1
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Noel JK, Haglund E. Topological Reaction Coordinate Captures the Folding Transition State Ensemble in a Pierced Lasso Protein. J Phys Chem B 2024; 128:117-124. [PMID: 38118146 DOI: 10.1021/acs.jpcb.3c06678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Proteins with a pierced lasso topology (PLT) have a covalent loop created by a disulfide bond, and the backbone circles back to thread the loop. This threaded topology has unique features compared to knotted topologies; notably, the topology is controlled by the chemical environment and the covalent loop remains intact even when denatured. In this work, we use the hormone leptin as our model PLT system and study its folding using molecular dynamics simulations that employ a structure-based (Go̅-like) model. We find that the reduced protein has a two-state folding mechanism with a transition state ensemble (TSE) that can be characterized by the reaction coordinate Q, the fraction of native contacts formed. In contrast, the oxidized protein, which must thread part of the polypeptide chain through a covalent loop, has a folding process that is poorly characterized by Q. Instead, we find that a topological coordinate that monitors the residue crossing the loop can identify the TSE of oxidized leptin. By precisely identifying the predicted TSE, one may now reliably calculate theoretical phi-values for the PLT protein, thereby enabling a comparison with experimental measurements. We find the loop-threading constraint leads to noncanonical phi-values that are uniformly small because this PLT protein has a flat energy landscape through the TSE.
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Affiliation(s)
- Jeffrey K Noel
- Structural Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii, Manoa, Honolulu, Hawaii 96822, United States
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2
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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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3
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Tripathi P, Mehrafrooz B, Aksimentiev A, Jackson SE, Gruebele M, Wanunu M. A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein. J Phys Chem Lett 2023; 14:10719-10726. [PMID: 38009629 PMCID: PMC11176711 DOI: 10.1021/acs.jpclett.3c02183] [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] [Indexed: 11/29/2023]
Abstract
Knotted proteins are rare but important species, yet how their complex topologies affect their physical properties is not fully understood. Here we combine single molecule nanopore experiments and all-atom MD simulations to study the electric-field-driven unfolding during the translocation through a model pore of individual protein knots important for methylating tRNA. One of these knots shows an unusual behavior that resembles the behavior of electrons hopping between two potential surfaces: as the electric potential driving the translocation reaction is increased, the rate eventually plateaus or slows back down in the "Marcus inverted regime". Our results shed light on the influence of topology in knotted proteins on their forced translocation through a pore connecting two electrostatic potential wells.
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Affiliation(s)
- Prabhat Tripathi
- Department of Chemistry, Indian Institute of Technology (Banaras Hindu University), Varanasi, UP-221005, India
| | - Behzad Mehrafrooz
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Sophie E. Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield `Road, Cambridge CB2 1EW, UK
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA-02115, USA
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4
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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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5
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Ozmaian M, Makarov DE. Long-lived metastable knots in polyampholyte chains. PLoS One 2023; 18:e0287200. [PMID: 37315055 PMCID: PMC10266668 DOI: 10.1371/journal.pone.0287200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023] Open
Abstract
Knots in proteins and DNA are known to have significant effect on their equilibrium and dynamic properties as well as on their function. While knot dynamics and thermodynamics in electrically neutral and uniformly charged polymer chains are relatively well understood, proteins are generally polyampholytes, with varied charge distributions along their backbones. Here we use simulations of knotted polymer chains to show that variation in the charge distribution on a polyampholyte chain with zero net charge leads to significant variation in the resulting knot dynamics, with some charge distributions resulting in long-lived metastable knots that escape the (open-ended) chain on a timescale that is much longer than that for knots in electrically neutral chains. The knot dynamics in such systems can be described, quantitatively, using a simple one-dimensional model where the knot undergoes biased Brownian motion along a "reaction coordinate", equal to the knot size, in the presence of a potential of mean force. In this picture, long-lived knots result from charge sequences that create large electrostatic barriers to knot escape. This model allows us to predict knot lifetimes even when those times are not directly accessible by simulations.
