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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 PMCID: PMC11265471 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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Salicari L, Baiesi M, Orlandini E, Trovato A. Folding kinetics of an entangled protein. PLoS Comput Biol 2023; 19:e1011107. [PMID: 37956216 PMCID: PMC10681328 DOI: 10.1371/journal.pcbi.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
The possibility of the protein backbone adopting lasso-like entangled motifs has attracted increasing attention. After discovering the surprising abundance of natively entangled protein domain structures, it was shown that misfolded entangled subpopulations might become thermosensitive or escape the homeostasis network just after translation. To investigate the role of entanglement in shaping folding kinetics, we introduce a novel indicator and analyze simulations of a coarse-grained, structure-based model for two small single-domain proteins. The model recapitulates the well-known two-state folding mechanism of a non-entangled SH3 domain. However, despite its small size, a natively entangled antifreeze RD1 protein displays a rich refolding behavior, populating two distinct kinetic intermediates: a short-lived, entangled, near-unfolded state and a longer-lived, non-entangled, near-native state. The former directs refolding along a fast pathway, whereas the latter is a kinetic trap, consistently with known experimental evidence of two different characteristic times. Upon trapping, the natively entangled loop folds without being threaded by the N-terminal residues. After trapping, the native entangled structure emerges by either backtracking to the unfolded state or threading through the already formed but not yet entangled loop. Along the fast pathway, trapping does not occur because the native contacts at the closure of the lasso-like loop fold after those involved in the N-terminal thread, confirming previous predictions. Despite this, entanglement may appear already in unfolded configurations. Remarkably, a longer-lived, near-native intermediate, with non-native entanglement properties, recalls what was observed in cotranslational folding.
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Affiliation(s)
- Leonardo Salicari
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Marco Baiesi
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Enzo Orlandini
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy “G. Galilei”, University of Padova, Padova, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Padova, Italy
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Salicari L, Trovato A. Entangled Motifs in Membrane Protein Structures. Int J Mol Sci 2023; 24:ijms24119193. [PMID: 37298146 DOI: 10.3390/ijms24119193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
Entangled motifs are found in one-third of protein domain structures, a reference set that contains mostly globular proteins. Their properties suggest a connection with co-translational folding. Here, we wish to investigate the presence and properties of entangled motifs in membrane protein structures. From existing databases, we build a non-redundant data set of membrane protein domains, annotated with the monotopic/transmembrane and peripheral/integral labels. We evaluate the presence of entangled motifs using the Gaussian entanglement indicator. We find that entangled motifs appear in one-fifth of transmembrane and one-fourth of monotopic proteins. Surprisingly, the main features of the distribution of the values of the entanglement indicator are similar to the reference case of general proteins. The distribution is conserved across different organisms. Differences with respect to the reference set emerge when considering the chirality of entangled motifs. Although the same chirality bias is found for single-winding motifs in both membrane and reference proteins, the bias is reversed, strikingly, for double-winding motifs only in the reference set. We speculate that these observations can be rationalized in terms of the constraints exerted on the nascent chain by the co-translational bio-genesis machinery, which is different for membrane and globular proteins.
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Affiliation(s)
- Leonardo Salicari
- Department of Physics and Astronomy 'Galileo Galilei', University of Padova, Via Marzolo 8, 35031 Padova, PD, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Via Marzolo 8, 35131 Padova, PD, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy 'Galileo Galilei', University of Padova, Via Marzolo 8, 35031 Padova, PD, Italy
- National Institute of Nuclear Physics (INFN), Padova Section, Via Marzolo 8, 35131 Padova, PD, Italy
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Topological Catenation Enhances Elastic Modulus of Single Linear Polycatenane. CHINESE JOURNAL OF POLYMER SCIENCE 2023. [DOI: 10.1007/s10118-023-2902-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Kuzmin E, VanderSluis B, Nguyen Ba AN, Wang W, Koch EN, Usaj M, Khmelinskii A, Usaj MM, van Leeuwen J, Kraus O, Tresenrider A, Pryszlak M, Hu MC, Varriano B, Costanzo M, Knop M, Moses A, Myers CL, Andrews BJ, Boone C. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science 2020; 368:eaaz5667. [PMID: 32586993 PMCID: PMC7539174 DOI: 10.1126/science.aaz5667] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/06/2020] [Indexed: 12/25/2022]
Abstract
Whole-genome duplication has played a central role in the genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated, and factors that influence the retention of persisting duplicates remain poorly understood. We describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping of digenic interactions for a deletion mutant of each paralog, and of trigenic interactions for the double mutant, provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs: a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.
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Affiliation(s)
- Elena Kuzmin
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alex N Nguyen Ba
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anton Khmelinskii
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | | | | | - Oren Kraus
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Amy Tresenrider
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael Pryszlak
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Ming-Che Hu
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Brenda Varriano
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alan Moses
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Center for Analysis of Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Transient knots in intrinsically disordered proteins and neurodegeneration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:79-103. [PMID: 32828471 DOI: 10.1016/bs.pmbts.2020.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We provide a brief overview of the topological features found in structured proteins and of the dynamical processes that involve knots. We then discuss the knotted states that arise in the intrinsically disordered polyglutamine and α-synuclein. We argue that the existence of the knotted conformations stalls degradation by proteases and thus enhances aggregation. This mechanism works if the length of a peptide chain exceeds a threshold, as in the Huntington disease. We also study the cavities that form within the conformations of the disordered proteins. The volume of the cavities varies in time in a way that is different than that of the radius of gyration or the end-to-end distance. In addition, we study the traffic between the conformational basins and identify patterns associated with the deep and shallow knots. The results are obtained by molecular dynamics simulations that use coarse-grained and all-atom models (with and without the explicit solvent).
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Norbiato F, Seno F, Trovato A, Baiesi M. Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures. Int J Mol Sci 2019; 21:ijms21010213. [PMID: 31892272 PMCID: PMC6981561 DOI: 10.3390/ijms21010213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/16/2019] [Accepted: 12/25/2019] [Indexed: 12/15/2022] Open
Abstract
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in structural biology. Recently, the hypothesis that energetic frustration might be a mechanism to avoid topological frustration has been put forward based on the empirical observation that loops involved in entanglements are stabilized by weak interactions between amino-acids at their extrema. To verify this idea, we use a toy lattice model for the folding of proteins into two almost identical structures, one entangled and one not. As expected, the folding time is longer when random sequences folds into the entangled structure. This holds also under an evolutionary pressure simulated by optimizing the folding time. It turns out that optmized protein sequences in the entangled structure are in fact characterized by frustrated interactions at the closures of entangled loops. This phenomenon is much less enhanced in the control case where the entanglement is not present. Our findings, which are in agreement with experimental observations, corroborate the idea that an evolutionary pressure shapes the folding funnel to avoid topological and kinetic traps.
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Affiliation(s)
- Federico Norbiato
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.N.); (F.S.); (A.T.)
| | - Flavio Seno
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.N.); (F.S.); (A.T.)
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Antonio Trovato
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.N.); (F.S.); (A.T.)
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Marco Baiesi
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy; (F.N.); (F.S.); (A.T.)
- INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
- Correspondence:
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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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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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