1
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Perlinska AP, Nguyen ML, Pilla SP, Staszor E, Lewandowska I, Bernat A, Purta E, Augustyniak R, Bujnicki JM, Sulkowska JI. Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. Front Mol Biosci 2024; 10:1223830. [PMID: 38903539 PMCID: PMC11187310 DOI: 10.3389/fmolb.2023.1223830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/04/2023] [Indexed: 06/22/2024] Open
Abstract
We have been aware of the existence of knotted proteins for over 30 years-but it is hard to predict what is the most complicated knot that can be formed in proteins. Here, we show new and the most complex knotted topologies recorded to date-double trefoil knots (31 #31). We found five domain arrangements (architectures) that result in a doubly knotted structure in almost a thousand proteins. The double knot topology is found in knotted membrane proteins from the CaCA family, that function as ion transporters, in the group of carbonic anhydrases that catalyze the hydration of carbon dioxide, and in the proteins from the SPOUT superfamily that gathers 31 knotted methyltransferases with the active site-forming knot. For each family, we predict the presence of a double knot using AlphaFold and RoseTTaFold structure prediction. In the case of the TrmD-Tm1570 protein, which is a member of SPOUT superfamily, we show that it folds in vitro and is biologically active. Our results show that this protein forms a homodimeric structure and retains the ability to modify tRNA, which is the function of the single-domain TrmD protein. However, how the protein folds and is degraded remains unknown.
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Affiliation(s)
| | - Mai Lan Nguyen
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Polish-Japanese Academy of Information Technology, Warsaw, Poland
| | - Smita P. Pilla
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Emilia Staszor
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | - Agata Bernat
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | | | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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2
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Niemyska W, Mukherjee S, Gren BA, Niewieczerzal S, Bujnicki JM, Sulkowska JI. Discovery of a trefoil knot in the RydC RNA: Challenging previous notions of RNA topology. J Mol Biol 2024; 436:168455. [PMID: 38272438 DOI: 10.1016/j.jmb.2024.168455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Knots are very common in polymers, including DNA and protein molecules. Yet, no genuine knot has been identified in natural RNA molecules to date. Upon re-examining experimentally determined RNA 3D structures, we discovered a trefoil knot 31, the most basic non-trivial knot, in the RydC RNA. This knotted RNA is a member of a small family of short bacterial RNAs, whose secondary structure is characterized by an H-type pseudoknot. Molecular dynamics simulations suggest a folding pathway of the RydC RNA that starts with a native twisted loop. Based on sequence analyses and computational RNA 3D structure predictions, we postulate that this trefoil knot is a conserved feature of all RydC-related RNAs. The first discovery of a knot in a natural RNA molecule introduces a novel perspective on RNA 3D structure formation and on fundamental research on the relationship between function and spatial structure of biopolymers.
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Affiliation(s)
- Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland
| | - Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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3
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da Silva FB, Simien JM, Viegas RG, Haglund E, Leite VBP. Exploring the folding landscape of leptin: Insights into threading pathways. J Struct Biol 2024; 216:108054. [PMID: 38065428 DOI: 10.1016/j.jsb.2023.108054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
The discovery of new protein topologies with entanglements and loop-crossings have shown the impact of local amino acid arrangement and global three-dimensional structures. This phenomenon plays a crucial role in understanding how protein structure relates to folding and function, affecting the global stability, and biological activity. Protein entanglements encompassing knots and non-trivial topologies add complexity to their folding free energy landscapes. However, the initial native contacts driving the threading event for entangled proteins remains elusive. The Pierced Lasso Topology (PLT) represents an entangled topology where a covalent linker creates a loop in which the polypeptide backbone is threaded through. Compared to true knotted topologies, PLTs are simpler topologies where the covalent-loop persists in all conformations. In this work, the PLT protein leptin, is used to visualize and differentiate the preference for slipknotting over plugging transition pathways along the folding route. We utilize the Energy Landscape Visualization Method (ELViM), a multidimensional projection technique, to visualize and distinguish early threaded conformations that cannot be observed in an in vitro experiment. Critical contacts for the leptin threading mechanisms were identified where the competing pathways are determined by the formation of a hairpin loop in the unfolded basin. Thus, prohibiting the dominant slipknotting pathway. Furthermore, ELViM offers insights into distinct folding pathways associated with slipknotting and plugging providing a novel tool for de novo design and in vitro experiments with residue specific information of threading events in silico.
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Affiliation(s)
- Fernando Bruno da Silva
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland; Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Jennifer M Simien
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Rafael G Viegas
- Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil; Federal Institute of Education, Science and Technology of São Paulo (IFSP), Catanduva, SP 15.808-305, Brazil
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States.
| | - Vitor Barbanti Pereira Leite
- Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil.
