu STD. Topologically knotted deubiquitinases exhibit unprecedented mechanostability to withstand the proteolysis by an AAA+ protease. Sci Rep 2018; 8:7076. [PMID: 29728659 PMCID: PMC5935755 DOI: 10.1038/s41598-018-25470-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 01/03/2023] Open
Abstract
More than one thousand knotted protein structures have been identified so far, but the functional roles of these knots remain elusive. It has been postulated that backbone entanglement may provide additional mechanostability. Here, we employed a bacterial proteasome, ClpXP, to mechanically unfold 52-knotted human ubiquitin C-terminal hydrolase (UCH) paralogs from their C-termini, followed by processive translocation into the proteolytic chamber for degradation. Our results revealed unprecedentedly slow kinetics of ClpXP-mediated proteolysis for the proteasome-associated UCHL5: ten thousand times slower than that of a green fluorescence protein (GFP), which has a comparable size to the UCH domain but much higher chemical and thermal stabilities. The ClpXP-dependent mechanostability positively correlates with the intrinsic unfolding rates of the substrates, spanning over several orders of magnitude for the UCHs. The broad range of mechanostability within the same protein family may be associated with the functional requirements for their differential malleabilities.
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Affiliation(s)
| | - Yen Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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26
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Soler MA, Rey A, Faísca PFN. Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding. Phys Chem Chem Phys 2018; 18:26391-26403. [PMID: 27722468 DOI: 10.1039/c6cp05086g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The chaperonin complex GroEL-GroES is able to accelerate the folding process of knotted proteins considerably. However, the folding mechanism inside the chaperonin cage is elusive. Here we use a combination of lattice and off-lattice Monte Carlo simulations of simple Gō models to study the effect of physical confinement and local flexibility on the folding process of protein model systems embedding a trefoil knot in their native structure. This study predicts that steric confinement plays a specific role in the folding of knotted proteins by increasing the knotting probability for very high degrees of confinement. This effect is observed for protein MJ0366 even above the melting temperature for confinement sizes compatible with the size of the GroEL/GroES chaperonin cage. An enhanced local flexibility produces the same qualitative effects on the folding process. In particular, we observe that knotting probability increases up to 40% in the transition state of protein MJ0366 when flexibility is enhanced. This is underlined by a structural change in the transition state, which becomes devoid of helical content. No relation between the knotting mechanism and flexibility was found in the context of the off-lattice model adopted in this work.
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Affiliation(s)
- Miguel A Soler
- Dipartimento di Scienze Mediche e Biologiche, Universita' di Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Antonio Rey
- Departamento de Química Física I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain.
| | - Patrícia F N Faísca
- Departamento de Física and BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.
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27
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Sulkowska JI, Sułkowski P. Entangled Proteins: Knots, Slipknots, Links, and Lassos. SPRINGER SERIES IN SOLID-STATE SCIENCES 2018. [DOI: 10.1007/978-3-319-76596-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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28
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Burban DJ, Jennings PA. Backbone assignments for the SPOUT methyltransferase MTT Tm , a knotted protein from Thermotoga maritima. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:151-154. [PMID: 28284017 DOI: 10.1007/s12104-017-9737-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
The SPOUT family of methyltransferase proteins is noted for containing a deep trefoil knot in their defining backbone fold. This unique fold is of high interest for furthering the understanding of knots in proteins. Here, we report the 1H, 13C, 15N assignments for MTT Tm , a canonical member of the SPOUT family. This protein is unique, as it is one of the smallest members of the family, making it an ideal system for probing the unique properties of the knot. Our present work represents the foundation for further studies into the topology of MTT Tm , and understanding how its structure affects both its folding and function.
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Affiliation(s)
- David J Burban
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, USA
| | - Patricia A Jennings
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, USA.
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29
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Dabrowski-Tumanski P, Sulkowska JI. To Tie or Not to Tie? That Is the Question. Polymers (Basel) 2017; 9:E454. [PMID: 30965758 PMCID: PMC6418553 DOI: 10.3390/polym9090454] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of entangled proteins. Around 6% of protein structures deposited in the PBD are entangled, forming knots, slipknots, lassos and links. We present theoretical methods and tools that enabled discovering and classifying such structures. We discuss the advantages and disadvantages of the non-trivial topology in proteins, based on available data about folding, stability, biological properties and evolutionary conservation. We also formulate intriguing and challenging questions on the border of biophysics, bioinformatics, biology and mathematics, which arise from the discovery of an entanglement in proteins. Finally, we discuss possible applications of entangled proteins in medicine and nanotechnology, such as the chance to design super stable proteins, whose stability could be controlled by chemical potential.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.