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Affiliation(s)
- Masoumeh Ozmaian
- College of Engineering, West Texas A&M University, Canyon, Texas, United States of America
| | - Dmitrii E. Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States of America
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, United States of America
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6
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Dahlstrom TJ, Capraro DT, Jennings PA, Finke JM. Knotting Optimization and Folding Pathways of a Go-Model with a Deep Knot. J Phys Chem B 2022; 126:10221-10236. [PMID: 36424347 DOI: 10.1021/acs.jpcb.2c05588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Formation of protein knots is an intriguing offshoot of the protein folding problem. Since experimental resolution on knot formation is limited, theoretical methods currently provide the most detailed insights into the knotting process. While suitable for shallow knots, molecular dynamics simulations have faced challenges capturing the formation of deep knots in proteins such as the minimally tied trefoil α/β methyltransferase from Thermotoga maritima (MTTTM). To improve the efficiency of MTTTM knotting in Cα Go-model simulations, mutant variants of the MTTTM Go-model were investigated. Through a structure-based analysis of knotted and unknotted states, four residues (K71, R72, E75, V76) were identified to increase the knotting efficiency from 2% to 83% when their contact energies were doubled and dihedral strength around the knot loop increased. The key features of this model are (i) a C-terminal slipknot intermediate that threads the knot in a highly unstructured intermediate, (ii) the inability to knot in native-like intermediate states, and (iii) a minor population in a long-lived trap that cannot knot. Examination of residue 71-76 contacts provides a small set of potential mutants that can directly test the model's validity. In addition, the knotting optimization process developed here has broad applicability in generating knotting-efficient models of other knotted proteins.
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Affiliation(s)
- Thomas J Dahlstrom
- Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States
| | - Dominique T Capraro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California92093, United States
| | - Particia A Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California92093, United States
| | - John M Finke
- Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States
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7
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Xu Y, Kang R, Ren L, Yang L, Yue T. Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations. Biomolecules 2021; 11:1688. [PMID: 34827686 PMCID: PMC8615548 DOI: 10.3390/biom11111688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The knot is one of the most remarkable topological features identified in an increasing number of proteins with important functions. However, little is known about how the knot is formed during protein folding, and untied or maintained in protein unfolding. By means of all-atom molecular dynamics simulation, here we employ methyltransferase YbeA as the knotted protein model to analyze changes of the knotted conformation coupled with protein unfolding under thermal and mechanical denaturing conditions. Our results show that the trefoil knot in YbeA is occasionally untied via knot loosening rather than sliding under enhanced thermal fluctuations. Through correlating protein unfolding with changes in the knot position and size, several aspects of barriers that jointly suppress knot untying are revealed. In particular, protein unfolding is always prior to knot untying and starts preferentially from separation of two α-helices (α1 and α5), which protect the hydrophobic core consisting of β-sheets (β1-β4) from exposure to water. These β-sheets form a loop through which α5 is threaded to form the knot. Hydrophobic and hydrogen bonding interactions inside the core stabilize the loop against loosening. In addition, residues at N-terminal of α5 define a rigid turning to impede α5 from sliding out of the loop. Site mutations are designed to specifically eliminate these barriers, and easier knot untying is achieved under the same denaturing conditions. These results provide new molecular level insights into the folding/unfolding of knotted proteins.
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Affiliation(s)
- Yan Xu
- College of Electronic Engineering and Automation, Shandong University of Science and Technology, Qingdao 266590, China;
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China;
| | - Runshan Kang
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China;
| | - Luyao Ren
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
| | - Lin Yang
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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8
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Especial JNC, Faísca PFN. A Specific Set of Heterogeneous Native Interactions Yields Efficient Knotting in Protein Folding. J Phys Chem B 2021; 125:7359-7367. [PMID: 34197706 DOI: 10.1021/acs.jpcb.1c03127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Native interactions are crucial for folding, and non-native interactions appear to be critical for efficiently knotting proteins. Therefore, it is important to understand both their roles in the folding of knotted proteins. It has been proposed that non-native interactions drive the correct order of contact formation, which is essential to avoid backtracking and efficiently self-tie. In this study, we ask if non-native interactions are strictly necessary to tangle a protein or if the correct order of contact formation can be assured by a specific set of native, but otherwise heterogeneous (i.e., having distinct energies), interactions. In order to address this problem, we conducted extensive Monte Carlo simulations of lattice models of protein-like sequences designed to fold into a preselected knotted conformation embedding a trefoil knot. We were able to identify a specific set of heterogeneous native interactions that drives efficient knotting and is able to fold the protein when combined with the remaining native interactions modeled as homogeneous. This specific set of heterogeneous native interactions is strictly enough to efficiently self-tie. A distinctive feature of these native interactions is that they do not backtrack because their energies ensure the correct order of contact formation. Furthermore, they stabilize a knotted intermediate state, which is en route to the native structure. Our results thus show that-at least in the context of the adopted model-non-native interactions are not necessary to knot a protein. However, when they are taken into account in protein energetics, it is possible to find specific, nonlocal non-native interactions that operate as a scaffold that assists the knotting step.