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4
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da Hora GCA, Oh M, Mifflin MC, Digal L, Roberts AG, Swanson JMJ. Lasso Peptides: Exploring the Folding Landscape of Nature's Smallest Interlocked Motifs. J Am Chem Soc 2024; 146:4444-4454. [PMID: 38166378 DOI: 10.1021/jacs.3c10126] [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] [Indexed: 01/04/2024]
Abstract
Lasso peptides make up a class of natural products characterized by a threaded structure. Given their small size and stability, chemical synthesis would offer tremendous potential for the development of novel therapeutics. However, the accessibility of the pre-folded lasso architecture has limited this advance. To better understand the folding process de novo, simulations are used herein to characterize the folding propensity of microcin J25 (MccJ25), a lasso peptide known for its antimicrobial properties. New algorithms are developed to unambiguously distinguish threaded from nonthreaded precursors and determine handedness, a key feature in natural lasso peptides. We find that MccJ25 indeed forms right-handed pre-lassos, in contrast to past predictions but consistent with all natural lasso peptides. Additionally, the native pre-lasso structure is shown to be metastable prior to ring formation but to readily transition to entropically favored unfolded and nonthreaded structures, suggesting that de novo lasso folding is rare. However, by altering the ring forming residues and appending thiol and thioester functionalities, we are able to increase the stability of pre-lasso conformations. Furthermore, conditions leading to protonation of a histidine imidazole side chain further stabilize the modified pre-lasso ensemble. This work highlights the use of computational methods to characterize lasso folding and demonstrates that de novo access to lasso structures can be facilitated by optimizing sequence, unnatural modifications, and reaction conditions like pH.
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Affiliation(s)
- Gabriel C A da Hora
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Myongin Oh
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Marcus C Mifflin
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Lori Digal
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jessica M J Swanson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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5
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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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6
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Hou Y, Xie T, He L, Tao L, Huang J. Topological links in predicted protein complex structures reveal limitations of AlphaFold. Commun Biol 2023; 6:1098. [PMID: 37898666 PMCID: PMC10613300 DOI: 10.1038/s42003-023-05489-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
AlphaFold is making great progress in protein structure prediction, not only for single-chain proteins but also for multi-chain protein complexes. When using AlphaFold-Multimer to predict protein‒protein complexes, we observed some unusual structures in which chains are looped around each other to form topologically intertwining links at the interface. Based on physical principles, such topological links should generally not exist in native protein complex structures unless covalent modifications of residues are involved. Although it is well known and has been well studied that protein structures may have topologically complex shapes such as knots and links, existing methods are hampered by the chain closure problem and show poor performance in identifying topologically linked structures in protein‒protein complexes. Therefore, we address the chain closure problem by using sliding windows from a local perspective and propose an algorithm to measure the topological-geometric features that can be used to identify topologically linked structures. An application of the method to AlphaFold-Multimer-predicted protein complex structures finds that approximately 1.72% of the predicted structures contain topological links. The method presented in this work will facilitate the computational study of protein‒protein interactions and help further improve the structural prediction of multi-chain protein complexes.
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Affiliation(s)
- Yingnan Hou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
| | - Tengyu Xie
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
| | - Liuqing He
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
| | - Liang Tao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China.
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China.
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7
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Flapan E, Mashaghi A, Wong H. A tile model of circuit topology for self-entangled biopolymers. Sci Rep 2023; 13:8889. [PMID: 37264056 DOI: 10.1038/s41598-023-35771-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
Building on the theory of circuit topology for intra-chain contacts in entangled proteins, we introduce tiles as a way to rigorously model local entanglements which are held in place by molecular forces. We develop operations that combine tiles so that entangled chains can be represented by algebraic expressions. Then we use our model to show that the only knot types that such entangled chains can have are [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and connected sums of these knots. This includes all proteins knots that have thus far been identified.
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Affiliation(s)
- Erica Flapan
- Mathematics and Statistics Department, Pomona College, Claremont, CA, 91711, USA.
| | - Alireza Mashaghi
- Faculty of Science, Leiden University, 2333CC, Leiden, The Netherlands
| | - Helen Wong
- Mathematical Sciences Department, Claremont McKenna College, Claremont, CA, 91711, USA
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8
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Sleiman JL, Burton RH, Caraglio M, Gutierrez Fosado YA, Michieletto D. Geometric Predictors of Knotted and Linked Arcs. ACS POLYMERS AU 2022; 2:341-350. [PMID: 36254317 PMCID: PMC9562465 DOI: 10.1021/acspolymersau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Inspired by how certain proteins “sense”
knots and
entanglements in DNA molecules, here, we ask if local geometric features
that may be used as a readout of the underlying topology of generic
polymers exist. We perform molecular simulations of knotted and linked
semiflexible polymers and study four geometric measures to predict
topological entanglements: local curvature, local density, local 1D
writhe, and nonlocal 3D writhe. We discover that local curvature is
a poor predictor of entanglements. In contrast, segments with maximum
local density or writhe correlate as much as 90% of the time with
the shortest knotted and linked arcs. We find that this accuracy is
preserved across different knot types and also under significant spherical
confinement, which is known to delocalize essential crossings in knotted
polymers. We further discover that nonlocal 3D writhe is the best
geometric readout of the knot location. Finally, we discuss how these
geometric features may be used to computationally analyze entanglements
in generic polymer melts and gels.
