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Mizgier NA, Jones CE, Furano AV. Co-expression of distinct L1 retrotransposon coiled coils can lead to their entanglement. Mob DNA 2023; 14:16. [PMID: 37864180 PMCID: PMC10588031 DOI: 10.1186/s13100-023-00303-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023] Open
Abstract
L1 (LINE1) non-LTR retrotransposons are ubiquitous genomic parasites and the dominant transposable element in humans having generated about 40% of their genomic DNA during their ~ 100 million years (Myr) of activity in primates. L1 replicates in germ line cells and early embryos, causing genetic diversity and defects, but can be active in some somatic stem cells, tumors and during aging. L1 encodes two proteins essential for retrotransposition: ORF2p, a reverse transcriptase that contains an endonuclease domain, and ORF1p, a coiled coil mediated homo trimer, which functions as a nucleic acid chaperone. Both proteins contain highly conserved domains and preferentially bind their encoding transcript to form an L1 ribonucleoprotein (RNP), which mediates retrotransposition. However, the coiled coil has periodically undergone episodes of substantial amino acid replacement to the extent that a given L1 family can concurrently express multiple ORF1s that differ in the sequence of their coiled coils. Here we show that such distinct ORF1p sequences can become entangled forming heterotrimers when co-expressed from separate vectors and speculate on how coiled coil entanglement could affect coiled coil evolution.
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Affiliation(s)
- Nikola A. Mizgier
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Charlie E. Jones
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anthony V. Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
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2
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Martinez-Goikoetxea M, Lupas AN. New protein families with hendecad coiled coils in the proteome of life. J Struct Biol 2023; 215:108007. [PMID: 37524272 DOI: 10.1016/j.jsb.2023.108007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/30/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Coiled coils are a widespread and well understood protein fold. Their short and simple repeats underpin considerable structural and functional diversity. The vast majority of coiled coils consist of 7-residue (heptad) sequence repeats, but in essence most combinations of 3- and 4-residue segments, each starting with a residue of the hydrophobic core, are compatible with coiled-coil structure. The most frequent among these other repeat patterns are 11-residue (hendecad, 3 + 4 + 4) repeats. Hendecads are frequently found in low copy number, interspersed between heptads, but some proteins consist largely or entirely of hendecad repeats. Here we describe the first large-scale survey of these proteins in the proteome of life. For this, we scanned the protein sequence database for sequences with 11-residue periodicity that lacked β-strand prediction. We then clustered these by pairwise similarity to construct a map of potential hendecad coiled-coil families. Here we discuss these according to their structural properties, their potential cellular roles, and the evolutionary mechanisms shaping their diversity. We note in particular the continuous amplification of hendecads, both within existing proteins and de novo from previously non-coding sequence, as a powerful mechanism in the genesis of new coiled-coil forms.
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Affiliation(s)
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany.
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3
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Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
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Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
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Shrestha BR, Liberelle B, Murschel F, Purisima EO, Sulea T, De Crescenzo G, Banquy X. Binding mechanism of a de novo coiled coil complex elucidated from surface forces measurements. J Colloid Interface Sci 2021; 581:218-25. [PMID: 32771733 DOI: 10.1016/j.jcis.2020.07.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 11/21/2022]
Abstract
We used the Surface Forces Apparatus to elucidate the interaction mechanism between grafted 5 heptad-long peptides engineered to spontaneously form a heterodimeric coiled-coil complex. The results demonstrated that when intimate contact between peptides is reached, binding occurs first via weakly interacting but more mobile distal heptads, suggesting an induced-fit association process. Precise control of the distance between peptide-coated surfaces allowed to quantitatively monitor the evolution of their biding energy. The binding energy of the coiled-coil complex increased in a stepwise fashion rather than monotonically with the overlapping distance, each step corresponding to the interaction between a quantized number of heptads. Surface forces data were corroborated to surface plasmon resonance measurements and molecular dynamics simulations and allowed the calculation of the energetic contribution of each heptad within the coiled-coil complex.