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Affiliation(s)
- João N C Especial
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal
| | - Patrícia F N Faísca
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.,BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal
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9
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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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10
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Caraglio M, Marcone B, Baldovin F, Orlandini E, Stella AL. Topological Disentanglement of Linear Polymers under Tension. Polymers (Basel) 2020; 12:E2580. [PMID: 33153057 PMCID: PMC7692779 DOI: 10.3390/polym12112580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 01/01/2023] Open
Abstract
We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semiflexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of crossings and the minimal knot contour length are the topological invariants playing a key role in the model. The crossings behave as particles diffusing along the chain and the application of appropriate boundary conditions at the ends of the chain accounts for the knot disentanglement. Starting from the number of particles and their positions, suitable rules allow reconstructing the type and location of the knot moving on the chain Our theory is extensively benchmarked with corresponding molecular dynamics simulations and the results show a remarkable agreement between the simulations and the theoretical predictions of the model.
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Affiliation(s)
- Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Boris Marcone
- Istituto Tecnico Economico Tecnologico Statale ‘L. Einaudi’, via Tommaso D’Aquino 8, I-36061 Bassano del Grappa, Italy;
| | - Fulvio Baldovin
- Dipartimento di Fisica e Astronomia and Sezione INFN Università di Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.B.); (E.O.); (A.L.S.)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN Università di Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.B.); (E.O.); (A.L.S.)
| | - Attilio L. Stella
- Dipartimento di Fisica e Astronomia and Sezione INFN Università di Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.B.); (E.O.); (A.L.S.)
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11
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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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12
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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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13
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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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14
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Abstract
The origin of protein backbone threading through a topological knot remains elusive. To understand the evolutionary origin of protein knots, in this issue of StructureKo et al. (2019) used circular permutation to untie a knotted protein. They showed that a domain-swapped dimer releases the knot and the associated high-energy state for substrate binding.
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15
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Caprice K, Aster A, Cougnon FBL, Kumpulainen T. Untying the Photophysics of Quinolinium-Based Molecular Knots and Links. Chemistry 2020; 26:1576-1587. [PMID: 31670851 DOI: 10.1002/chem.201904456] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Indexed: 01/08/2023]
Abstract
Complex molecular knots and links are still difficult to synthesize and the properties arising from their topology are mostly unknown. Here, we report on a comparative photophysical study carried out on a family of closely related quinolinium-based knots and links to determine the impact exerted by topology on the molecular backbone. Our results indicate that topology has a negligible influence on the behavior of loosely braided molecules, which mostly behave like their unbraided equivalents. On the other hand, tightly braided molecules display distinct features. Their higher packing density results in a pronounced ability to resist deformation, a significant reduction in the solvent-accessible surface area and favors close-range π-π interactions between the quinolinium units and neighboring aromatics. Finally, the sharp alteration in behavior between loosely and tightly braided molecules sheds light on the factors contributing to braiding tightness.