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Affiliation(s)
- Joseph L. Sleiman
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Robin H. Burton
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Yair Augusto Gutierrez Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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9
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Greń BA, Dabrowski-Tumanski P, Niemyska W, Sulkowska JI. Lasso Proteins-Unifying Cysteine Knots and Miniproteins. Polymers (Basel) 2021; 13:3988. [PMID: 34833285 PMCID: PMC8621785 DOI: 10.3390/polym13223988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Complex lasso proteins are a recently identified class of biological compounds that are present in considerable fraction of proteins with disulfide bridges. In this work, we look at complex lasso proteins as a generalization of well-known cysteine knots and miniproteins (lasso peptides). In particular, we show that complex lasso proteins with the same crucial topological features-cysteine knots and lasso peptides-are antimicrobial proteins, which suggests that they act as a molecular plug. Based on an analysis of the stability of the lasso piercing residue, we also introduce a method to determine which lasso motif is potentially functional. Using this method, we show that the lasso motif in antimicrobial proteins, as well in that in cytokines, is functionally relevant. We also study the evolution of lasso motifs, their conservation, and the usefulness of the lasso fingerprint, which extracts all topologically non-triviality concerning covalent loops. The work is completed by the presentation of extensive statistics on complex lasso proteins to analyze, in particular, the strange propensity for "negative" piercings. We also identify 21 previously unknown complex lasso proteins with an ester and a thioester bridge.
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Affiliation(s)
- Bartosz Ambroży Greń
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; (B.A.G.); (P.D.-T.)
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | | | - Wanda Niemyska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | - Joanna Ida Sulkowska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; (B.A.G.); (P.D.-T.)
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10
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Chubak I, Likos CN, Smrek J. Topological and threading effects in polydisperse ring polymer solutions. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1883140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Iurii Chubak
- Faculty of Physics, University of Vienna, Vienna, Austria
| | | | - Jan Smrek
- Faculty of Physics, University of Vienna, Vienna, Austria
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11
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Dabrowski-Tumanski P, Rubach P, Niemyska W, Gren BA, Sulkowska JI. Topoly: Python package to analyze topology of polymers. Brief Bioinform 2021; 22:bbaa196. [PMID: 32935829 PMCID: PMC8138882 DOI: 10.1093/bib/bbaa196] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 12/27/2022] Open
Abstract
The increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.cent.uw.edu.pl.
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Affiliation(s)
| | | | | | | | - Joanna Ida Sulkowska
- Corresponding author: Joanna Ida Sulkowska, Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland; Faculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland. Tel.: +48-22-55-43678 E-mail:
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12
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13
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Simien JM, Haglund E. Topological Twists in Nature. Trends Biochem Sci 2021; 46:461-471. [PMID: 33419636 DOI: 10.1016/j.tibs.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
Abstract
The first entangled protein was observed about 30 years ago, resulting in an increased interest for uncovering the biological functions and biophysical properties of these complex topologies. Recently, the Pierced Lasso Topology (PLT) was discovered in which a covalent bond forms an intramolecular loop, leaving one or both termini free to pierce the loop. This topology is related to knots and other entanglements. PLTs exist in many well-researched systems where the PLTs have previously been unnoticed. PLTs represents 18% of all disulfide containing proteins across all kingdoms of life. In this review, we investigate the biological implications of this specific topology in which the PLT-forming disulfide may act as a molecular switch for protein function and consequently human health.
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Affiliation(s)
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI, USA.
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14
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Liu Y, Wu W, Hong S, Fang J, Zhang F, Liu G, Seo J, Zhang W. Lasso Proteins: Modular Design, Cellular Synthesis, and Topological Transformation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Wen‐Hao Wu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Sumin Hong
- Department of Chemistry Pohang University of Science and Technology (POSTECH) Pohang 37673 Republic of Korea
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Geng‐Xin Liu
- Center for Advanced Low-dimension Materials State Key Laboratory for Modification of Chemical Fibers and Polymer Materials College of Material Science and Engineering Donghua University Shanghai 201620 China
| | - Jongcheol Seo
- Department of Chemistry Pohang University of Science and Technology (POSTECH) Pohang 37673 Republic of Korea
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry & Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
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15
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Niemyska W, Millett KC, Sulkowska JI. GLN: a method to reveal unique properties of lasso type topology in proteins. Sci Rep 2020; 10:15186. [PMID: 32938999 PMCID: PMC7494857 DOI: 10.1038/s41598-020-71874-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/17/2020] [Indexed: 02/02/2023] Open
Abstract
Geometry and topology are the main factors that determine the functional properties of proteins. In this work, we show how to use the Gauss linking integral (GLN) in the form of a matrix diagram-for a pair of a loop and a tail-to study both the geometry and topology of proteins with closed loops e.g. lassos. We show that the GLN method is a significantly faster technique to detect entanglement in lasso proteins in comparison with other methods. Based on the GLN technique, we conduct comprehensive analysis of all proteins deposited in the PDB and compare it to the statistical properties of the polymers. We show how high and low GLN values correlate with the internal exibility of proteins, and how the GLN in the form of a matrix diagram can be used to study folding and unfolding routes. Finally, we discuss how the GLN method can be applied to study entanglement between two structures none of which are closed loops. Since this approach is much faster than other linking invariants, the next step will be evaluation of lassos in much longer molecules such as RNA or loops in a single chromosome.
