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Harracksingh AN, Singh A, Mayorova T, Bejoy B, Hornbeck J, Elkhatib W, McEdwards G, Gauberg J, Taha ARW, Islam IM, Erclik T, Currie MA, Noyes M, Senatore A. The binding of Mint/X11 PDZ domains to Ca V 2 calcium channels predates bilaterian animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582151. [PMID: 38463976 PMCID: PMC10925089 DOI: 10.1101/2024.02.26.582151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
PDZ domain mediated interactions with voltage-gated calcium (Ca V ) channel C-termini play important roles in localizing and compartmentalizing membrane Ca 2+ signaling. The first such interaction discovered was between the neuronal multi-domain protein Mint-1, and the presynaptc calcium channel Ca V 2.2 in mammals. Although the physiological significance of this interaction is unclear, its occurrence in vertebrates and bilaterian invertebrates suggests important and conserved functions. In this study, we explore the evolutionary origins of Mint and its interaction with Ca V 2 channels. Phylogenetic and structural in silico analyses revealed that Mint is an animal-specific gene, like Ca V 2 channels, which bears a highly divergent N-terminus but strongly conserved C-terminus comprised of a phosphotyrosine binding domain, two tandem PDZ domains (PDZ-1 and PDZ-2), and a C-terminal auto-inhibitory element that binds and inhibits PDZ-1. Also deeply conserved are other Mint interacting proteins, namely amyloid precursor and related proteins, presenilins, neurexin, as well as CASK and Veli which form a tripartite complex with Mint in bilaterians. Through yeast 2-hybrid and bacterial 2-hybrid experiments, we show that Mint and Ca V 2 channels from cnidarians and placozoans interact in vitro , and in situ hybridization revealed co-expression of corresponding transcripts in dissociated neurons from the cnidarian Nematostella vectensis . Unexpectedly, the Mint orthologue from the ctenophore Hormiphora californiensis was able to strongly bind the divergent C-terminal ligands of cnidarian and placozoan Ca V 2 channels, despite neither the ctenophore Mint, nor the placozoan and cnidarian orthologues, binding the ctenophore Ca V 2 channel C-terminus. Altogether, our analyses provide a model for the emergence of this interaction in early animals first via adoption of a PDZ ligand by Ca V 2 channels, followed by sequence changes in the ligand that caused a modality switch for binding to Mint.
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Ji Z, Belfield EJ, Zhang S, Bouvier J, Li S, Schnell J, Fu X, Harberd NP. Evolution of a plant growth-regulatory protein interaction specificity. NATURE PLANTS 2023; 9:2059-2070. [PMID: 37903985 PMCID: PMC10724065 DOI: 10.1038/s41477-023-01556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023]
Abstract
Specific protein-protein interactions (PPIs) enable biological regulation. However, the evolution of PPI specificity is little understood. Here we trace the evolution of the land-plant growth-regulatory DELLA-SLY1/GID2 PPI, revealing progressive increase in specificity of affinity of SLY1/GID2 for a particular DELLA form. While early-diverging SLY1s display relatively broad-range DELLA affinity, later-diverging SLY1s tend towards increasingly stringent affinity for a specific DELLA A' form generated by the growth-promoting phytohormone gibberellin (GA). Our novel mutational strategy reveals amino acid substitutions contributing to the evolution of Arabidopsis thaliana SLY1 A' specificity, also showing that routes permitting reversion to broader affinity became increasingly constrained over evolutionary time. We suggest that progressive affinity narrowing may be an important evolutionary driver of PPI specificity and that increase in SLY1/GID2-DELLA specificity enabled the enhanced flexibility of plant physiological environmental adaptation conferred by the GA-DELLA growth-regulatory mechanism.