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30
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Abstract
ATP-dependent proteases translocate proteins through a narrow pore for their controlled destruction. However, how a protein substrate containing a knotted topology affects this process remains unknown. Here, we characterized the effects of the trefoil-knotted protein MJ0366 from Methanocaldococcus jannaschii on the operation of the ClpXP protease from Escherichia coli ClpXP completely degrades MJ0366 when pulling from the C-terminal ssrA-tag. However, when a GFP moiety is appended to the N terminus of MJ0366, ClpXP releases intact GFP with a 47-residue tail. The extended length of this tail suggests that ClpXP tightens the trefoil knot against GFP, which prevents GFP unfolding. Interestingly, if the linker between the knot core of MJ0366 and GFP is longer than 36 residues, ClpXP tightens and translocates the knot before it reaches GFP, enabling the complete unfolding and degradation of the substrate. These observations suggest that a knot-induced stall during degradation of multidomain proteins by AAA proteases may constitute a novel mechanism to produce partially degraded products with potentially new functions.
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31
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Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange. Molecules 2017; 22:molecules22081357. [PMID: 28813004 PMCID: PMC6152064 DOI: 10.3390/molecules22081357] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/17/2022] Open
Abstract
Galectins are β-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their affinities for lactose, a common galectin inhibitor, vary significantly. Here, we aimed to examine the molecular basis of differential lactose affinities amongst galectins using solution-based techniques. Consistent dissociation constants of lactose binding were derived from nuclear magnetic resonance (NMR) spectroscopy, intrinsic tryptophan fluorescence, isothermal titration calorimetry and bio-layer interferometry for human galectin-1 (hGal1), galectin-7 (hGal7), and the N-terminal and C-terminal domains of galectin-8 (hGal8NTD and hGal8CTD, respectively). Furthermore, the dissociation rates of lactose binding were extracted from NMR lineshape analyses. Structural mapping of chemical shift perturbations revealed long-range perturbations upon lactose binding for hGal1 and hGal8NTD. We further demonstrated using the NMR-based hydrogen–deuterium exchange (HDX) that lactose binding increases the exchange rates of residues located on the opposite side of the ligand-binding pocket for hGal1 and hGal8NTD, indicative of allostery. Additionally, lactose binding induces significant stabilisation of hGal8CTD across the entire domain. Our results suggested that lactose binding reduced the internal dynamics of hGal8CTD on a very slow timescale (minutes and slower) at the expense of reduced binding affinity due to the unfavourable loss of conformational entropy.
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32
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Lee YTC, Chang CY, Chen SY, Pan YR, Ho MR, Hsu STD. Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome. Sci Rep 2017; 7:45174. [PMID: 28338014 PMCID: PMC5364529 DOI: 10.1038/srep45174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 02/07/2023] Open
Abstract
Human ubiquitin C-terminal hydrolyase UCH-L5 is a topologically knotted deubiquitinase that is activated upon binding to the proteasome subunit Rpn13. The length of its intrinsically disordered cross-over loop is essential for substrate recognition. Here, we showed that the catalytic domain of UCH-L5 exhibits higher equilibrium folding stability with an unfolding rate on the scale of 10−8 s−1, over four orders of magnitudes slower than its paralogs, namely UCH-L1 and -L3, which have shorter cross-over loops. NMR relaxation dynamics analysis confirmed the intrinsic disorder of the cross-over loop. Hydrogen deuterium exchange analysis further revealed a positive correlation between the length of the cross-over loop and the degree of local fluctuations, despite UCH-L5 being thermodynamically and kinetically more stable than the shorter UCHs. Considering the role of UCH-L5 in removing K48-linked ubiquitin to prevent proteasomal degradation of ubiquitinated substrates, our findings offered mechanistic insights into the evolution of UCH-L5. Compared to its paralogs, it is entropically stabilized to withstand mechanical unfolding by the proteasome while maintaining structural plasticity. It can therefore accommodate a broad range of substrate geometries at the cost of unfavourable entropic loss.
