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Newcombe EA, Fernandes CB, Lundsgaard JE, Brakti I, Lindorff-Larsen K, Langkilde AE, Skriver K, Kragelund BB. Insight into Calcium-Binding Motifs of Intrinsically Disordered Proteins. Biomolecules 2021; 11:1173. [PMID: 34439840 PMCID: PMC8391695 DOI: 10.3390/biom11081173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 01/28/2023] Open
Abstract
Motifs within proteins help us categorize their functions. Intrinsically disordered proteins (IDPs) are rich in short linear motifs, conferring them many different roles. IDPs are also frequently highly charged and, therefore, likely to interact with ions. Canonical calcium-binding motifs, such as the EF-hand, often rely on the formation of stabilizing flanking helices, which are a key characteristic of folded proteins, but are absent in IDPs. In this study, we probe the existence of a calcium-binding motif relevant to IDPs. Upon screening several carefully selected IDPs using NMR spectroscopy supplemented with affinity quantification by colorimetric assays, we found calcium-binding motifs in IDPs which could be categorized into at least two groups-an Excalibur-like motif, sequentially similar to the EF-hand loop, and a condensed-charge motif carrying repetitive negative charges. The motifs show an affinity for calcium typically in the ~100 μM range relevant to regulatory functions and, while calcium binding to the condensed-charge motif had little effect on the overall compaction of the IDP chain, calcium binding to Excalibur-like motifs resulted in changes in compaction. Thus, calcium binding to IDPs may serve various structural and functional roles that have previously been underreported.
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Affiliation(s)
- Estella A. Newcombe
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark;
| | - Catarina B. Fernandes
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Jeppe E. Lundsgaard
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Inna Brakti
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
| | - Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark;
| | - Karen Skriver
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Birthe B. Kragelund
- Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200 Copenhagen, Denmark; (E.A.N.); (C.B.F.); (J.E.L.); (I.B.); (K.L.-L.); (K.S.)
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
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Pedersen CP, Seiffert P, Brakti I, Bugge K. Production of Intrinsically Disordered Proteins for Biophysical Studies: Tips and Tricks. Methods Mol Biol 2020; 2141:195-209. [PMID: 32696358 DOI: 10.1007/978-1-0716-0524-0_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) have no single, fixed tertiary structure, yet they take on many vital functions in biology. In recent years, considerable effort has been put into the structural characterization of their conformational ensembles, to understand the link between the transient, short- and long-range organizations of IDPs and their functions. Such biophysical studies require substantial amounts of pure protein, representing a major bottleneck in the studies of IDPs. However, the unique physicochemical properties resulting from their compositional bias may be exploited for simple yet effective purification strategies. In this chapter, we provide tips and tricks for IDP production and describe the most important analyses to carry out before bringing an IDP of interest to the laboratory. We outline four purification protocols utilizing the unique properties of IDPs as well as some commonly encountered challenges and pitfalls.
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Affiliation(s)
- Christian Parsbæk Pedersen
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Pernille Seiffert
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Inna Brakti
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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Bugge K, Brakti I, Fernandes CB, Dreier JE, Lundsgaard JE, Olsen JG, Skriver K, Kragelund BB. Interactions by Disorder - A Matter of Context. Front Mol Biosci 2020; 7:110. [PMID: 32613009 PMCID: PMC7308724 DOI: 10.3389/fmolb.2020.00110] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Living organisms depend on timely and organized interactions between proteins linked in interactomes of high complexity. The recent increased precision by which protein interactions can be studied, and the enclosure of intrinsic structural disorder, suggest that it is time to zoom out and embrace protein interactions beyond the most central points of physical encounter. The present paper discusses protein-protein interactions in the view of structural disorder with an emphasis on flanking regions and contexts of disorder-based interactions. Context constitutes an overarching concept being of physicochemical, biomolecular, and physiological nature, but it also includes the immediate molecular context of the interaction. For intrinsically disordered proteins, which often function by exploiting short linear motifs, context contributes in highly regulatory and decisive manners and constitute a yet largely unrecognized source of interaction potential in a multitude of biological processes. Through selected examples, this review emphasizes how multivalency, charges and charge clusters, hydrophobic patches, dynamics, energetic frustration, and ensemble redistribution of flanking regions or disordered contexts are emerging as important contributors to allosteric regulation, positive and negative cooperativity, feedback regulation and negative selection in binding. The review emphasizes that understanding context, and in particular the role the molecular disordered context and flanking regions take on in protein interactions, constitute an untapped well of energetic modulation potential, also of relevance to drug discovery and development.
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Affiliation(s)
- Katrine Bugge
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Inna Brakti
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Catarina B. Fernandes
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesper E. Dreier
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe E. Lundsgaard
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Johan G. Olsen
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Karen Skriver
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B. Kragelund
- REPIN, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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