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Affiliation(s)
- Wanda Niemyska
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Kenneth C Millett
- Department of Mathematics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Joanna I Sulkowska
- 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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16
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Liu Y, Duan Z, Fang J, Zhang F, Xiao J, Zhang WB. Cellular Synthesis and X-ray Crystal Structure of a Designed Protein Heterocatenane. Angew Chem Int Ed Engl 2020; 59:16122-16127. [PMID: 32506656 DOI: 10.1002/anie.202005490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/24/2023]
Abstract
Herein, we report the biosynthesis of protein heterocatenanes using a programmed sequence of multiple post-translational processing events including intramolecular chain entanglement, in situ backbone cleavage, and spontaneous cyclization. The approach is general, autonomous, and can obviate the need for any additional enzymes. The catenane topology was convincingly proven using a combination of SDS-PAGE, LC-MS, size exclusion chromatography, controlled proteolytic digestion, and protein crystallography. The X-ray crystal structure clearly shows two mechanically interlocked protein rings with intact folded domains. It opens new avenues in the nascent field of protein-topology engineering.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zelin Duan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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17
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Liu Y, Duan Z, Fang J, Zhang F, Xiao J, Zhang W. Cellular Synthesis and X‐ray Crystal Structure of a Designed Protein Heterocatenane. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Zelin Duan
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking-Tsinghua Center for Life Sciences Peking University Beijing 100871 P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking-Tsinghua Center for Life Sciences Peking University Beijing 100871 P. R. China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
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18
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Liu Y, Wu WH, Hong S, Fang J, Zhang F, Liu GX, Seo J, Zhang WB. Lasso Proteins: Modular Design, Cellular Synthesis, and Topological Transformation. Angew Chem Int Ed Engl 2020; 59:19153-19161. [PMID: 32602613 DOI: 10.1002/anie.202006727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/30/2020] [Indexed: 02/06/2023]
Abstract
Entangled proteins have attracted significant research interest. Herein, we report the first rationally designed lasso proteins, or protein [1]rotaxanes, by using a p53dim-entwined dimer for intramolecular entanglement and a SpyTag-SpyCatcher reaction for side-chain ring closure. The lasso structures were confirmed by proteolytic digestion, mutation, NMR spectrometry, and controlled ligation. Their dynamic properties were probed by experiments such as end-capping, proteolytic digestion, and heating/cooling. As a versatile topological intermediate, a lasso protein could be converted to a rotaxane, a heterocatenane, and a "slide-ring" network. Being entirely genetically encoded, this robust and modular lasso-protein motif is a valuable addition to the topological protein repertoire and a promising candidate for protein-based biomaterials.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Wen-Hao Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Sumin Hong
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Geng-Xin Liu
- Center for Advanced Low-dimension Materials, State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Material Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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19
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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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20
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Rosa A, Smrek J, Turner MS, Michieletto D. Threading-Induced Dynamical Transition in Tadpole-Shaped Polymers. ACS Macro Lett 2020; 9:743-748. [PMID: 33828901 PMCID: PMC8016395 DOI: 10.1021/acsmacrolett.0c00197] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/30/2020] [Indexed: 01/06/2023]
Abstract
The relationship between polymer topology and bulk rheology remains a key question in soft matter physics. Architecture-specific constraints (or threadings) are thought to control the dynamics of ring polymers in ring-linear blends, which thus affects the viscosity to range between that of the pure rings and a value larger, but still comparable to, that of the pure linear melt. Here we consider qualitatively different systems of linear and ring polymers, fused together in "chimeric" architectures. The simplest example of this family is a "tadpole"-shaped polymer, a single ring fused to the end of a single linear chain. We show that polymers with this architecture display a threading-induced dynamical transition that substantially slows chain relaxation. Our findings shed light on how threadings control dynamics and may inform design principles for chimeric polymers with topologically tunable bulk rheological properties.
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Affiliation(s)
- Angelo Rosa
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), Via Bonomea 265, 34136 Trieste, Italy
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Matthew S Turner
- Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemical Engineering, Kyoto University, Kyoto 606-8501, Japan
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- Department of Mathematical Sciences, University of Bath, North Rd, Bath BA2 7AY, United Kingdom
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21
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Rubach P, Zajac S, Jastrzebski B, Sulkowska JI, Sułkowski P. Genus for biomolecules. Nucleic Acids Res 2020; 48:D1129-D1135. [PMID: 31584078 PMCID: PMC6943057 DOI: 10.1093/nar/gkz845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 10/02/2019] [Indexed: 01/03/2023] Open
Abstract
The ‘Genus for biomolecules’ database (http://genus.fuw.edu.pl) collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule, this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all and RNA structures deposited in the Protein Data Bank (PDB). This database presents also various statistics and extensive information about the biological function of the analyzed biomolecules. The database is regularly self-updating, once new structures are deposited in the PDB. Moreover, users can analyze their own structures.