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Affiliation(s)
- Kenji Caprice
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest Ansermet, Geneva, Switzerland
| | - Alexander Aster
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest Ansermet, Geneva, Switzerland
| | - Fabien B L Cougnon
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest Ansermet, Geneva, Switzerland
| | - Tatu Kumpulainen
- Department of Physical Chemistry, University of Geneva, 30 Quai Ernest Ansermet, Geneva, Switzerland
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16
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Xu Y, Li S, Yan Z, Ge B, Huang F, Yue T. Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations. J Phys Chem Lett 2019; 10:5815-5822. [PMID: 31525988 DOI: 10.1021/acs.jpclett.9b02209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The topological knot is thought to play a stabilizing role in maintaining the global fold and nature of proteins with the underlying mechanism yet to be elucidated. Given that most proteins containing trefoil knots exist and function as homodimers with a large part of the dimer interface occupied by the knotted region, we reason that the knotted conformation cooperates with dimerization in protein stabilization. Here, we take YbeA from Escherichia coli as the knotted protein model, using molecular dynamics (MD) simulations to compare the stability of two pairs of dimeric proteins having the same sequence and secondary structures but differing in the presence or absence of a trefoil knot in each subunit. The dimer interface of YbeA is identified to involve favorable contacts among three α-helices (α1, α3, and α5), one of which (α5) is threaded through a loop connected with α3 to form the knot. Upon removal of the knot by appropriate change of the knot-making crossing of the polypeptide chain, relevant domains are less constrained and exhibit enhanced fluctuations to decrease contacts at the interface. Unknotted subunits are less compact and undergo structural changes to ease the dimer separation. Such a stabilizing effect is evidenced by steered MD simulations, showing that the mechanical force required for dimer separation is significantly reduced by removing the knot. In addition to the knotted conformation, dimerization further improves the protein stability by restricting the α1-α5 separation, which is defined as a leading step for protein unfolding. These results provide important insights into the structure-function relationship of dimerization in knotted proteins.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
- College of Electronic Engineering and Automation , Shandong University of Science and Technology , Qingdao 266590 , China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Zengshuai Yan
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
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17
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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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18
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Karasev MM, Stepanenko OV, Rumyantsev KA, Turoverov KK, Verkhusha VV. Near-Infrared Fluorescent Proteins and Their Applications. BIOCHEMISTRY (MOSCOW) 2019; 84:S32-S50. [PMID: 31213194 DOI: 10.1134/s0006297919140037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
High transparency, low light-scattering, and low autofluorescence of mammalian tissues in the near-infrared (NIR) spectral range (~650-900 nm) open a possibility for in vivo imaging of biological processes at the micro- and macroscales to address basic and applied problems in biology and biomedicine. Recently, probes that absorb and fluoresce in the NIR optical range have been engineered using bacterial phytochromes - natural NIR light-absorbing photoreceptors that regulate metabolism in bacteria. Since the chromophore in all these proteins is biliverdin, a natural product of heme catabolism in mammalian cells, they can be used as genetically encoded fluorescent probes, similarly to GFP-like fluorescent proteins. In this review, we discuss photophysical and biochemical properties of NIR fluorescent proteins, reporters, and biosensors and analyze their characteristics required for expression of these molecules in mammalian cells. Structural features and molecular engineering of NIR fluorescent probes are discussed. Applications of NIR fluorescent proteins and biosensors for studies of molecular processes in cells, as well as for tissue and organ visualization in whole-body imaging in vivo, are described. We specifically focus on the use of NIR fluorescent probes in advanced imaging technologies that combine fluorescence and bioluminescence methods with photoacoustic tomography.
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Affiliation(s)
- M M Karasev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Medicum, University of Helsinki, Helsinki, 00290, Finland
| | - O V Stepanenko
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - K A Rumyantsev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - K K Turoverov
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia. .,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - V V Verkhusha
- Medicum, University of Helsinki, Helsinki, 00290, Finland. .,Albert Einstein College of Medicine, Bronx, NY 10461, USA
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19
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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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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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Xu Y, Li S, Yan Z, Luo Z, Ren H, Ge B, Huang F, Yue T. Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations. Biophys J 2018; 115:1681-1689. [PMID: 30314655 PMCID: PMC6225051 DOI: 10.1016/j.bpj.2018.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/11/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022] Open
Abstract
A growing number of proteins have been identified as knotted in their native structures, with such entangled topological features being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal, and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot. One protein is YbeA from Escherichia coli, containing a deep trefoil knot within the sequence, and the other is the modified protein with the knot of YbeA being removed. Under certain chemical denaturing conditions, the unknotted protein fully unfolds whereas the knotted protein does not, suggesting a higher intrinsic stability for the protein having a knot. Both proteins unfold under enhanced thermal fluctuations but at different rates and with distinct pathways. Opening the hydrophobic core via separation between two α-helices is identified as a crucial step initiating the protein unfolding, which, however, is restrained for the knotted protein by topological and geometrical frustrations. Energy barriers for denaturing the protein are reduced by removing the knot, as evidenced by mechanical unfolding simulations. Finally, yet importantly, no obvious change in size or location of the knot was observed during denaturing processes, indicating that YbeA may remain knotted for a relatively long time during and after denaturation.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Shixin Li
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zengshuai Yan
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zhen Luo
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Hao Ren
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Baosheng Ge
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China; Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China.
