1
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [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: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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3
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Olsen JG, Prestel A, Kassem N, Broendum SS, Shamim HM, Simonsen S, Grysbæk M, Mortensen J, Rytkjær LL, Haxholm GW, Marabini R, Holmberg C, Carr AM, Crehuet R, Nielsen O, Kragelund BB. Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs. Nucleic Acids Res 2024; 52:2030-2044. [PMID: 38261971 PMCID: PMC10939359 DOI: 10.1093/nar/gkae011] [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: 05/11/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Noah Kassem
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sebastian S Broendum
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hossain Mohammad Shamim
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Signe Simonsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Grysbæk
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Josefine Mortensen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Louise Lund Rytkjær
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Gitte W Haxholm
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Holmberg
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex, John Maynard Smith Building, Falmer, BN1 9RQ, Brighton
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, c/ Jordi Girona 18-26, 08034 Barcelona
| | - Olaf Nielsen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
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4
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Mendoza-Salazar I, Fragozo A, González-Martínez AP, Trejo-Martínez I, Arreola R, Pavón L, Almagro JC, Vallejo-Castillo L, Aguilar-Alonso FA, Pérez-Tapia SM. Almost 50 Years of Monomeric Extracellular Ubiquitin (eUb). Pharmaceuticals (Basel) 2024; 17:185. [PMID: 38399400 PMCID: PMC10892293 DOI: 10.3390/ph17020185] [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: 12/26/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Monomeric ubiquitin (Ub) is a 76-amino-acid highly conserved protein found in eukaryotes. The biological activity of Ub first described in the 1970s was extracellular, but it quickly gained relevance due to its intracellular role, i.e., post-translational modification of intracellular proteins (ubiquitination) that regulate numerous eukaryotic cellular processes. In the following years, the extracellular role of Ub was relegated to the background, until a correlation between higher survival rate and increased serum Ub concentrations in patients with sepsis and burns was observed. Although the mechanism of action (MoA) of extracellular ubiquitin (eUb) is not yet well understood, further studies have shown that it may ameliorate the inflammatory response in tissue injury and multiple sclerosis diseases. These observations, compounded with the high stability and low immunogenicity of eUb due to its high conservation in eukaryotes, have made this small protein a relevant candidate for biotherapeutic development. Here, we review the in vitro and in vivo effects of eUb on immunologic, cardiovascular, and nervous systems, and discuss the potential MoAs of eUb as an anti-inflammatory, antimicrobial, and cardio- and brain-protective agent.
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Affiliation(s)
- Ivette Mendoza-Salazar
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Ana Fragozo
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Aneth P González-Martínez
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Ismael Trejo-Martínez
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Rodrigo Arreola
- Subdirección de Investigaciones Clínicas, Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Calzada México-Xochimilco 101, Colonia San Lorenzo Huipulco, Tlalpan, Mexico City 14370, Mexico
| | - Lenin Pavón
- Laboratorio de Psicoinmunología, Dirección de Investigaciones en Neurociencias, Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Mexico City 14370, Mexico
| | - Juan C Almagro
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- GlobalBio, Inc., 320 Concord Ave, Cambridge, MA 02138, USA
| | - Luis Vallejo-Castillo
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Francisco A Aguilar-Alonso
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
| | - Sonia M Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Laboratorio Nacional para Servicios Especializados de Investigación, Desarrollo e Innovación (I + D + i) para Farmoquímicos y Biotecnológicos, LANSEIDI-FarBiotec-CONACyT, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Alcaldía Miguel Hidalgo, Mexico City 11340, Mexico
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5
