1
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Sikora M, Klimentova E, Uchal D, Sramkova D, Perlinska AP, Nguyen ML, Korpacz M, Malinowska R, Nowakowski S, Rubach P, Simecek P, Sulkowska JI. Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model. Protein Sci 2024; 33:e4998. [PMID: 38888487 PMCID: PMC11184937 DOI: 10.1002/pro.4998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/14/2024] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
Abstract
Knotted proteins, although scarce, are crucial structural components of certain protein families, and their roles continue to be a topic of intense research. Capitalizing on the vast collection of protein structure predictions offered by AlphaFold (AF), this study computationally examines the entire UniProt database to create a robust dataset of knotted and unknotted proteins. Utilizing this dataset, we develop a machine learning (ML) model capable of accurately predicting the presence of knots in protein structures solely from their amino acid sequences. We tested the model's capabilities on 100 proteins whose structures had not yet been predicted by AF and found agreement with our local prediction in 92% cases. From the point of view of structural biology, we found that all potentially knotted proteins predicted by AF can be classified only into 17 families. This allows us to discover the presence of unknotted proteins in families with a highly conserved knot. We found only three new protein families: UCH, DUF4253, and DUF2254, that contain both knotted and unknotted proteins, and demonstrate that deletions within the knot core could potentially account for the observed unknotted (trivial) topology. Finally, we have shown that in the majority of knotted families (11 out of 15), the knotted topology is strictly conserved in functional proteins with very low sequence similarity. We have conclusively demonstrated that proteins AF predicts as unknotted are structurally accurate in their unknotted configurations. However, these proteins often represent nonfunctional fragments, lacking significant portions of the knot core (amino acid sequence).
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Affiliation(s)
- Maciej Sikora
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
| | - Eva Klimentova
- Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrnoCzech Republic
| | - Dawid Uchal
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Physics, University of WarsawWarsawPoland
| | - Denisa Sramkova
- Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk UniversityBrnoCzech Republic
| | | | - Mai Lan Nguyen
- Centre of New Technologies, University of WarsawWarsawPoland
| | - Marta Korpacz
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
| | - Roksana Malinowska
- Centre of New Technologies, University of WarsawWarsawPoland
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
| | - Szymon Nowakowski
- Faculty of Mathematics, Informatics and Mechanics, University of WarsawWarsawPoland
- Faculty of Physics, University of WarsawWarsawPoland
| | - Pawel Rubach
- Centre of New Technologies, University of WarsawWarsawPoland
- Warsaw School of EconomicsWarsawPoland
| | - Petr Simecek
- Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic
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2
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Gren BA, Antczak M, Zok T, Sulkowska JI, Szachniuk M. Knotted artifacts in predicted 3D RNA structures. PLoS Comput Biol 2024; 20:e1011959. [PMID: 38900780 DOI: 10.1371/journal.pcbi.1011959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/01/2024] [Indexed: 06/22/2024] Open
Abstract
Unlike proteins, RNAs deposited in the Protein Data Bank do not contain topological knots. Recently, admittedly, the first trefoil knot and some lasso-type conformations have been found in experimental RNA structures, but these are still exceptional cases. Meanwhile, algorithms predicting 3D RNA models have happened to form knotted structures not so rarely. Interestingly, machine learning-based predictors seem to be more prone to generate knotted RNA folds than traditional methods. A similar situation is observed for the entanglements of structural elements. In this paper, we analyze all models submitted to the CASP15 competition in the 3D RNA structure prediction category. We show what types of topological knots and structure element entanglements appear in the submitted models and highlight what methods are behind the generation of such conformations. We also study the structural aspect of susceptibility to entanglement. We suggest that predictors take care of an evaluation of RNA models to avoid publishing structures with artifacts, such as unusual entanglements, that result from hallucinations of predictive algorithms.