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24
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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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25
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The Pathways of the iRFP713 Unfolding Induced by Different Denaturants. Int J Mol Sci 2018; 19:ijms19092776. [PMID: 30223568 PMCID: PMC6163377 DOI: 10.3390/ijms19092776] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
Near-infrared fluorescent proteins (NIR FPs) based on the complexes of bacterial phytochromes with their natural biliverdin chromophore are widely used as genetically encoded optical probes for visualization of cellular processes and deep-tissue imaging of cells and organs in living animals. In this work, we show that the steady-state and kinetic dependencies of the various spectral characteristics of iRFP713, developed from the bacterial phytochrome RpBphP2 and recorded at protein unfolding induced by guanidine hydrochloride (GdnHCl), guanidine thiocyanate (GTC), and urea, differ substantially. A study of the unfolding of three single-tryptophan mutant forms of iRFP713 expectedly revealed that protein unfolding begins with the dissociation of the native dimer, while the monomers remain compact. A further increase in the denaturant concentration leads to the formation of an intermediate state of iRFP713 having hydrophobic areas exposed on the protein surface (I). The total surface charge of iRFP713 (pI 5.86) changes from negative to positive with an increase in the concentration of GdnHCl and GTC because the negative charge of glutamic and aspartic acids is neutralized by forming salt bridges between the carboxyl groups and GdnH+ ions and because the guanidinium cations bind to amide groups of glutamines and asparagines. The coincidence of both the concentration of the denaturants at which the intermediate state of iRFP713 accumulates and the concentration of GdnH+ ions at which the neutralization of the surface charge of the protein in this state is ensured results in strong protein aggregation. This is evidently realized by iRFP713 unfolding by GTC. At the unfolding of the protein by GdnHCl, an intermediate state is populated at higher denaturant concentrations and a strong aggregation is not observed. As expected, protein aggregates are not formed in the presence of the urea. The aggregation of the protein upon neutralization of the charge on the macromolecule surface is the main indicator of the intermediate state of protein. The unfolded state of iRFP713, whose formation is accompanied by a significant decrease in the parameter A, was found to have a different residual structure in the denaturants used.
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26
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Wu J, Cheng C, Liu G, Zhang P, Chen T. The folding pathways and thermodynamics of semiflexible polymers. J Chem Phys 2018; 148:184901. [PMID: 29764123 DOI: 10.1063/1.5018114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm. However, the population of the intermediates in the unfolding process is very low, insufficient to induce unfolding arm rollover. The total types of folding pathways from the coil state to the toroidal state for a semiflexible polymer chain remain unchanged by varying the solvent quality or temperature, whereas the kinetic partitioning into different folding events can be tuned significantly. In the process of knotting, three types of mechanisms, namely, plugging, slipknotting, and sliding, are discovered. Along the folding evolution, a semiflexible homopolymer chain can knot at any stage of folding upon leaving the extended coil state, and the probability to find a knot increases with chain compactness. In addition, we find rich types of knotted topologies during the folding of a semiflexible homopolymer chain. This study should be helpful in gaining insight into the general principles of biopolymer folding.
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Affiliation(s)
- 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, People's Republic of China
| | - 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, People's Republic of 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, People's Republic of China
| | - Ping Zhang
- 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, People's Republic of 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, People's Republic of China
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27
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Tubiana L, Polles G, Orlandini E, Micheletti C. KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:72. [PMID: 29884956 DOI: 10.1140/epje/i2018-11681-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .
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Affiliation(s)
- Luca Tubiana
- Computational Physics Department, University of Vienna, Sensengasse 8/10, 1090, Vienna, Austria.
| | - Guido Polles
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 90089, Los Angeles, CA, USA
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, 35131, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, Via Bonomea 265, I-34136, Trieste, Italy
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28
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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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29
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The energy cost of polypeptide knot formation and its folding consequences. Nat Commun 2017; 8:1581. [PMID: 29146980 PMCID: PMC5691195 DOI: 10.1038/s41467-017-01691-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/09/2017] [Indexed: 11/08/2022] Open
Abstract
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain—an event that can potentially impair its folding—and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol−1. Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin. This cost is predicted to remain above 3 kcal mol−1 for denatured proteins as large as 900 residues. Therefore, we conclude that naturally knotted proteins cannot attain their knot randomly in the unfolded state but must pay the cost of knotting through contacts along their folding landscape. The effect of knots on protein stability and folding kinetics is not well understood. Here the authors combine optical tweezer experiments and calculations to experimentally determine the energy cost for knot formation, which indicates that knotted proteins evolved specific folding pathways because knot formation in unfolded chains is unfavorable.