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Affiliation(s)
- Paweł Rubach
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.,Warsaw School of Economics, Al. Niepodległości 162, 02-554 Warsaw, Poland
| | - Sebastian Zajac
- Warsaw School of Economics, Al. Niepodległości 162, 02-554 Warsaw, Poland
| | - Borys Jastrzebski
- 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.,Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Piotr Sułkowski
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.,Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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22
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Danielsson J, Noel JK, Simien JM, Duggan BM, Oliveberg M, Onuchic JN, Jennings PA, Haglund E. The Pierced Lasso Topology Leptin has a Bolt on Dynamic Domain Composed by the Disordered Loops I and III. J Mol Biol 2020; 432:3050-3063. [PMID: 32081588 DOI: 10.1016/j.jmb.2020.01.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/18/2020] [Accepted: 01/24/2020] [Indexed: 02/08/2023]
Abstract
Leptin is an important signaling hormone, mostly known for its role in energy expenditure and satiety. Furthermore, leptin plays a major role in other proteinopathies, such as cancer, marked hyperphagia, impaired immune function, and inflammation. In spite of its biological relevance in human health, there are no NMR resonance assignments of the human protein available, obscuring high-resolution characterization of the soluble protein and/or its conformational dynamics, suggested as being important for receptor interaction and biological activity. Here, we report the nearly complete backbone resonance assignments of human leptin. Chemical shift-based secondary structure prediction confirms that in solution leptin forms a four-helix bundle including a pierced lasso topology. The conformational dynamics, determined on several timescales, show that leptin is monomeric, has a rigid four-helix scaffold, and a dynamic domain, including a transiently formed helix. The dynamic domain is anchored to the helical scaffold by a secondary hydrophobic core, pinning down the long loops of leptin to the protein body, inducing motional restriction without a well-defined secondary or tertiary hydrogen bond stabilized structure. This dynamic region is well suited for and may be involved in functional allosteric dynamics upon receptor binding.
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Affiliation(s)
- Jens Danielsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | | | | | - Brendan Michael Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, USA
| | - Mikael Oliveberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, USA; Department of Physics and Astronomy, Department of Chemistry, And Department of Biosciences, Rice University, Houston, USA
| | - Patricia Ann Jennings
- Department of Chemistry and Biochemistry, The University of California at San Diego, La Jolla, USA
| | - Ellinor Haglund
- The Department of Chemistry, University of Hawaii, Manoa, Honolulu, USA.
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23
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Sulkowska JI. On folding of entangled proteins: knots, lassos, links and θ-curves. Curr Opin Struct Biol 2020; 60:131-141. [PMID: 32062143 DOI: 10.1016/j.sbi.2020.01.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/15/2022]
Abstract
Around 6% of protein structures deposited in the PDB are entangled, forming knots, slipknots, lassos, links, and θ-curves. In each of these cases, the protein backbone weaves through itself in a complex way, and at some point passes through a closed loop, formed by other regions of the protein structure. Such a passing can be interpreted as crossing a topological barrier. How proteins overcome such barriers, and therefore different degrees of frustration, challenged scientists and has shed new light on the field of protein folding. In this review, we summarize the current knowledge about the free energy landscape of proteins with non-trivial topology. We describe identified mechanisms which lead proteins to self-tying. We discuss the influence of excluded volume, such as crowding and chaperones, on tying, based on available data. We briefly discuss the diversity of topological complexity of proteins and their evolution. We also list available tools to investigate non-trivial topology. Finally, we formulate intriguing and challenging questions at the boundary of biophysics, bioinformatics, biology, and mathematics, which arise from the discovery of entangled proteins.
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Affiliation(s)
- Joanna Ida Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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24
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Perego C, Potestio R. Computational methods in the study of self-entangled proteins: a critical appraisal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:443001. [PMID: 31269476 DOI: 10.1088/1361-648x/ab2f19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The existence of self-entangled proteins, the native structure of which features a complex topology, unveils puzzling, and thus fascinating, aspects of protein biology and evolution. The discovery that a polypeptide chain can encode the capability to self-entangle in an efficient and reproducible way during folding, has raised many questions, regarding the possible function of these knots, their conservation along evolution, and their role in the folding paradigm. Understanding the function and origin of these entanglements would lead to deep implications in protein science, and this has stimulated the scientific community to investigate self-entangled proteins for decades by now. In this endeavour, advanced experimental techniques are more and more supported by computational approaches, that can provide theoretical guidelines for the interpretation of experimental results, and for the effective design of new experiments. In this review we provide an introduction to the computational study of self-entangled proteins, focusing in particular on the methodological developments related to this research field. A comprehensive collection of techniques is gathered, ranging from knot theory algorithms, that allow detection and classification of protein topology, to Monte Carlo or molecular dynamics strategies, that constitute crucial instruments for investigating thermodynamics and kinetics of this class of proteins.
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Affiliation(s)
- Claudio Perego
- Max Panck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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25
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Niewieczerzał S, Sulkowska JI. Supercoiling in a Protein Increases its Stability. PHYSICAL REVIEW LETTERS 2019; 123:138102. [PMID: 31697559 DOI: 10.1103/physrevlett.123.138102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Indexed: 06/10/2023]
Abstract
The supercoiling motif is the most complex type of nontrivial topology found in proteins with at least one disulfide bond and, to the best of our knowledge, it has not been studied before. We show that a protein from extremophilic species with such a motif can fold; however, the supercoiling changes a smooth landscape observed in reduced conditions into a two-state folding process in the oxidative conditions, with a deep intermediate state. The protein takes advantage of the hairpinlike motif to overcome the topological barrier and thus to supercoil. We find that the depth of the supercoiling motif, i.e., the length of the threaded terminus, has a crucial impact on the folding rates of the studied protein. We show that fluctuations of the minimal surface area can be used to measure local stability, and we find that supercoiling introduces stability into the protein. We suggest that the supercoiling motif enables the studied protein to live in physically extreme conditions, which are detrimental to most life on Earth.