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Affiliation(s)
- Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maciej Antczak
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Marta Szachniuk
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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3
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Rana V, Sitarik I, Petucci J, Jiang Y, Song H, O'Brien EP. Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance. J Mol Biol 2024; 436:168459. [PMID: 38296158 DOI: 10.1016/j.jmb.2024.168459] [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: 09/03/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
One-third of protein domains in the CATH database contain a recently discovered tertiary topological motif: non-covalent lasso entanglements, in which a segment of the protein backbone forms a loop closed by non-covalent interactions between residues and is threaded one or more times by the N- or C-terminal backbone segment. Unknown is how frequently this structural motif appears across the proteomes of organisms. And the correlation of these motifs with various classes of protein function and biological processes have not been quantified. Here, using a combination of protein crystal structures, AlphaFold2 predictions, and Gene Ontology terms we show that in E. coli, S. cerevisiae and H. sapiens that 71%, 52% and 49% of globular proteins contain one-or-more non-covalent lasso entanglements in their native fold, and that some of these are highly complex with multiple threading events. Further, proteins containing these tertiary motifs are consistently enriched in certain functions and biological processes across these organisms and depleted in others, strongly indicating an influence of evolutionary selection pressures acting positively and negatively on the distribution of these motifs. Together, these results demonstrate that non-covalent lasso entanglements are widespread and indicate they may be extensively utilized for protein function and subcellular processes, thus impacting phenotype.
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Affiliation(s)
- Viraj Rana
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Justin Petucci
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, United States
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Hyebin Song
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States; Department of Statistics, Pennsylvania State University, University Park, PA, United States.
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, United States; Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States.
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4
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Zayats V, Sikora M, Perlinska AP, Stasiulewicz A, Gren BA, Sulkowska JI. Conservation of knotted and slipknotted topology in transmembrane transporters. Biophys J 2023; 122:4528-4541. [PMID: 37919904 PMCID: PMC10719070 DOI: 10.1016/j.bpj.2023.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023] Open
Abstract
The existence of nontrivial topology is well accepted in globular proteins but not in membrane proteins. Our comprehensive topological analysis of the Protein Data Bank structures reveals 18 families of transmembrane proteins with nontrivial topology, showing that they constitute a significant number of membrane proteins. Moreover, we found that they comprise one of the largest groups of secondary active transporters. We classified them based on their knotted fingerprint into four groups: three slipknotted and one knotted. Unexpectedly, we found that the same protein can possess two distinct slipknot motifs that correspond to its outward- and inward-open conformational state. Based on the analysis of structures and knotted fingerprints, we show that slipknot topology is directly involved in the conformational transition and substrate transfer. Therefore, entanglement can be used to classify proteins and to find their structure-function relationship. Furthermore, based on the topological analysis of the transmembrane protein structures predicted by AlphaFold, we identified new potentially slipknotted protein families.
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Affiliation(s)
- Vasilina Zayats
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maciej Sikora
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | | | - Adam Stasiulewicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland; Department of Drug Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
| | - Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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5
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Dabrowski-Tumanski P, Stasiak A. AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology. Molecules 2023; 28:7462. [PMID: 38005184 PMCID: PMC10672856 DOI: 10.3390/molecules28227462] [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: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
AlphaFold is a groundbreaking deep learning tool for protein structure prediction. It achieved remarkable accuracy in modeling many 3D structures while taking as the user input only the known amino acid sequence of proteins in question. Intriguingly though, in the early steps of each individual structure prediction procedure, AlphaFold does not respect topological barriers that, in real proteins, result from the reciprocal impermeability of polypeptide chains. This study aims to investigate how this failure to respect topological barriers affects AlphaFold predictions with respect to the topology of protein chains. We focus on such classes of proteins that, during their natural folding, reproducibly form the same knot type on their linear polypeptide chain, as revealed by their crystallographic analysis. We use partially artificial test constructs in which the mutual non-permeability of polypeptide chains should not permit the formation of complex composite knots during natural protein folding. We find that despite the formal impossibility that the protein folding process could produce such knots, AlphaFold predicts these proteins to form complex composite knots. Our study underscores the necessity for cautious interpretation and further validation of topological features in protein structures predicted by AlphaFold.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Faculty of Mathematics and Natural Sciences, School of Exact Sciences, Cardinal Wyszynski University in Warsaw, Wóycickiego 1/3, 01-938 Warsaw, Poland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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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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Ubertini MA, Rosa A. Spatial Organization of Slit-Confined Melts of Ring Polymers with Nonconserved Topology: A Lattice Monte Carlo Study. Macromolecules 2023; 56:7860-7869. [PMID: 37841537 PMCID: PMC10569094 DOI: 10.1021/acs.macromol.3c01320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/08/2023] [Indexed: 10/17/2023]
Abstract
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density, we explore the influence of confinement on single-chain conformations and interchain interactions. We demonstrate that confinement makes chains globally larger and more elongated while enhancing both contacts and knottedness propensities. As for multichain properties, we show that ring-ring contacts decrease with the confinement, yet neighboring rings overlap more as confinement grows. These aspects are accompanied by a marked decrease in the links formed between pairs of neighboring rings. In connection with the quantitative relation between links and entanglements in polymer melts recently established by us [Ubertini M. A.; Rosa A.Macromolecules2023, 56, 3354-3362], we propose that confinement can be used to set polymer networks that act softer under mechanical stress and suggest a viable experimental setup to validate our results.