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30
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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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31
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Niewieczerzal S, Sulkowska JI. Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume. PLoS One 2017; 12:e0176744. [PMID: 28489858 PMCID: PMC5425179 DOI: 10.1371/journal.pone.0176744] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/14/2017] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations are used to explore the effects of chaperonin-like cages on knotted proteins with very low sequence similarity, different depths of a knot but with a similar fold, and the same type of topology. The investigated proteins are VirC2, DndE and MJ0366 with two depths of a knot. A comprehensive picture how encapsulation influences folding rates is provided based on the analysis of different cage sizes and temperature conditions. Neither of these two effects with regard to knotted proteins has been studied by means of molecular dynamics simulations with coarse-grained structure-based models before. We show that encapsulation in a chaperonin is sufficient to self-tie and untie small knotted proteins (VirC2, DndE), for which the equilibrium process is not accessible in the bulk solvent. Furthermore, we find that encapsulation reduces backtracking that arises from the destabilisation of nucleation sites, smoothing the free energy landscape. However, this effect can also be coupled with temperature rise. Encapsulation facilitates knotting at the early stage of folding and can enhance an alternative folding route. Comparison to unknotted proteins with the same fold shows directly how encapsulation influences the free energy landscape. In addition, we find that as the size of the cage decreases, folding times increase almost exponentially in a certain range of cage sizes, in accordance with confinement theory and experimental data for unknotted proteins.
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Affiliation(s)
- Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna I. Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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32
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Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Sci Rep 2017; 7:969. [PMID: 28428565 PMCID: PMC5430550 DOI: 10.1038/s41598-017-01186-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/23/2017] [Indexed: 11/24/2022] Open
Abstract
Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site. One monomer provides the SAM-binding site, whereas the conserved C-terminal tail of the second monomer provides residues essential for catalysis. Our findings elucidate the mechanism by which a small protein dimer assembles a functionally asymmetric architecture.
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33
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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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34
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Cao PF, Rong LH, Mangadlao JD, Advincula RC. Synthesizing a Trefoil Knotted Block Copolymer via Ring-Expansion Strategy. Macromolecules 2017. [DOI: 10.1021/acs.macromol.6b02029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Peng-Fei Cao
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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35
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Haglund E, Pilko A, Wollman R, Jennings PA, Onuchic JN. Pierced Lasso Topology Controls Function in Leptin. J Phys Chem B 2017; 121:706-718. [PMID: 28035835 DOI: 10.1021/acs.jpcb.6b11506] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein engineering is a powerful tool in drug design and therapeutics, where disulphide bridges are commonly introduced to stabilize proteins. However, these bonds also introduce covalent loops, which are often neglected. These loops may entrap the protein backbone on opposite sides, leading to a "knotted" topology, forming a so-called Pierced Lasso (PL). In this elegant system, the "knot" is held together with a single disulphide bridge where part of the polypeptide chain is threaded through. The size and position of these covalent loops can be manipulated through protein design in vitro, whereas nature uses polymorphism to switch the PL topology. The PL protein leptin shows genetic modification of an N-terminal residue, adding a third cysteine to the same sequence. In an effort to understand the mechanism of threading of these diverse topologies, we designed three loop variants to mimic the polymorphic sequence. This adds elegance to the system under study, as it allows the generation of three possible covalent loops; they are the original wild-type C-terminal loop protein, the fully circularized unthreaded protein, and the N-terminal loop protein, responsible for different lasso topologies. The size of the loop changes the threading mechanism from a slipknotting to a plugging mechanism, with increasing loop size. Interestingly, the ground state of the native protein structure is largely unaffected, but biological assays show that the activity is maximized by properly controlled dynamics in the threaded state. A threaded topology with proper conformational dynamics is important for receptor interaction and activation of the signaling pathways in vivo.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biosciences, Rice University , Houston, Texas, United States
| | - Anna Pilko
- Department of Chemistry and Biochemistry, The University of California, San Diego (UCSD) , La Jolla, California, United States
| | - Roy Wollman
- Department of Chemistry and Biochemistry, The University of California, San Diego (UCSD) , La Jolla, California, United States
| | - Patricia Ann Jennings