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Affiliation(s)
- Szymon Niewieczerzał
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna I Sulkowska
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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26
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Niewieczerzal S, Niemyska W, Sulkowska JI. Defining and detecting links in chromosomes. Sci Rep 2019; 9:11753. [PMID: 31409805 PMCID: PMC6692345 DOI: 10.1038/s41598-019-47999-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/03/2019] [Indexed: 11/09/2022] Open
Abstract
Sophisticated methods for mapping chromatin contacts enable to generate data of the genome structure that provide deep insights into the formation of chromatin interactions within cell nuclei. Due to the recent progress in this field, three-dimensional genomic structures of individual haploid mouse embryonic stem cells have been determined. Here, we analyze these data (8 cells) and determine comprehensive landscape of entanglements between interphase chromosomes. We find a significant number of stable links formed by chromosome pairs. Some links are even conserved between cells. Moreover, examples of stable multiple links, with at least three chromosomes engaged, are also identified. Types of links and their location along chromosomes are determined based on computations of HOMFLY-PT polynomials and Gauss Linking Numbers. Furthermore, stability of links is studied between different models, cells, and based on relaxation simulations of the genomic structure in a simplified structure-based representation. Identified links suggest that small fraction of chromosomes are entangled not only locally. How topoisomerases engineer such configurations remains an open question. Furthermore, presented methods can be used as a quantitative assessment - descriptor - to distinguish the quality of modeled data.
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Affiliation(s)
- Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, 02-097, Warsaw, Poland
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland. .,Departament of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
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27
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Perego C, Potestio R. Searching the Optimal Folding Routes of a Complex Lasso Protein. Biophys J 2019; 117:214-228. [PMID: 31235180 PMCID: PMC6700606 DOI: 10.1016/j.bpj.2019.05.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/29/2019] [Accepted: 05/30/2019] [Indexed: 10/27/2022] Open
Abstract
Understanding how polypeptides can efficiently and reproducibly attain a self-entangled conformation is a compelling biophysical challenge that might shed new light on our general knowledge of protein folding. Complex lassos, namely self-entangled protein structures characterized by a covalent loop sealed by a cysteine bridge, represent an ideal test system in the framework of entangled folding. Indeed, because cysteine bridges form in oxidizing conditions, they can be used as on/off switches of the structure topology to investigate the role played by the backbone entanglement in the process. In this work, we have used molecular dynamics to simulate the folding of a complex lasso glycoprotein, granulocyte-macrophage colony-stimulating factor, modeling both reducing and oxidizing conditions. Together with a well-established Gō-like description, we have employed the elastic folder model, a coarse-grained, minimalistic representation of the polypeptide chain driven by a structure-based angular potential. The purpose of this study is to assess the kinetically optimal pathways in relation to the formation of the native topology. To this end, we have implemented an evolutionary strategy that tunes the elastic folder model potentials to maximize the folding probability within the early stages of the dynamics. The resulting protein model is capable of folding with high success rate, avoiding the kinetic traps that hamper the efficient folding in the other tested models. Employing specifically designed topological descriptors, we could observe that the selected folding routes avoid the topological bottleneck by locking the cysteine bridge after the topology is formed. These results provide valuable insights on the selection of mechanisms in self-entangled protein folding while, at the same time, the proposed methodology can complement the usage of established minimalistic models and draw useful guidelines for more detailed simulations.
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Affiliation(s)
- Claudio Perego
- Polymer Theory Department, Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Raffaello Potestio
- Department of Physics, University of Trento, Trento, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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28
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PconsFam: An Interactive Database of Structure Predictions of Pfam Families. J Mol Biol 2019; 431:2442-2448. [DOI: 10.1016/j.jmb.2019.01.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 11/17/2022]
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29
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Dabrowski-Tumanski P, Gren B, Sulkowska JI. Statistical Properties of Lasso-Shape Polymers and Their Implications for Complex Lasso Proteins Function. Polymers (Basel) 2019; 11:E707. [PMID: 30999683 PMCID: PMC6523798 DOI: 10.3390/polym11040707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
Abstract
The shape and properties of closed loops depend on various topological factors. One of them is loop-threading, which is present in complex lasso proteins. In this work, we analyze the probability of loop-threading by the tail and its influence on the shape of the loop measured by the radius of gyration, distention, asphericity, and prolateness. In particular, we show that the probability of a trivial lasso for phantom polymer is non-zero even for an infinite structure, as well as that the threading flattens the loop by restricting its motion in one dimension. These results are further used to show that there are fewer non-trivial protein lassos than expected and select potentially functional complex lasso proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | - Bartosz Gren
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
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30