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Affiliation(s)
- Yun-Tzai Cloud Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Chia-Yun Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, 10617, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun-Ru Pan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Meng-Ru Ho
- 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, 10617, Taiwan
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33
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Ramírez MP, Rivera M, Quiroga-Roger D, Bustamante A, Vega M, Baez M, Puchner EM, Wilson CAM. Single molecule force spectroscopy reveals the effect of BiP chaperone on protein folding. Protein Sci 2017; 26:1404-1412. [PMID: 28176394 DOI: 10.1002/pro.3137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/18/2017] [Accepted: 02/03/2017] [Indexed: 11/10/2022]
Abstract
BiP (Immunoglobulin Binding Protein) is a member of the Hsp70 chaperones that participates in protein folding in the endoplasmic reticulum. The function of BiP relies on cycles of ATP hydrolysis driving the binding and release of its substrate proteins. It still remains unknown how BiP affects the protein folding pathway and there has been no direct demonstration showing which folding state of the substrate protein is bound by BiP, as previous work has used only peptides. Here, we employ optical tweezers for single molecule force spectroscopy experiments to investigate how BiP affects the folding mechanism of a complete protein and how this effect depends on nucleotides. Using the protein MJ0366 as the substrate for BiP, we performed pulling and relaxing cycles at constant velocity to unfold and refold the substrate. In the absence of BiP, MJ0366 unfolded and refolded in every cycle. However, when BiP was added, the frequency of folding events of MJ0366 significantly decreased, and the loss of folding always occurred after a successful unfolding event. This process was dependent on ATP and ADP, since when either ATP was decreased or ADP was added, the duration of periods without folding events increased. Our results show that the affinity of BiP for the substrate protein increased in these conditions, which correlates with previous studies in bulk. Therefore, we conclude that BiP binds to the unfolded state of MJ0366 and prevents its refolding, and that this effect is dependent on both the type and concentration of nucleotides.
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Affiliation(s)
- María Paz Ramírez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile.,Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Maira Rivera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Diego Quiroga-Roger
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Andrés Bustamante
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Marcela Vega
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
| | - Elias M Puchner
- Laboratory of Cellular and Molecular Biophysics, School of Physics & Astronomy, University of Minnesota, Twin Cities, Minnesota
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, RM, Chile
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34
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Hsu STD. Protein knotting through concatenation significantly reduces folding stability. Sci Rep 2016; 6:39357. [PMID: 27982106 PMCID: PMC5159899 DOI: 10.1038/srep39357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
Concatenation by covalent linkage of two protomers of an intertwined all-helical HP0242 homodimer from Helicobacter pylori results in the first example of an engineered knotted protein. While concatenation does not affect the native structure according to X-ray crystallography, the folding kinetics is substantially slower compared to the parent homodimer. Using NMR hydrogen-deuterium exchange analysis, we showed here that concatenation destabilises significantly the knotted structure in solution, with some regions close to the covalent linkage being destabilised by as much as 5 kcal mol-1. Structural mapping of chemical shift perturbations induced by concatenation revealed a pattern that is similar to the effect induced by concentrated chaotrophic agent. Our results suggested that the design strategy of protein knotting by concatenation may be thermodynamically unfavourable due to covalent constrains imposed on the flexible fraying ends of the template structure, leading to rugged free energy landscape with increased propensity to form off-pathway folding intermediates.
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Affiliation(s)
- Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
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35
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Thiruselvam V, Kumarevel T, Karthe P, Kuramitsu S, Yokoyama S, Ponnuswamy MN. Crystal structure analysis of a hypothetical protein (MJ0366) from Methanocaldococcus jannaschii revealed a novel topological arrangement of the knot fold. Biochem Biophys Res Commun 2016; 482:264-269. [PMID: 27845039 DOI: 10.1016/j.bbrc.2016.11.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 11/10/2016] [Indexed: 01/30/2023]
Abstract
The crystal structure of a hypothetical protein MJ0366, derived from Methanocaldococcus jannaschii was solved at 1.9 Å resolution using synchrotron radiation. MJ0366 was crystallized as a monomer and has knot structural arrangement. Intriguingly, the solved structure consists of novel 'KNOT' fold conformation. The 31 trefoil knot was observed in the structure. The N-terminal and C-terminal ends did not participate in knot formation.
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Affiliation(s)
- Viswanathan Thiruselvam
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, India
| | - Thirumananseri Kumarevel
- RIKEN Structural Biology Laboratory, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan.
| | - Ponnuraj Karthe
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, 600025, India
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
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36
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Jackson SE, Suma A, Micheletti C. How to fold intricately: using theory and experiments to unravel the properties of knotted proteins. Curr Opin Struct Biol 2016; 42:6-14. [PMID: 27794211 DOI: 10.1016/j.sbi.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/06/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022]
Abstract
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out.
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Affiliation(s)
- Sophie E Jackson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
| | - Antonio Suma
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy.
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37
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Folding analysis of the most complex Stevedore's protein knot. Sci Rep 2016; 6:31514. [PMID: 27527519 PMCID: PMC4985754 DOI: 10.1038/srep31514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/21/2016] [Indexed: 12/21/2022] Open
Abstract
DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS. Three single-tryptophan variants (W34, W53, and W196) were generated to probe non-cooperative unfolding events localized around the three fluorophores. Kinetic fluorescence measurements indicated that the transition from the intermediate I' to the unfolded state is rate limiting. Our multiparametric folding analyses suggest that DehI unfolds through a linear folding pathway with two distinct folding intermediates by initial hydrophobic collapse followed by nucleation condensation, and that knotting precedes the formation of secondary structures.