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Qiu C, Yuan Y, Liang Z, Lee SW, Ploplis VA, Castellino FJ. Variations in the secondary structures of PAM proteins influence their binding affinities to human plasminogen. J Struct Biol 2019; 206:193-203. [PMID: 30880082 DOI: 10.1016/j.jsb.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
M-proteins (M-Prts) are major virulence determinants of Group A Streptococcus pyogenes (GAS) that are covalently anchored to the cell wall at their conserved COOH-termini while the NH2-terminal regions extend through the capsule into extracellular space. Functional M-Prts are also secreted and/or released from GAS cells where they exist as helical coiled-coil dimers in solution. Certain GAS strains (Pattern D) uniquely express an M-protein (plasminogen-binding group A streptococcal M-protein; PAM) that directly interacts with human plasminogen (hPg), a process strongly implicated in the virulence of these strains. M-Prt expressed by the emm gene is employed to serotype over 250 known strains of GAS, ∼20 of which are hitherto found to express PAMs. We have developed a modular structural model of the PAM dimer that describes the roles of different domains of this protein in various functions. While the helical COOH-terminal domains of PAM are essential for dimerization in solution, regions of its NH2-terminal domains also exhibit a weak potential to dimerize. We find that temperature controls the open (unwound) or closed (wound) states of the functional NH2-terminal domains of PAM. As temperature increases, α-helices are dramatically reduced, which concomitantly destabilizes the helical coiled-coil PAM dimers. PAMs with two a-repeats within the variable NH2-terminal A-domain (class I/III) bind to hPg tightly, but natural PAM isolates with a single a-repeat in this domain (class II) display dramatic changes in hPg binding with temperature. We conclude that coexistence of two a-repeats in PAM is critical to achieve optimal binding to hPg, especially in its monomeric form, at the biologically relevant temperature.
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Affiliation(s)
- Cunjia Qiu
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Yue Yuan
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Zhong Liang
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States.
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Abstract
Many new methods for the sequence-based prediction of the secondary and supersecondary structures have been developed over the last several years. These and older sequence-based predictors are widely applied for the characterization and prediction of protein structure and function. These efforts have produced countless accurate predictors, many of which rely on state-of-the-art machine learning models and evolutionary information generated from multiple sequence alignments. We describe and motivate both types of predictions. We introduce concepts related to the annotation and computational prediction of the three-state and eight-state secondary structure as well as several types of supersecondary structures, such as β hairpins, coiled coils, and α-turn-α motifs. We review 34 predictors focusing on recent tools and provide detailed information for a selected set of 14 secondary structure and 3 supersecondary structure predictors. We conclude with several practical notes for the end users of these predictive methods.
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Affiliation(s)
- Christopher J Oldfield
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Ke Chen
- School of Computer Science and Software Engineering, Tianjin Polytechnic University, Tianjin, People's Republic of China
| | - Lukasz Kurgan
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA.
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7
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Lilliu E, Villeri V, Pelassa I, Cesano F, Scarano D, Fiumara F. Polyserine repeats promote coiled coil-mediated fibril formation and length-dependent protein aggregation. J Struct Biol 2018; 204:572-84. [PMID: 30194983 DOI: 10.1016/j.jsb.2018.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/06/2018] [Accepted: 09/01/2018] [Indexed: 12/13/2022]
Abstract
Short polyserine (polyS) repeats are frequently found in proteins and longer ones are produced in neurological disorders such as Huntington disease (HD) owing to translational frameshifting or non-ATG-dependent translation, together with polyglutamine (polyQ) and polyalanine (polyA) repeats, forming intracellular aggregates. However, the physiological and pathological structures of polyS repeats are not clearly understood. Early studies highlighted their structural versatility, similar to other homopolymers whose conformation is influenced by the surrounding protein context. As polyS stretches are frequently near polyQ and polyA repeats, which can be part of coiled coil (CC) structures, and the frameshift-derived polyS repeats in HD directly flank CC heptads important for aggregation, we investigate here the structural and aggregation properties of polyS in the context of CC structures. We have taken advantage of peptide models, previously used to study polyQ and polyA in CCs, in which we inserted polyS repeats of variable length and studied them in comparison with polyQ and polyA peptides. We found that polyS repeats promote CC-mediated polymerization and fibrillization as revealed by circular dichroism, chemical crosslinking, and atomic force microscopy. Furthermore, they promote CC-based, length-dependent intracellular aggregation, which is negligible with 7 and widespread with 49 serines. These findings show that polyS repeats can participate in the formation of CCs, as previously found for polyQ and polyA, conferring to peptides distinctive structural properties with aggregation kinetics that are intermediate between those of polyA and polyQ CCs, and contribute to an overall structural definition of the pathophysiogical roles of homopolymeric repeats in CC structures.