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Dabrowski-Tumanski P, Sulkowska JI. The APS-bracket – A topological tool to classify lasso proteins, RNAs and other tadpole-like structures. REACT FUNCT POLYM 2018. [DOI: 10.1016/j.reactfunctpolym.2018.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Dabrowski-Tumanski P, Piejko M, Niewieczerzal S, Stasiak A, Sulkowska JI. Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting from the Ribosome Exit Channel. J Phys Chem B 2018; 122:11616-11625. [PMID: 30198720 DOI: 10.1021/acs.jpcb.8b07634] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The mechanism of folding of deeply knotted proteins into their native structure is still not understood. Current thinking about protein folding is dominated by the Anfinsen dogma, stating that the structure of the folded proteins is uniquely dictated by the amino acid sequence of a given protein and that the folding is driven uniquely by the energy gained from interactions between amino acids that contact each other in the native structure of the protein. The role of ribosomes in protein folding was only seen as permitting the folding to progress from the N-terminal part of nascent protein chains. We propose here that ribosomes can participate actively in the folding of knotted proteins by actively threading nascent chains emerging from the ribosome exit channels through loops formed by a synthesized earlier portion of the same protein. Our simulations of folding of deeply knotted protein Tp0624 positively verify the proposed ribosome-driven active threading mechanism leading to the formation of deeply knotted proteins.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Maciej Piejko
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Szymon Niewieczerzal
- Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
| | - Andrzej Stasiak
- Center for Integrative Genomics , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Joanna I Sulkowska
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 , Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2c , 02-097 , Warsaw , Poland
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33
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Haglund E, Nguyen L, Schafer NP, Lammert H, Jennings PA, Onuchic JN. Uncovering the molecular mechanisms behind disease-associated leptin variants. J Biol Chem 2018; 293:12919-12933. [PMID: 29950524 PMCID: PMC6102133 DOI: 10.1074/jbc.ra118.003957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/14/2018] [Indexed: 01/21/2023] Open
Abstract
The pleiotropic hormone leptin has a pivotal role in regulating energy balance by inhibiting hunger and increasing energy expenditure. Homozygous mutations found in the leptin gene are associated with extreme obesity, marked hyperphagia, and impaired immune function. Although these mutations have been characterized in vivo, a detailed understanding of how they affect leptin structure and function remains elusive. In the current work, we used NMR, differential scanning calorimetry, molecular dynamics simulations, and bioinformatics calculations to characterize the effects of these mutations on leptin structure and function and binding to its cognate receptor. We found that mutations identified in patients with congenital leptin deficiency not only cause leptin misfolding or aggregation, but also cause changes in the dynamics of leptin residues on the receptor-binding interface. Therefore, we infer that mutation-induced leptin deficiency may arise from several distinct mechanisms including (i) blockade of leptin receptor interface II, (ii) decreased affinity in the second step of leptin's interaction with its receptor, (iii) leptin destabilization, and (iv) unsuccessful threading through the covalent loop, leading to leptin misfolding/aggregation. We propose that this expanded framework for understanding the mechanisms underlying leptin deficiency arising from genetic mutations may be useful in designing therapeutics for leptin-associated disorders.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics, and Biosciences, Rice University, Houston, Texas 77005.
| | - Lannie Nguyen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093
| | - Nicholas Peter Schafer
- Center for Theoretical Biological Physics, and Biosciences, Rice University, Houston, Texas 77005
| | - Heiko Lammert
- Center for Theoretical Biological Physics, and Biosciences, Rice University, Houston, Texas 77005
| | - Patricia Ann Jennings
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093.
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, and Biosciences, Rice University, Houston, Texas 77005; Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas 77005.
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34
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Sulkowska JI, Niewieczerzal S, Jarmolinska AI, Siebert JT, Virnau P, Niemyska W. KnotGenome: a server to analyze entanglements of chromosomes. Nucleic Acids Res 2018; 46:W17-W24. [PMID: 29905836 PMCID: PMC6030981 DOI: 10.1093/nar/gky511] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/05/2018] [Accepted: 05/23/2018] [Indexed: 02/03/2023] Open
Abstract
The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial. Entangled chromosomes are presented graphically in an intuitive way. It is also possible to relax structure with short molecular dynamics runs before the analysis. KnotGenome is freely available at http://knotgenom.cent.uw.edu.pl/.
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Affiliation(s)
- Joanna I Sulkowska
- 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
| | - Szymon Niewieczerzal
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - 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, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Jonathan T Siebert
- Johannes Gutenberg-Universität Mainz, Institut für Physik, Staudingerweg 9, Mainz, 55128, Germany
| | - Peter Virnau
- Johannes Gutenberg-Universität Mainz, Institut für Physik, Staudingerweg 9, Mainz, 55128, Germany
| | - Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
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35
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Jarmolinska AI, Kadlof M, Dabrowski-Tumanski P, Sulkowska JI. GapRepairer: a server to model a structural gap and validate it using topological analysis. Bioinformatics 2018; 34:3300-3307. [DOI: 10.1093/bioinformatics/bty334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 04/27/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Aleksandra I Jarmolinska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Warsaw, Poland
| | - Michal Kadlof
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
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36
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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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37
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Burban DJ, Jennings PA. Backbone assignments for the SPOUT methyltransferase MTT Tm , a knotted protein from Thermotoga maritima. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:151-154. [PMID: 28284017 DOI: 10.1007/s12104-017-9737-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
The SPOUT family of methyltransferase proteins is noted for containing a deep trefoil knot in their defining backbone fold. This unique fold is of high interest for furthering the understanding of knots in proteins. Here, we report the 1H, 13C, 15N assignments for MTT Tm , a canonical member of the SPOUT family. This protein is unique, as it is one of the smallest members of the family, making it an ideal system for probing the unique properties of the knot. Our present work represents the foundation for further studies into the topology of MTT Tm , and understanding how its structure affects both its folding and function.