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Affiliation(s)
- Mattia Alberto Ubertini
- Scuola Internazionale Superiore
di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Rosa
- Scuola Internazionale Superiore
di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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8
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McDonald SM, Augustine EK, Lanners Q, Rudin C, Catherine Brinson L, Becker ML. Applied machine learning as a driver for polymeric biomaterials design. Nat Commun 2023; 14:4838. [PMID: 37563117 PMCID: PMC10415291 DOI: 10.1038/s41467-023-40459-8] [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: 02/08/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Polymers are ubiquitous to almost every aspect of modern society and their use in medical products is similarly pervasive. Despite this, the diversity in commercial polymers used in medicine is stunningly low. Considerable time and resources have been extended over the years towards the development of new polymeric biomaterials which address unmet needs left by the current generation of medical-grade polymers. Machine learning (ML) presents an unprecedented opportunity in this field to bypass the need for trial-and-error synthesis, thus reducing the time and resources invested into new discoveries critical for advancing medical treatments. Current efforts pioneering applied ML in polymer design have employed combinatorial and high throughput experimental design to address data availability concerns. However, the lack of available and standardized characterization of parameters relevant to medicine, including degradation time and biocompatibility, represents a nearly insurmountable obstacle to ML-aided design of biomaterials. Herein, we identify a gap at the intersection of applied ML and biomedical polymer design, highlight current works at this junction more broadly and provide an outlook on challenges and future directions.
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Affiliation(s)
| | - Emily K Augustine
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
| | - Quinn Lanners
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Cynthia Rudin
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - L Catherine Brinson
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
| | - Matthew L Becker
- Department of Chemistry, Duke University, Durham, NC, USA.
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA.
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9
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Jedrzejewski M, Belza B, Lewandowska I, Sadlej M, Perlinska AP, Augustyniak R, Christian T, Hou YM, Kalek M, Sulkowska JI. Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study. Comput Struct Biotechnol J 2023; 21:3999-4008. [PMID: 37649713 PMCID: PMC10462857 DOI: 10.1016/j.csbj.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/01/2023] Open
Abstract
The Nep1 protein is essential for the formation of eukaryotic and archaeal small ribosomal subunits, and it catalyzes the site-directed SAM-dependent methylation of pseudouridine (Ψ) during pre-rRNA processing. It possesses a non-trivial topology, namely, a 31 knot in the active site. Here, we address the issue of seemingly unfeasible deprotonation of Ψ in Nep1 active site by a distant aspartate residue (D101 in S. cerevisiae), using a combination of bioinformatics, computational, and experimental methods. We identified a conserved hydroxyl-containing amino acid (S233 in S. cerevisiae, T198 in A. fulgidus) that may act as a proton-transfer mediator. Molecular dynamics simulations, based on the crystal structure of S. cerevisiae, and on a complex generated by molecular docking in A. fulgidus, confirmed that this amino acid can shuttle protons, however, a water molecule in the active site may also serve this role. Quantum-chemical calculations based on density functional theory and the cluster approach showed that the water-mediated pathway is the most favorable for catalysis. Experimental kinetic and mutational studies reinforce the requirement for the aspartate D101, but not S233. These findings provide insight into the catalytic mechanisms underlying proton transfer over extended distances and comprehensively elucidate the mode of action of Nep1.