- Department of Chemistry and Biochemistry, The University of California, San Diego (UCSD) , La Jolla, California, United States
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biosciences, Rice University , Houston, Texas, United States
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36
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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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37
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Untangling the Influence of a Protein Knot on Folding. Biophys J 2016; 110:1044-51. [PMID: 26958882 DOI: 10.1016/j.bpj.2016.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 01/01/2016] [Accepted: 01/14/2016] [Indexed: 10/22/2022] Open
Abstract
Entanglement and knots occur across all aspects of the physical world. Despite the common belief that knots are too complicated for incorporation into proteins, knots have been identified in the native fold of a growing number of proteins. The discovery of proteins with this unique backbone characteristic has challenged the preconceptions about the complexity of biological structures, as well as current folding theories. Given the intricacies of the knotted geometry, the interplay between a protein's fold, structure, and function is of particular interest. Interestingly, for most of these proteins, the knotted region appears critical both in folding and function, although full understanding of these contributions is still incomplete. Here, we experimentally reveal the impact of the knot on the landscape, the origin of the bistable nature of the knotted protein, and broaden the view of knot formation as uniquely decoupled from folding.
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38
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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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39
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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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40
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Baiesi M, Orlandini E, Trovato A, Seno F. Linking in domain-swapped protein dimers. Sci Rep 2016; 6:33872. [PMID: 27659606 PMCID: PMC5034241 DOI: 10.1038/srep33872] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/05/2016] [Indexed: 11/24/2022] Open
Abstract
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, makes such dimers suitable candidates to validate the possibility that mutual entanglement between chains may play a similar role for protein complexes. We suggest that such entanglement is captured by the linking number. This represents, for two closed curves, the number of times that each curve winds around the other. We show that closing the curves is not necessary, as a novel parameter G', termed Gaussian entanglement, is strongly correlated with the linking number. Based on 110 non redundant domain-swapped dimers, our analysis evidences a high fraction of chains with a significant intertwining, that is with |G'| > 1. We report that Nature promotes configurations with negative mutual entanglement and surprisingly, it seems to suppress intertwining in long protein dimers. Supported by numerical simulations of dimer dissociation, our results provide a novel topology-based classification of protein-swapped dimers together with some preliminary evidence of its impact on their physical and biological properties.
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Affiliation(s)
- Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- INFN-Sezione di Padova, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- INFN-Sezione di Padova, Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- CNISM-Unità di Padova, Padova, Italy
| | - Flavio Seno
- Department of Physics and Astronomy, University of Padova, Padova, Italy
- CNISM-Unità di Padova, Padova, Italy
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41
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Pieters BJGE, van Eldijk MB, Nolte RJM, Mecinović J. Natural supramolecular protein assemblies. Chem Soc Rev 2016; 45:24-39. [PMID: 26497225 DOI: 10.1039/c5cs00157a] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Supramolecular protein assemblies are an emerging area within the chemical sciences, which combine the topological structures of the field of supramolecular chemistry and the state-of-the-art chemical biology approaches to unravel the formation and function of protein assemblies. Recent chemical and biological studies on natural multimeric protein structures, including fibers, rings, tubes, catenanes, knots, and cages, have shown that the quaternary structures of proteins are a prerequisite for their highly specific biological functions. In this review, we illustrate that a striking structural diversity of protein assemblies is present in nature. Furthermore, we describe structure-function relationship studies for selected classes of protein architectures, and we highlight the techniques that enable the characterisation of supramolecular protein structures.
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Affiliation(s)
- Bas J G E Pieters
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Mark B van Eldijk
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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42
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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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43
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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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44
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Chwastyk M, Cieplak M. Multiple folding pathways of proteins with shallow knots and co-translational folding. J Chem Phys 2016; 143:045101. [PMID: 26233164 DOI: 10.1063/1.4927153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.