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Jacobsen NL, Bloch M, Millard PS, Ruidiaz SF, Elsborg JD, Boomsma W, Hendus‐Altenburger R, Hartmann‐Petersen R, Kragelund BB. Phosphorylation of Schizosaccharomyces pombe Dss1 mediates direct binding to the ubiquitin-ligase Dma1 in vitro. Protein Sci 2023; 32:e4733. [PMID: 37463013 PMCID: PMC10443397 DOI: 10.1002/pro.4733] [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: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Intrinsically disordered proteins (IDPs) are often multifunctional and frequently posttranslationally modified. Deleted in split hand/split foot 1 (Dss1-Sem1 in budding yeast) is a highly multifunctional IDP associated with a range of protein complexes. However, it remains unknown if the different functions relate to different modified states. In this work, we show that Schizosaccharomyces pombe Dss1 is a substrate for casein kinase 2 in vitro, and we identify three phosphorylated threonines in its linker region separating two known disordered ubiquitin-binding motifs. Phosphorylations of the threonines had no effect on ubiquitin-binding but caused a slight destabilization of the C-terminal α-helix and mediated a direct interaction with the forkhead-associated (FHA) domain of the RING-FHA E3-ubiquitin ligase defective in mitosis 1 (Dma1). The phosphorylation sites are not conserved and are absent in human Dss1. Sequence analyses revealed that the Txx(E/D) motif, which is important for phosphorylation and Dma1 binding, is not linked to certain branches of the evolutionary tree. Instead, we find that the motif appears randomly, supporting the mechanism of ex nihilo evolution of novel motifs. In support of this, other threonine-based motifs, although frequent, are nonconserved in the linker, pointing to additional functions connected to this region. We suggest that Dss1 acts as an adaptor protein that docks to Dma1 via the phosphorylated FHA-binding motifs, while the C-terminal α-helix is free to bind mitotic septins, thereby stabilizing the complex. The presence of Txx(D/E) motifs in the disordered regions of certain septin subunits may be of further relevance to the formation and stabilization of these complexes.
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Affiliation(s)
- Nina L. Jacobsen
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Magnus Bloch
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Peter S. Millard
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Sarah F. Ruidiaz
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
| | - Jonas D. Elsborg
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagen ØDenmark
| | | | - Rasmus Hartmann‐Petersen
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR LaboratoryUniversity of CopenhagenCopenhagen NDenmark
- REPINUniversity of CopenhagenCopenhagen NDenmark
- The Linderstrøm Lang Centre for Protein Science, Department of BiologyUniversity of CopenhagenCopenhagen NDenmark
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6
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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7
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Intrinsically Disordered Proteins: An Overview. Int J Mol Sci 2022; 23:ijms232214050. [PMID: 36430530 PMCID: PMC9693201 DOI: 10.3390/ijms232214050] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
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8
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Roesgaard MA, Lundsgaard JE, Newcombe EA, Jacobsen NL, Pesce F, Tranchant EE, Lindemose S, Prestel A, Hartmann-Petersen R, Lindorff-Larsen K, Kragelund BB. Deciphering the Alphabet of Disorder-Glu and Asp Act Differently on Local but Not Global Properties. Biomolecules 2022; 12:biom12101426. [PMID: 36291634 PMCID: PMC9599281 DOI: 10.3390/biom12101426] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 12/29/2022] Open
Abstract
Compared to folded proteins, the sequences of intrinsically disordered proteins (IDPs) are enriched in polar and charged amino acids. Glutamate is one of the most enriched amino acids in IDPs, while the chemically similar amino acid aspartate is less enriched. So far, the underlying functional differences between glutamates and aspartates in IDPs remain poorly understood. In this study, we examine the differential effects of aspartate and glutamates in IDPs by comparing the function and conformational ensemble of glutamate and aspartate variants of the disordered protein Dss1, using a range of assays, including interaction studies, nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and molecular dynamics simulation. First, we analyze the sequences of the rapidly growing database of experimentally verified IDPs (DisProt) and show that glutamate enrichment is not caused by a taxonomy bias in IDPs. From analyses of local and global structural properties as well as cell growth and protein-protein interactions using a model acidic IDP from yeast and three Glu/Asp variants, we find that while the Glu/Asp variants support similar function and global dimensions, the variants differ in their binding affinities and population of local transient structural elements. We speculate that these local structural differences may play roles in functional diversity, where glutamates can support increased helicity, important for folding and binding, while aspartates support extended structures and form helical caps, as well as playing more relevant roles in, e.g., transactivation domains and ion-binding.
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