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Affiliation(s)
- Mateusz Jedrzejewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Barbara Belza
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Iwona Lewandowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Marta Sadlej
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Agata P. Perlinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Rafal Augustyniak
- Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 4201 Henry Ave, Philadelphia, PA 19144, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 4201 Henry Ave, Philadelphia, PA 19144, USA
| | - Marcin Kalek
- 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
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10
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Halder R, Nissley DA, Sitarik I, Jiang Y, Rao Y, Vu QV, Li MS, Pritchard J, O'Brien EP. How soluble misfolded proteins bypass chaperones at the molecular level. Nat Commun 2023; 14:3689. [PMID: 37344452 DOI: 10.1038/s41467-023-38962-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Subpopulations of soluble, misfolded proteins can bypass chaperones within cells. The extent of this phenomenon and how it happens at the molecular level are unknown. Through a meta-analysis of the experimental literature we find that in all quantitative protein refolding studies there is always a subpopulation of soluble but misfolded protein that does not fold in the presence of one or more chaperones, and can take days or longer to do so. Thus, some misfolded subpopulations commonly bypass chaperones. Using multi-scale simulation models we observe that the misfolded structures that bypass various chaperones can do so because their structures are highly native like, leading to a situation where chaperones do not distinguish between the folded and near-native-misfolded states. More broadly, these results provide a mechanism by which long-time scale changes in protein structure and function can persist in cells because some misfolded states can bypass components of the proteostasis machinery.
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Affiliation(s)
- Ritaban Halder
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel A Nissley
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Ian Sitarik
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yang Jiang
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yiyun Rao
- Molecular, Cellular and Integrative Biosciences Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences; Al. Lotnikow 32/46, 02-668, Warsaw, Poland
- Institute for Computational Sciences and Technology; Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Justin Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, 16802, USA
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA.
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
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11
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Ubertini MA, Rosa A. Topological Analysis and Recovery of Entanglements in Polymer Melts. Macromolecules 2023; 56:3354-3362. [PMID: 37181245 PMCID: PMC10173697 DOI: 10.1021/acs.macromol.3c00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/24/2023] [Indexed: 05/16/2023]
Abstract
The viscous flow of polymer chains in dense melts is dominated by topological constraints whenever the single-chain contour length, N, becomes larger than the characteristic scale Ne, defining comprehensively the macroscopic rheological properties of the highly entangled polymer systems. Even though they are naturally connected to the presence of hard constraints like knots and links within the polymer chains, the difficulty of integrating the rigorous language of mathematical topology with the physics of polymer melts has limited somehow a genuine topological approach to the problem of classifying these constraints and to how they are related to the rheological entanglements. In this work, we tackle this problem by studying the occurrence of knots and links in lattice melts of randomly knotted and randomly concatenated ring polymers with various bending stiffness values. Specifically, by introducing an algorithm that shrinks the chains to their minimal shapes that do not violate topological constraints and by analyzing those in terms of suitable topological invariants, we provide a detailed characterization of the topological properties at the intrachain level (knots) and of links between pairs and triplets of distinct chains. Then, by employing the Z1 algorithm on the minimal conformations to extract the entanglement length Ne, we show that the ratio N/Ne, the number of entanglements per chain, can be remarkably well reconstructed in terms of only two-chain links.