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Affiliation(s)
- Zhe Ji
- Department of Biology, University of Oxford, Oxford, UK
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
| | | | - Siyu Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, PR China
| | | | - Shan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, PR China
| | - Jason Schnell
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China
- New Cornerstone Science Laboratory, Beijing, P. R. China
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Nam K, Wolf-Watz M. Protein dynamics: The future is bright and complicated! STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:014301. [PMID: 36865927 PMCID: PMC9974214 DOI: 10.1063/4.0000179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions occurring on micro to milliseconds. An outstanding challenge in contemporary biophysics and structural biology is a quantitative understanding of the linkages among protein structure, dynamics, and function. These linkages are becoming increasingly explorable due to conceptual and methodological advances. In this Perspective article, we will point toward future directions of the field of protein dynamics with an emphasis on enzymes. Research questions in the field are becoming increasingly complex such as the mechanistic understanding of high-order interaction networks in allosteric signal propagation through a protein matrix, or the connection between local and collective motions. In analogy to the solution to the "protein folding problem," we argue that the way forward to understanding these and other important questions lies in the successful integration of experiment and computation, while utilizing the present rapid expansion of sequence and structure space. Looking forward, the future is bright, and we are in a period where we are on the doorstep to, at least in part, comprehend the importance of dynamics for biological function.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
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Nocedal I, Laub MT. Ancestral reconstruction of duplicated signaling proteins reveals the evolution of signaling specificity. eLife 2022; 11:e77346. [PMID: 35686729 PMCID: PMC9208753 DOI: 10.7554/elife.77346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/27/2022] [Indexed: 01/30/2023] Open
Abstract
Gene duplication is crucial to generating novel signaling pathways during evolution. However, it remains unclear how the redundant proteins produced by gene duplication ultimately acquire new interaction specificities to establish insulated paralogous signaling pathways. Here, we used ancestral sequence reconstruction to resurrect and characterize a bacterial two-component signaling system that duplicated in α-proteobacteria. We determined the interaction specificities of the signaling proteins that existed before and immediately after this duplication event and then identified key mutations responsible for establishing specificity in the two systems. Just three mutations, in only two of the four interacting proteins, were sufficient to establish specificity of the extant systems. Some of these mutations weakened interactions between paralogous systems to limit crosstalk. However, others strengthened interactions within a system, indicating that the ancestral interaction, although functional, had the potential to be strengthened. Our work suggests that protein-protein interactions with such latent potential may be highly amenable to duplication and divergence.
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Affiliation(s)
- Isabel Nocedal
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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Karlsson E, Sorgenfrei FA, Andersson E, Dogan J, Jemth P, Chi CN. The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved. Commun Biol 2022; 5:286. [PMID: 35354917 PMCID: PMC8967867 DOI: 10.1038/s42003-022-03217-y] [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: 09/08/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022] Open
Abstract
Evolution of proteins is constrained by their structure and function. While there is a consensus that the plasticity of intrinsically disordered proteins relaxes the structural constraints on evolution there is a paucity of data on the molecular details of these processes. The Nuclear Coactivator Binding Domain (NCBD) from CREB-binding protein is a protein interaction domain, which contains a hydrophobic core but is not behaving as a typical globular domain, and has been described as 'molten-globule like'. The highly dynamic properties of NCBD makes it an interesting model system for evolutionary structure-function investigation of intrinsically disordered proteins. We have here compared the structure and biophysical properties of an ancient version of NCBD present in a bilaterian animal ancestor living around 600 million years ago with extant human NCBD. Using a combination of NMR spectroscopy, circular dichroism and kinetics we show that although NCBD has increased its thermodynamic stability, it has retained its dynamic biophysical properties in the ligand-free state in the evolutionary lineage leading from the last common bilaterian ancestor to humans. Our findings suggest that the dynamic properties of NCBD have been maintained by purifying selection and thus are important for its function, which includes mediating several distinct protein-protein interactions.
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Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Frieda A Sorgenfrei
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.,acib GmbH, Krenngasse 37, 8010 Graz c/o University of Graz, Institute of Chemistry, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Jakob Dogan
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden. .,Department of Pharmaceutical Biosciences, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.
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