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Affiliation(s)
- Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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45
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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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46
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Nikoofard N, Mashaghi A. Topology sorting and characterization of folded polymers using nano-pores. NANOSCALE 2016; 8:4643-4649. [PMID: 26853059 DOI: 10.1039/c5nr08828c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied: one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the molecule passes through the nano-pore. The topology of a folded polymer chain is defined as the arrangement of the intramolecular contacts, known as circuit topology. In the case where intramolecular contacts remain intact, we show that the dynamics of passage through a nano-pore varies for molecules with differing topologies: a phenomenon that can be exploited to enrich certain topologies in mixtures. We find that the nano-pore allows reading of the topology for short chains. Moreover, when the passage is coupled with unfolding, the nano-pore enables discrimination between pure states, i.e., states in which the majority of contacts are arranged identically. In this case, as we show here, it is also possible to read the positions of the contact sites along a chain. Our results demonstrate the applicability of nano-pore technology to characterize and sort molecules based on their topology.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 51167-87317, Iran
| | - Alireza Mashaghi
- Harvard Medical School, Harvard University, Boston, MA 02115, USA.
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47
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Aguirre C, Goto Y, Costas M. Thermal and chemical unfolding pathways of PaSdsA1 sulfatase, a homo-dimer with topologically interlinked chains. FEBS Lett 2016; 590:202-14. [PMID: 26823168 DOI: 10.1002/1873-3468.12041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/17/2015] [Accepted: 12/07/2015] [Indexed: 11/11/2022]
Abstract
Understanding the mechanisms as to how interlinked proteins entangle and fold is a challenge. PaSdsA1 sulfatase is a homo-dimer containing two zinc atoms per monomer. The monomer chains are interlinked in a dimerization domain. To study the unfolding pathways denaturation experiments were performed. In the native protein three forms coexist in chemical equilibrium, each with a different number of zinc atoms. In the chemical unfolding of the holo-dimers the entanglement of the chains is preserved and acts as a 'folding seed', allowing the unfolding process to be reversible. Thermal irreversible unfolding of the holo-dimers favours dissociation, producing monomers that are SDS-stabilized. The thermal unfolding of these monomers is reversible. However, it is not possible to form dimers from unfolded monomers.
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Affiliation(s)
- César Aguirre
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F, México
| | - Yuji Goto
- Protein Folding Laboratory, Institute for Protein Research, Osaka University, Japan
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México D. F, México
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48
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Potestio R, Tubiana L. Discretized knot motion on a tensioned fiber induced by transverse waves. SOFT MATTER 2016; 12:669-673. [PMID: 26510521 DOI: 10.1039/c5sm01766a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Topological entanglement is a ubiquitous feature of many biological as well as artificial polymers and fibers. While the equilibrium properties of entangled chains have been the subject of several studies, little is known about their out-of-equilibrium behavior. Here, we address the problem of a stretched knotted fiber driven by a periodic force applied to one of its termini. We show that the onset of standing waves kinetically traps the knot in spatially localized states where the amplitude of the oscillations is maximal, while the knot normal diffusive dynamics is replaced by a discrete jump dynamics.
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Affiliation(s)
- Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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49
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Chi H, Wang X, Li J, Ren H, Huang F. Folding of newly translated membrane protein CCR5 is assisted by the chaperonin GroEL-GroES. Sci Rep 2015; 5:17037. [PMID: 26585937 PMCID: PMC4653635 DOI: 10.1038/srep17037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/23/2015] [Indexed: 01/20/2023] Open
Abstract
The in vitro folding of newly translated human CC chemokine receptor type 5
(CCR5), which belongs to the physiologically important family of G protein-coupled
receptors (GPCRs), has been studied in a cell-free system supplemented with the
surfactant Brij-35. The freshly synthesized CCR5 can spontaneously fold into its
biologically active state but only slowly and inefficiently. However, on addition of
the GroEL-GroES molecular chaperone system, the folding of the nascent CCR5 was
significantly enhanced, as was the structural stability and functional expression of
the soluble form of CCR5. The chaperonin GroEL was partially effective on its own,
but for maximum efficiency both the GroEL and its GroES lid were necessary. These
results are direct evidence for chaperone-assisted membrane protein folding and
therefore demonstrate that GroEL-GroES may be implicated in the folding of membrane
proteins.
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Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jiqiang Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, P. R. China
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50
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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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