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12
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Zhao Y, Rothörl J, Besenius P, Virnau P, Daoulas KC. Can Polymer Helicity Affect Topological Chirality of Polymer Knots? ACS Macro Lett 2023; 12:234-240. [PMID: 36706453 PMCID: PMC9948535 DOI: 10.1021/acsmacrolett.2c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We investigate the effect of helicity in isolated polymers on the topological chirality of their knots with computer simulations. Polymers are described by generic worm-like chains (WLC), where helical conformations are promoted by chiral coupling between segments that are neighbors along the chain contour. The sign and magnitude of the coupling coefficient u determine the sense and strength of helicity. The corrugation of the helix is adjusted via the radius R of a spherical, hard excluded volume around each WLC segment. Open and compact helices are, respectively, obtained for R that is either zero or smaller than the length of the WLC bond, and R that is a few times larger than the bond length. We use a Monte Carlo algorithm to sample polymer conformations for different values of u, spanning the range from achiral polymers to chains with well-developed helices. Monitoring the average helix torsion and fluctuations of chiral order as a function of u, for two very different chain lengths, demonstrates that the coil-helix transition in this model is not a phase transition but a crossover. Statistical analysis of conformations forming the simplest chiral knots, 31, 51, and 52, demonstrates that topological mirror symmetry is broken─knots formed by helices with a given sense prefer one handedness over the other. For the 31 and 51 knots, positive helical sense favors positive handedness. Intriguingly, an opposite trend is observed for 52 knots, where positive helical sense promotes negative handedness. We argue that this special coupling between helicity and topological chirality stems from a generic mechanism: conformations where some of the knot crossings are found in "braids" formed by two tightly interwoven sections of the polymer.
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Affiliation(s)
- Yani Zhao
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jan Rothörl
- Department
of Physics, Johannes Gutenberg University
Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Pol Besenius
- Department
of Chemistry, Johannes Gutenberg University
Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Peter Virnau
- Department
of Physics, Johannes Gutenberg University
Mainz, Staudingerweg 9, 55128 Mainz, Germany,E-mail:
| | - Kostas Ch. Daoulas
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany,E-mail: . Phone: +49
(0)6131 379218
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13
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Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots. Polymers (Basel) 2022; 14:polym14194201. [PMID: 36236148 PMCID: PMC9572405 DOI: 10.3390/polym14194201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement strength and compressive forces in a range covering weak, intermediate and strong confinement together with weak and strong compressive forces. The results find that while the common metrics of polymer chain in cylindrical and helical channels are very similar, the DNA in helical channels exhibits greatly different topology in terms of chain knottedness, writhe and handedness of knots. The results show that knots with a preferred chirality in terms of average writhe can be produced by using channels with a chosen handedness.
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14
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Walker CC, Fobe TL, Shirts MR. How Cooperatively Folding Are Homopolymer Molecular Knots? Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher C. Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303 United States
| | - Theodore L. Fobe
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303 United States
| | - Michael R. Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303 United States
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15
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Rauscher PM, de Pablo JJ. Random Knotting in Fractal Ring Polymers. Macromolecules 2022; 55:8409-8417. [PMID: 36186575 PMCID: PMC9520986 DOI: 10.1021/acs.macromol.2c01676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/23/2022] [Indexed: 11/28/2022]
Abstract
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Many ring polymer
systems of physical and biological
interest exhibit
both pronounced topological effects and nontrivial self-similarity,
but the relationship between these two phenomena has not yet been
clearly established. Here, we use theory and simulation to formulate
such a connection by studying a fundamental topological property—the
random knotting probability—for ring polymers with varying
fractal dimension, df. Using straightforward scaling arguments, we generalize a classic
mathematical result, showing that the probability of a trivial knot
decays exponentially with chain size, N, for all
fractal dimensions: P0(N) ∝ exp(−N/N0). However, no such simple considerations can account for
the dependence of the knotting length, N0, on df, necessitating
a more involved analytical calculation. This analysis reveals a complicated
double-exponential dependence, which is well supported by numerical
data. By contrast, functional forms typical of simple scaling theories
fail to adequately describe the observations. These findings are equally
valid for two-dimensional ring polymer systems, where “knotting”
is defined as the intersection of any two segments.