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38
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Abstract
Spontaneous folding of a polypeptide chain into a knotted structure remains one of the most puzzling and fascinating features of protein folding. The folding of knotted proteins is on the timescale of minutes and thus hard to reproduce with atomistic simulations that have been able to reproduce features of ultrafast folding in great detail. Furthermore, it is generally not possible to control the topology of the unfolded state. Single-molecule force spectroscopy is an ideal tool for overcoming this problem: by variation of pulling directions, we controlled the knotting topology of the unfolded state of the 52-knotted protein ubiquitin C-terminal hydrolase isoenzyme L1 (UCH-L1) and have therefore been able to quantify the influence of knotting on its folding rate. Here, we provide direct evidence that a threading event associated with formation of either a 31 or 52 knot, or a step closely associated with it, significantly slows down the folding of UCH-L1. The results of the optical tweezers experiments highlight the complex nature of the folding pathway, many additional intermediate structures being detected that cannot be resolved by intrinsic fluorescence. Mechanical stretching of knotted proteins is also of importance for understanding the possible implications of knots in proteins for cellular degradation. Compared with a simple 31 knot, we measure a significantly larger size for the 52 knot in the unfolded state that can be further tightened with higher forces. Our results highlight the potential difficulties in degrading a 52 knot compared with a 31 knot.
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39
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Lou SC, Wetzel S, Zhang H, Crone EW, Lee YT, Jackson SE, Hsu STD. The Knotted Protein UCH-L1 Exhibits Partially Unfolded Forms under Native Conditions that Share Common Structural Features with Its Kinetic Folding Intermediates. J Mol Biol 2016; 428:2507-2520. [PMID: 27067109 DOI: 10.1016/j.jmb.2016.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 04/02/2016] [Indexed: 10/22/2022]
Abstract
The human ubiquitin C-terminal hydrolase, UCH-L1, is an abundant neuronal deubiquitinase that is associated with Parkinson's disease. It contains a complex Gordian knot topology formed by the polypeptide chain alone. Using a combination of fluorescence-based kinetic measurements, we show that UCH-L1 has two distinct kinetic folding intermediates that are transiently populated on parallel pathways between the denatured and native states. NMR hydrogen-deuterium exchange (HDX) experiments indicate the presence of partially unfolded forms (PUFs) of UCH-L1 under native conditions. HDX measurements as a function of urea concentration were used to establish the structure of the PUFs and pulse-labelled HDX NMR was used to show that the PUFs and the folding intermediates are likely the same species. In both cases, a similar stable core encompassing most of the central β-sheet is highly structured and α-helix 3, which is partially formed, packs against it. In contrast to the stable β-sheet core, the peripheral α-helices display significant local fluctuations leading to rapid exchange. The results also suggest that the main difference between the two kinetic intermediates is structure and packing of α-helices 3 and 7 and the degree of structure in β-strand 5. Together, the fluorescence and NMR results establish that UCH-L1 neither folds through a continuum of pathways nor by a single discrete pathway. Its folding is complex, the β-sheet core forms early and is present in both intermediate states, and the rate-limiting step which is likely to involve the threading of the chain to form the 52-knot occurs late on the folding pathway.
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Affiliation(s)
- Shih-Chi Lou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Svava Wetzel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Hongyu Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Elizabeth W Crone
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Yun-Tzai Lee
- Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Sophie E Jackson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Shang-Te Danny Hsu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
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40
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Dabrowski-Tumanski P, Jarmolinska AI, Sulkowska JI. Prediction of the optimal set of contacts to fold the smallest knotted protein. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354109. [PMID: 26291339 DOI: 10.1088/0953-8984/27/35/354109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.
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Affiliation(s)
- P Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland. Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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41
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Wang LW, Liu YN, Lyu PC, Jackson SE, Hsu STD. Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354106. [PMID: 26290953 DOI: 10.1088/0953-8984/27/35/354106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.
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Affiliation(s)
- Liang-Wei Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan. Institute of Biochemical Science, National Taiwan University, Taipei 116, Taiwan. Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
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42
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Shih PM, Wang I, Lee YTC, Hsieh SJ, Chen SY, Wang LW, Huang CT, Chien CT, Chang CY, Hsu STD. Random-Coil Behavior of Chemically Denatured Topologically Knotted Proteins Revealed by Small-Angle X-ray Scattering. J Phys Chem B 2015; 119:5437-43. [DOI: 10.1021/acs.jpcb.5b01984] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Po-Min Shih
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Iren Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Yun-Tzai Cloud Lee
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Shu-Ju Hsieh
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Szu-Yu Chen
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Liang-Wei Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Chih-Ting Huang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Chih-Ta Chien
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Chia-Yun Chang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 106, Taiwan
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