1
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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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2
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Gao M, Li P, Su Z, Huang Y. Topological frustration leading to backtracking in a coupled folding-binding process. Phys Chem Chem Phys 2022; 24:2630-2637. [PMID: 35029261 DOI: 10.1039/d1cp04927e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in all species. Their discovery challenges the traditional "sequence-structure-function" paradigm of protein science because IDPs play important roles in various biological processes without preformed folded structures. Bioinformatic analysis reveals that the intrinsically conformational disorder of IDPs as well as their conformational transition upon binding to their targets is encoded by their amino acid sequences. The rRNase domain of colicin E3 and the immunity protein Im3 are a pair of proteins involved in bacterial survival. While the N-terminal segment and the central segment of E3 make comparable intermolecular contacts with Im3 in the bound state, binding of E3 with Im3 is dominantly triggered by the central segment of E3. In this work, to further investigate the binding mechanism of disordered E3 with Im3, we performed systematic free energy and transition path analysis through coarse-grained molecular dynamics simulations. We observed backtracking of the N-terminal segment of E3 in the binding process, whose occurrence depends on salt concentration. Conformational analysis revealed that initial binding of the N-terminal segment of E3 to Im3 usually leads to misorientation of a central hairpin of E3 on Im3, which generates topological frustration and results in backtracking of the N-terminal segment. Our results not only provide deeper mechanistic insights into the coupled folding-binding process of the E3/Im3 complex, but also suggest that topological frustration could be present in the coupled folding-binding process of IDPs and play an important role in regulating the binding transition pathways.
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Affiliation(s)
- Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Ping Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan 430068, China.
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Department of Biological Engineering, Hubei University of Technology, Wuhan 430068, China
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3
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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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4
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Heidari M, Schiessel H, Mashaghi A. Circuit Topology Analysis of Polymer Folding Reactions. ACS CENTRAL SCIENCE 2020; 6:839-847. [PMID: 32607431 PMCID: PMC7318069 DOI: 10.1021/acscentsci.0c00308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Indexed: 06/03/2023]
Abstract
Circuit topology is emerging as a versatile measure to classify the internal structures of folded linear polymers such as proteins and nucleic acids. The topology framework can be applied to a wide range of problems, most notably molecular folding reactions that are central to biology and molecular engineering. In this Outlook, we discuss the state-of-the art of the technology and elaborate on the opportunities and challenges that lie ahead.
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Affiliation(s)
- Maziar Heidari
- Leiden
Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden2300 RA, The Netherlands
- Laboratoire
Gulliver, UMR 7083, ESPCI Paris and PSL
University, 75005 Paris, France
| | - Helmut Schiessel
- Institute
Lorentz for Theoretical Physics, Faculty of Science, Leiden University, Leiden 2333 CA, The Netherlands
| | - Alireza Mashaghi
- Leiden
Academic Centre for Drug Research, Faculty of Science, Leiden University, Leiden2300 RA, The Netherlands
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5
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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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6
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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: 36] [Impact Index Per Article: 9.0] [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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7
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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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8
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Especial J, Nunes A, Rey A, Faísca PF. Hydrophobic confinement modulates thermal stability and assists knotting in the folding of tangled proteins. Phys Chem Chem Phys 2019; 21:11764-11775. [PMID: 31114834 DOI: 10.1039/c9cp01701a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
There is growing support for the idea that the in vivo folding process of knotted proteins is assisted by chaperonins, but the mechanism of chaperonin assisted folding remains elusive. Here, we conduct extensive Monte Carlo simulations of lattice and off-lattice models to explore the effects of confinement and hydrophobic intermolecular interactions with the chaperonin cage in the folding and knotting processes. We find that moderate to high protein-cavity interactions (which are likely to be established in the beginning of the chaperonin working cycle) cause an energetic destabilization of the protein that overcomes the entropic stabilization driven by excluded volume, and leads to a decrease of the melting temperature relative to bulk conditions. Moreover, mild-to-moderate hydrophobic interactions with the cavity (which would be established later in the cycle) lead to a significant enhancement of knotting probability in relation to bulk conditions while simultaneously moderating the effect of steric confinement in the enhancement of thermal stability. Our results thus indicate that the chaperonin may be able to assist knotting without simultaneously thermally stabilizing potential misfolded states to a point that would hamper productive folding thus compromising its functional role.
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Affiliation(s)
- João Especial
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.
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9
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Abstract
How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. Motivated by the computer simulations of Bölinger et al. [Bölinger D, et al. (2010) PLoS Comput Biol 6:e1000731] for the folding of the [Formula: see text]-knotted α-haloacid dehalogenase (DehI) protein, we introduce a topological description of knot folding that could describe pathways for the formation of all currently known protein knot types and predicts knot types that might be identified in the future. We analyze fingerprint data from crystal structures of protein knots as evidence that particular protein knots may fold according to specific pathways from our theory. Our results confirm Taylor's twisted hairpin theory of knot folding for the [Formula: see text]-knotted proteins and the [Formula: see text]-knotted ketol-acid reductoisomerases and present alternative folding mechanisms for the [Formula: see text]-knotted phytochromes and the [Formula: see text]- and [Formula: see text]-knotted proteins.