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Affiliation(s)
- Phillip M. Rauscher
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Materials Science Division (MSD) and Center for Molecular Engineering (CME), Argonne National Laboratory, Lemont, Illinois 60439, United States
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16
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Guo F, Wu J, Yang Z, Li K, Zhang L. Penetration of linear chains into semiflexible knotted rings in linear-ring blends. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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17
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Pulse labeling reveals the tail end of protein folding by proteome profiling. Cell Rep 2022; 40:111096. [PMID: 35858568 PMCID: PMC9893312 DOI: 10.1016/j.celrep.2022.111096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Accurate and efficient folding of nascent protein sequences into their native states requires support from the protein homeostasis network. Herein we probe which newly translated proteins are thermo-sensitive, making them susceptible to misfolding and aggregation under heat stress using pulse-SILAC mass spectrometry. We find a distinct group of proteins that is highly sensitive to this perturbation when newly synthesized but not once matured. These proteins are abundant and highly structured. Notably, they display a tendency to form β sheet secondary structures, have more complex folding topology, and are enriched for chaperone-binding motifs, suggesting a higher demand for chaperone-assisted folding. These polypeptides are also more often components of stable protein complexes in comparison with other proteins. Combining these findings suggests the existence of a specific subset of proteins in the cell that is particularly vulnerable to misfolding and aggregation following synthesis before reaching the native state.
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18
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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
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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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19
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Celoria D, Mahler BI. A statistical approach to knot confinement via persistent homology. Proc Math Phys Eng Sci 2022; 478:20210709. [PMID: 35645602 PMCID: PMC9116441 DOI: 10.1098/rspa.2021.0709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/08/2022] [Indexed: 11/12/2022] Open
Abstract
In this paper, we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing radii. Specifically, we extract features from the persistent homology (PH) of the Vietoris-Rips complexes built from point clouds associated with knots. Statistical analysis of our data shows the existence of increasing correlations between geometric quantities associated with the embedding and PH-based features, as a function of the knots' lengths. We further study the variation of these correlations for different knot types. Finally, this framework also allows us to define a simple notion of deviation from ideal configurations of knots.
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Affiliation(s)
- Daniele Celoria
- Mathematical Institute, University of Oxford, Radcliffe Observatory, Andrew Wiles Building, Woodstock Rd, Oxford OX2 6GG, UK
| | - Barbara I Mahler
- Mathematical Institute, University of Oxford, Radcliffe Observatory, Andrew Wiles Building, Woodstock Rd, Oxford OX2 6GG, UK
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20
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Niemyska W, Rubach P, Gren BA, Nguyen ML, Garstka W, Bruno da Silva F, Rawdon EJ, Sulkowska JI. AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. Nucleic Acids Res 2022; 50:W44-W50. [PMID: 35609987 PMCID: PMC9252816 DOI: 10.1093/nar/gkac388] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022] Open
Abstract
AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https://alphaknot.cent.uw.edu.pl/.
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Affiliation(s)
- Wanda Niemyska
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Pawel Rubach
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.,Warsaw School of Economics,Al. Niepodleglosci 162, 02-554, Warsaw, Poland
| | - Bartosz A Gren
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
| | - Mai Lan Nguyen
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.,Polish-Japanese Academy of Information Technology, Koszykowa 86, 02-008 Warsaw, Poland
| | - Wojciech Garstka
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.,Inter-faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | | | - Eric J Rawdon
- University of St. Thomas, 2115 Summit Ave, Saint Paul, MN 55105, USA
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland
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21
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Michieletto D, Fosado YAG, Melas E, Baiesi M, Tubiana L, Orlandini E. Dynamic and facilitated binding of topoisomerase accelerates topological relaxation. Nucleic Acids Res 2022; 50:4659-4668. [PMID: 35474478 PMCID: PMC9071436 DOI: 10.1093/nar/gkac260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expected of proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo.