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Affiliation(s)
- David J Burban
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, USA
| | - Patricia A Jennings
- Department of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA, USA.
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38
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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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39
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Goundaroulis D, Gügümcü N, Lambropoulou S, Dorier J, Stasiak A, Kauffman L. Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids. Polymers (Basel) 2017; 9:polym9090444. [PMID: 30965745 PMCID: PMC6418563 DOI: 10.3390/polym9090444] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/16/2022] Open
Abstract
In this paper we introduce a method that offers a detailed overview of the entanglement of an open protein chain. Further, we present a purely topological model for classifying open protein chains by also taking into account any bridge involving the backbone. To this end, we implemented the concepts of planar knotoids and bonded knotoids. We show that the planar knotoids technique provides more refined information regarding the knottedness of a protein when compared to established methods in the literature. Moreover, we demonstrate that our topological model for bonded proteins is robust enough to distinguish all types of lassos in proteins.
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Affiliation(s)
- Dimos Goundaroulis
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Neslihan Gügümcü
- Department of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Sofia Lambropoulou
- Department of Mathematics, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece.
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Louis Kauffman
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL 60607-7045, USA.
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40
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Abstract
Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links-entangled structures, more complex than knots, which consist of several components. We derive conditions that proteins need to meet to be able to form links. We search through the entire Protein Data Bank and identify several sequentially nonhomologous chains that form a Hopf link and a Solomon link. We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. We also explain how the presence of links affects the folding pathways of proteins. Finally, we define necessary conditions to form Borromean rings in proteins and show that no structure in the Protein Data Bank forms a link of this type.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - Joanna I Sulkowska
- Faculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland;
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
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41
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Abstract
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.
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42
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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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43
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Abstract
We identify new entangled motifs in proteins that we call complex lassos. Lassos arise in proteins with disulfide bridges (or in proteins with amide linkages), when termini of a protein backbone pierce through an auxiliary surface of minimal area, spanned on a covalent loop. We find that as much as 18% of all proteins with disulfide bridges in a non-redundant subset of PDB form complex lassos, and classify them into six distinct geometric classes, one of which resembles supercoiling known from DNA. Based on biological classification of proteins we find that lassos are much more common in viruses, plants and fungi than in other kingdoms of life. We also discuss how changes in the oxidation/reduction potential may affect the function of proteins with lassos. Lassos and associated surfaces of minimal area provide new, interesting and possessing many potential applications geometric characteristics not only of proteins, but also of other biomolecules.
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44
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Allen CD, Chen MY, Trick AY, Le DT, Ferguson AL, Link AJ. Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3. ACS Chem Biol 2016; 11:3043-3051. [PMID: 27588549 DOI: 10.1021/acschembio.6b00588] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are a class of knot-like polypeptides in which the C-terminal tail of the peptide threads through a ring formed by an isopeptide bond between the N-terminal amine group and a side chain carboxylic acid. The small size (∼20 amino acids) and simple topology of lasso peptides make them a good model system for studying the unthreading of entangled polypeptides, both with experiments and atomistic simulation. Here, we present an in-depth study of the thermal unthreading behavior of two lasso peptides astexin-2 and astexin-3. Quantitative kinetics and energetics of the unthreading process were determined for variants of these peptides using a series of chromatography and mass spectrometry experiments and biased molecular dynamics (MD) simulations. In addition, we show that the Tyr15Phe variant of astexin-3 unthreads via an unprecedented "tail pulling" mechanism. MD simulations on a model ring-thread system coupled with machine learning approaches also led to the discovery of physicochemical descriptors most important for peptide unthreading.
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Affiliation(s)
- Caitlin D. Allen
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Maria Y. Chen
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Alexander Y. Trick
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Dan Thanh Le
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - A. James Link
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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45
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Dabrowski-Tumanski P, Jarmolinska AI, Niemyska W, Rawdon EJ, Millett KC, Sulkowska JI. LinkProt: a database collecting information about biological links. Nucleic Acids Res 2016; 45:D243-D249. [PMID: 27794552 PMCID: PMC5210653 DOI: 10.1093/nar/gkw976] [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: 09/08/2016] [Revised: 10/06/2016] [Accepted: 10/13/2016] [Indexed: 01/01/2023] Open
Abstract
Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structures. Moreover, the complex topology can be defined also as one additional structural level. The LinkProt database (http://linkprot.cent.uw.edu.pl) collects and displays information about protein links - topologically non-trivial structures made by up to four chains and complexes of chains (e.g. in capsids). The database presents deterministic links (with loops closed, e.g. by two disulfide bonds), links formed probabilistically and macromolecular links. The structures are classified according to their topology and presented using the minimal surface area method. The database is also equipped with basic tools which allow users to analyze the topology of arbitrary (bio)polymers.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - 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, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.,Institute of Mathematics, University of Silesia, Bankowa 14, 40-007, Katowice, Poland
| | - Eric J Rawdon
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Kenneth C Millett
- Department of Mathematics, University of California, Santa Barbara, CA 93106, USA
| | - Joanna I Sulkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland .,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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