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Borkúti P, Kristó I, Szabó A, Kovács Z, Vilmos P. FERM domain-containing proteins are active components of the cell nucleus. Life Sci Alliance 2024; 7:e202302489. [PMID: 38296350 PMCID: PMC10830384 DOI: 10.26508/lsa.202302489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
The FERM domain is a conserved and widespread protein module that appeared in the common ancestor of amoebae, fungi, and animals, and is therefore now found in a wide variety of species. The primary function of the FERM domain is localizing to the plasma membrane through binding lipids and proteins of the membrane; thus, for a long time, FERM domain-containing proteins (FDCPs) were considered exclusively cytoskeletal. Although their role in the cytoplasm has been extensively studied, the recent discovery of the presence and importance of cytoskeletal proteins in the nucleus suggests that FDCPs might also play an important role in nuclear function. In this review, we collected data on their nuclear localization, transport, and possible functions, which are still scattered throughout the literature, with special regard to the role of the FERM domain in these processes. With this, we would like to draw attention to the exciting, new dimension of the role of FDCPs, their nuclear activity, which could be an interesting novel direction for future research.
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Affiliation(s)
| | | | - Anikó Szabó
- HUN-REN Biological Research Centre, Szeged, Hungary
| | - Zoltán Kovács
- HUN-REN Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Péter Vilmos
- HUN-REN Biological Research Centre, Szeged, Hungary
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2
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Hu X, Xu Y, Wang C, Liu Y, Zhang L, Zhang J, Wang W, Chen Q, Liu H. Combined prediction and design reveals the target recognition mechanism of an intrinsically disordered protein interaction domain. Proc Natl Acad Sci U S A 2023; 120:e2305603120. [PMID: 37722056 PMCID: PMC10523638 DOI: 10.1073/pnas.2305603120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/14/2023] [Indexed: 09/20/2023] Open
Abstract
An increasing number of protein interaction domains and their targets are being found to be intrinsically disordered proteins (IDPs). The corresponding target recognition mechanisms are mostly elusive because of challenges in performing detailed structural analysis of highly dynamic IDP-IDP complexes. Here, we show that by combining recently developed computational approaches with experiments, the structure of the complex between the intrinsically disordered C-terminal domain (CTD) of protein 4.1G and its target IDP region in NuMA can be dissected at high resolution. First, we carry out systematic mutational scanning using dihydrofolate reductase-based protein complementarity analysis to identify essential interaction regions and key residues. The results are found to be highly consistent with an α/β-type complex structure predicted by AlphaFold2 (AF2). We then design mutants based on the predicted structure using a deep learning protein sequence design method. The solved crystal structure of one mutant presents the same core structure as predicted by AF2. Further computational prediction and experimental assessment indicate that the well-defined core structure is conserved across complexes of 4.1G CTD with other potential targets. Thus, we reveal that an intrinsically disordered protein interaction domain uses an α/β-type structure module formed through synergistic folding to recognize broad IDP targets. Moreover, we show that computational prediction and experiment can be jointly applied to segregate true IDP regions from the core structural domains of IDP-IDP complexes and to uncover the structure-dependent mechanisms of some otherwise elusive IDP-IDP interactions.
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Affiliation(s)
- Xiuhong Hu
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Yang Xu
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Chenchen Wang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Yufeng Liu
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Lu Zhang
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Jiahai Zhang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Wenning Wang
- Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai200438, China
| | - Quan Chen
- Department of Rheumatology and Immunology, Division of Life Sciences and Medicine, The First Affiliated Hospital, University of Science and Technology of China, Hefei, Anhui230001, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui230027, China
| | - Haiyan Liu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui230027, China
- School of Data Science, University of Science and Technology of China, Hefei, Anhui230027, China
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Partida-Hanon A, Treviño MA, Mompeán M, Jiménez MÁ, Bruix M. Structural insight into the XTACC3/XMAP215 interaction from CD and NMR studies on model peptides. Biopolymers 2017; 107. [PMID: 28922450 DOI: 10.1002/bip.23039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 11/07/2022]
Abstract
TACC3 is a centrosomal adaptor protein that plays important roles during mitotic spindle assembly. It interacts with chTOG/XMAP215, which catalyzes the addition of tubulin dimers during microtubule growth. A 3D coiled-coil model for this interaction is available but the structural details are not well described. To characterize this interaction at atomic resolution, we have designed a simplified version of the system based on small peptides. Four different peptides have been studied by circular dichroism and nuclear magnetic resonance both singly and in all possible combinations; namely, five peptide pairs and two trios. In cosolvents, all single peptides tend to adopt helical conformations resembling those of the full-length protein. However, neither the single peptides nor pairs of peptides form coiled coils. We show that the simultaneous presence of all preformed helices is a prerequisite for binding. The simplest 3D model for the interaction, based on the NMR results, is proposed. Interestingly, the peptide's structure remains unaffected by mutations at essential positions for TACC3 activity. This suggests that the lack of interaction of this TACC3 mutant with XMAP does not correlate with changes in the protein structure and that specific interactions are likely responsible for the interaction and stability of the complex.
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Affiliation(s)
| | - Miguel A Treviño
- Department of Biological Physical Chemistry, IQFR-CSIC, Madrid, 28006, Spain
| | - Miguel Mompeán
- Department of Biological Physical Chemistry, IQFR-CSIC, Madrid, 28006, Spain
| | - Ma Ángeles Jiménez
- Department of Biological Physical Chemistry, IQFR-CSIC, Madrid, 28006, Spain
| | - Marta Bruix
- Department of Biological Physical Chemistry, IQFR-CSIC, Madrid, 28006, Spain
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Wu S, Wang D, Liu J, Feng Y, Weng J, Li Y, Gao X, Liu J, Wang W. The Dynamic Multisite Interactions between Two Intrinsically Disordered Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shaowen Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
| | - Dongdong Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
| | - Jin Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
| | - Yitao Feng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
| | - Yu Li
- King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Thuwal 23955 Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Thuwal 23955 Saudi Arabia
| | - Jianwei Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai 200433 China
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Wu S, Wang D, Liu J, Feng Y, Weng J, Li Y, Gao X, Liu J, Wang W. The Dynamic Multisite Interactions between Two Intrinsically Disordered Proteins. Angew Chem Int Ed Engl 2017; 56:7515-7519. [PMID: 28493424 DOI: 10.1002/anie.201701883] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 01/10/2023]
Abstract
Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well-characterized folding upon binding to dynamic fuzzy complexes. To date, most studies concern the binding of an IDP to a structured protein, while the interaction between two IDPs is poorly understood. In this study, NMR, smFRET, and molecular dynamics (MD) simulation are combined to characterize the interaction between two IDPs, the C-terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by molecular dynamics and mutagenesis studies. This study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.
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Affiliation(s)
- Shaowen Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Dongdong Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Jin Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Yitao Feng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Yu Li
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Jianwei Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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