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Affiliation(s)
| | | | - Elias Melas
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy,INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Luca Tubiana
- Physics Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy,Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | - Enzo Orlandini
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy,INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
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22
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Hagita K, Murashima T, Ogino M, Omiya M, Ono K, Deguchi T, Jinnai H, Kawakatsu T. Efficient compressed database of equilibrated configurations of ring-linear polymer blends for MD simulations. Sci Data 2022; 9:40. [PMID: 35136085 PMCID: PMC8825841 DOI: 10.1038/s41597-022-01138-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
To effectively archive configuration data during molecular dynamics (MD) simulations of polymer systems, we present an efficient compression method with good numerical accuracy that preserves the topology of ring-linear polymer blends. To compress the fraction of floating-point data, we used the Jointed Hierarchical Precision Compression Number - Data Format (JHPCN-DF) method to apply zero padding for the tailing fraction bits, which did not affect the numerical accuracy, then compressed the data with Huffman coding. We also provided a dataset of well-equilibrated configurations of MD simulations for ring-linear polymer blends with various lengths of linear and ring polymers, including ring complexes composed of multiple rings such as polycatenane. We executed 109 MD steps to obtain 150 equilibrated configurations. The combination of JHPCN-DF and SZ compression achieved the best compression ratio for all cases. Therefore, the proposed method enables efficient archiving of MD trajectories. Moreover, the publicly available dataset of ring-linear polymer blends can be employed for studies of mathematical methods, including topology analysis and data compression, as well as MD simulations. Measurement(s) | equilibrated configurations of ring-linear polymer blends | Technology Type(s) | molecular dynamics simulation | Factor Type(s) | length of linear and ring polymer |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.18742097
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Affiliation(s)
- Katsumi Hagita
- Department of Applied Physics, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka, 239-8686, Japan.
| | - Takahiro Murashima
- Department of Physics, Tohoku University, 6-3, Aramaki-aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Masao Ogino
- Faculty of Informatics, Daido University, 10-3 Takiharu-cho, Minami-ku, Nagoya, 457-8530, Japan
| | - Manabu Omiya
- Information Initiative Center, Hokkaido University, Kita 11, Nishi 5, Kita-ku, Sapporo, 060-0811, Japan
| | - Kenji Ono
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Tetsuo Deguchi
- Department of Physics, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hiroshi Jinnai
- Institute of Multidisciplinary for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, 6-3, Aramaki-aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
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23
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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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24
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Hagita K, Murashima T. Molecular Dynamics Simulations of Ring Shapes on a Ring Fraction in Ring–Linear Polymer Blends. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00656] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Katsumi Hagita
- Department of Applied Physics, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka 239-8686, Japan
| | - Takahiro Murashima
- Department of Physics, Tohoku University, 6-3, Aramaki-aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
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25
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Murashima T, Hagita K, Kawakatsu T. Viscosity Overshoot in Biaxial Elongational Flow: Coarse-Grained Molecular Dynamics Simulation of Ring–Linear Polymer Mixtures. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00267] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Takahiro Murashima
- Department of Physics, Tohoku University, 6-3, Aramaki-aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Katsumi Hagita
- Department of Applied Physics, National Defense Academy, 1-10-20, Hashirimizu, Yokosuka 239-8686, Japan
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, 6-3, Aramaki-aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
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26
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Hagita K, Murashima T. Multi-ring configurations and penetration of linear chains into rings on bonded ring systems and polycatenanes in linear chain matrices. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123705] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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27
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Favier B. Spontaneous knotting of a flexible fiber in chaotic flows. Phys Rev E 2021; 103:043101. [PMID: 34005912 DOI: 10.1103/physreve.103.043101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/18/2021] [Indexed: 01/21/2023]
Abstract
We consider the problem of an inextensible but flexible fiber advected by a steady chaotic flow, and ask the simple question of whether the fiber can spontaneously knot itself. Using a one-dimensional Cosserat model, a simple local viscous drag model and discrete contact forces, we explore the probability of finding knots at any given time when the fiber is interacting with the ABC class of flows. The bending rigidity is shown to have a marginal effect compared to that of increasing the fiber length. Complex knots are formed up to 11 crossings, but some knots are more probable than others. The finite-time Lyapunov exponent of the flow is shown to have a positive effect on the knot probability. Finally, contact forces appear to be crucial since knotted configurations can remain stable for times much longer than the turnover time of the flow, something that is not observed when the fiber can freely cross itself.
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Affiliation(s)
- Benjamin Favier
- Aix Marseille Univ, CNRS, Centrale Marseille, IRPHE, Marseille, France
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