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Abstract
Intermediate filaments (IFs), together with microtubules and actin microfilaments, are the three main cytoskeletal components in metazoan cells. IFs are formed by a distinct protein family, which is made up of 70 members in humans. Most IF proteins are tissue- or organelle-specific, which includes lamins, the IF proteins of the nucleus. The building block of IFs is an elongated dimer, which consists of a central α-helical 'rod' domain flanked by flexible N- and C-terminal domains. The conserved rod domain is the 'signature feature' of the IF family. Bioinformatics analysis reveals that the rod domain of all IF proteins contains three α-helical segments of largely conserved length, interconnected by linkers. Moreover, there is a conserved pattern of hydrophobic repeats within each segment, which includes heptads and hendecads. This defines the presence of both left-handed and almost parallel coiled-coil regions along the rod length. Using X-ray crystallography on multiple overlapping fragments of IF proteins, the atomic structure of the nearly complete rod domain has been determined. Here, we discuss some specific challenges of this procedure, such as crystallization and diffraction data phasing by molecular replacement. Further insights into the structure of the coiled coil and the terminal domains have been obtained using electron paramagnetic resonance measurements on the full-length protein, with spin labels attached at specific positions. This atomic resolution information, as well as further interesting findings, such as the variation of the coiled-coil stability along the rod length, provide clues towards interpreting the data on IF assembly, collected by a range of methods. However, a full description of this process at the molecular level is not yet at hand.
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Affiliation(s)
- Dmytro Guzenko
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Anastasia A Chernyatina
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven, Belgium.
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9
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Kükenshöner T, Wohlwend D, Niemöller C, Dondapati P, Speck J, Adeniran AV, Nieth A, Gerhardt S, Einsle O, Müller KM, Arndt KM. Improving coiled coil stability while maintaining specificity by a bacterial hitchhiker selection system. J Struct Biol 2014; 186:335-48. [PMID: 24631970 DOI: 10.1016/j.jsb.2014.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 12/12/2022]
Abstract
The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of α-helix encoding sequences was designed and selected for interference with the coiled coil domain (CC) of a melanoma-associated basic-helix-loop-helix-leucine-zipper (bHLHLZ) protein, the microphthalmia associated transcription factor (MITF). One predominant sequence (iM10) was enriched during selection and showed remarkable protease resistance, high solubility and thermal stability while maintaining its specificity. Furthermore, it exhibited nanomolar range affinity towards the target peptide. A mutation screen indicated that target-binding helices of increased homodimer stability and improved expression rates were preferred in the selection process. The crystal structure of the iM10/MITF-CC heterodimer (2.1Å) provided important structural insights and validated our design predictions. Importantly, iM10 did not only bind to the MITF coiled coil, but also to the markedly more stable HLHLZ domain of MITF. Characterizing the selected variants of the semi-rational library demonstrated the potential of the innovative bacterial selection approach.
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Affiliation(s)
- Tim Kükenshöner
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Daniel Wohlwend
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Christoph Niemöller
- Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Padmarupa Dondapati
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Janina Speck
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Adebola V Adeniran
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anita Nieth
- Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefan Gerhardt
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany; Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Kristian M Müller
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Germany
| | - Katja M Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Institute for Biology III, University of Freiburg, Freiburg im Breisgau, Germany; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg im Breisgau, Germany.
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