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10
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Dabrowski-Tumanski P, Gren B, Sulkowska JI. Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function. Polymers (Basel) 2019; 11:E707. [PMID: 30999683 PMCID: PMC6523798 DOI: 10.3390/polym11040707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
Abstract
The shape and properties of closed loops depend on various topological factors. One of them is loop-threading, which is present in complex lasso proteins. In this work, we analyze the probability of loop-threading by the tail and its influence on the shape of the loop measured by the radius of gyration, distention, asphericity, and prolateness. In particular, we show that the probability of a trivial lasso for phantom polymer is non-zero even for an infinite structure, as well as that the threading flattens the loop by restricting its motion in one dimension. These results are further used to show that there are fewer non-trivial protein lassos than expected and select potentially functional complex lasso proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | - Bartosz Gren
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
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11
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12
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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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13
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Cheng C, Wu J, Liu G, Shi S, Chen T. Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement. J Phys Chem B 2018; 122:7654-7667. [DOI: 10.1021/acs.jpcb.8b04147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Chenqian Cheng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Gaoyuan Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Suqing Shi
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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14
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Zhao Y, Dabrowski-Tumanski P, Niewieczerzal S, Sulkowska JI. The exclusive effects of chaperonin on the behavior of proteins with 52 knot. PLoS Comput Biol 2018; 14:e1005970. [PMID: 29547629 PMCID: PMC5874080 DOI: 10.1371/journal.pcbi.1005970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 03/28/2018] [Accepted: 01/12/2018] [Indexed: 02/05/2023] Open
Abstract
The folding of proteins with a complex knot is still an unresolved question. Based on representative members of Ubiquitin C-terminal Hydrolases (UCHs) that contain the 52 knot in the native state, we explain how UCHs are able to unfold and refold in vitro reversibly within the structure-based model. In particular, we identify two, topologically different folding/unfolding pathways and corroborate our results with experiment, recreating the chevron plot. We show that confinement effect of chaperonin or weak crowding greatly facilitates folding, simultaneously slowing down the unfolding process of UCHs, compared with bulk conditions. Finally, we analyze the existence of knots in the denaturated state of UCHs. The results of the work show that the crowded environment of the cell should have a positive effect on the kinetics of complex knotted proteins, especially when proteins with deeper knots are found in this family. Self-tying of knotted proteins remains a challenge both for theoreticians and experimentalist. In this work, we study the proteins with complex, the 52 knot, in a bulk and confined within a chaperonin box. We show that in our model we recreate the experimental results, identify two topologically distinct folding pathways and explain the beneficial role of confinement for complex knotted proteins. Encapsulation provides a possibility to fold via alternative pathway—folding via trefoil intermediate knot (N-terminal pathway) from entropic reason while folding via the C-terminal (direct tying) appears with the same probability. The results of this work show, how crowded environment in the real cell may enhance self-tying of proteins. The results are also the first step to the identification of possible oligomerization-prone forms of UCHs, which may cause neurodegenerative diseases.
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Affiliation(s)
- Yani Zhao
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- * E-mail:
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15
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Lipid bilayer composition modulates the unfolding free energy of a knotted α-helical membrane protein. Proc Natl Acad Sci U S A 2018; 115:E1799-E1808. [PMID: 29432185 DOI: 10.1073/pnas.1714668115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
α-Helical membrane proteins have eluded investigation of their thermodynamic stability in lipid bilayers. Reversible denaturation curves have enabled some headway in determining unfolding free energies. However, these parameters have been limited to detergent micelles or lipid bicelles, which do not possess the same mechanical properties as lipid bilayers that comprise the basis of natural membranes. We establish reversible unfolding of the membrane transporter LeuT in lipid bilayers, enabling the comparison of apparent unfolding free energies in different lipid compositions. LeuT is a bacterial ortholog of neurotransmitter transporters and contains a knot within its 12-transmembrane helical structure. Urea is used as a denaturant for LeuT in proteoliposomes, resulting in the loss of up to 30% helical structure depending upon the lipid bilayer composition. Urea unfolding of LeuT in liposomes is reversible, with refolding in the bilayer recovering the original helical structure and transport activity. A linear dependence of the unfolding free energy on urea concentration enables the free energy to be extrapolated to zero denaturant. Increasing lipid headgroup charge or chain lateral pressure increases the thermodynamic stability of LeuT. The mechanical and charge properties of the bilayer also affect the ability of urea to denature the protein. Thus, we not only gain insight to the long-sought-after thermodynamic stability of an α-helical protein in a lipid bilayer but also provide a basis for studies of the folding of knotted proteins in a membrane environment.
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16
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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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17
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18
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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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