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Clements CM, Henen MA, Vögeli B, Shellman YG. The Structural Dynamics, Complexity of Interactions, and Functions in Cancer of Multi-SAM Containing Proteins. Cancers (Basel) 2023; 15:3019. [PMID: 37296980 PMCID: PMC10252437 DOI: 10.3390/cancers15113019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
SAM domains are crucial mediators of diverse interactions, including those important for tumorigenesis or metastasis of cancers, and thus SAM domains can be attractive targets for developing cancer therapies. This review aims to explore the literature, especially on the recent findings of the structural dynamics, regulation, and functions of SAM domains in proteins containing more than one SAM (multi-SAM containing proteins, MSCPs). The topics here include how intrinsic disorder of some SAMs and an additional SAM domain in MSCPs increase the complexity of their interactions and oligomerization arrangements. Many similarities exist among these MSCPs, including their effects on cancer cell adhesion, migration, and metastasis. In addition, they are all involved in some types of receptor-mediated signaling and neurology-related functions or diseases, although the specific receptors and functions vary. This review also provides a simple outline of methods for studying protein domains, which may help non-structural biologists to reach out and build new collaborations to study their favorite protein domains/regions. Overall, this review aims to provide representative examples of various scenarios that may provide clues to better understand the roles of SAM domains and MSCPs in cancer in general.
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Affiliation(s)
- Christopher M. Clements
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.A.H.); (B.V.)
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (M.A.H.); (B.V.)
| | - Yiqun G. Shellman
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
- Charles C. Gates Regenerative Medicine and Stem Cell Biology Institute, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Hayashi S, Matsubara T, Fukuda K, Maeda T, Funahashi K, Hashimoto M, Takashima Y, Kikuchi K, Fujita M, Matsumoto T, Kuroda R. A genome-wide association study identifying single nucleotide polymorphisms in the PPFIBP2 gene was predictive for interstitial lung disease in rheumatoid arthritis patients. Rheumatol Adv Pract 2022; 6:rkac088. [PMID: 36382269 PMCID: PMC9651976 DOI: 10.1093/rap/rkac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Genetic polymorphisms might serve as useful prognostic markers for the timely diagnosis of RA. The purpose of this study was to identify genomic factors predictive of the occurrence of interstitial lung disease (ILD) in RA by performing a genome-wide association study of genetic variants, including single nucleotide polymorphisms (SNPs). Methods The study population included 306 RA patients. All patients were treated with conventional DMARDs, including 6–16 mg MTX per week. Clinical data and venous blood samples were collected from all patients before administration of DMARDs. A total of 278 347 SNPs were analysed to determine their association with ILD occurrence. Results Several SNPs were strongly associated with ILD occurrence (P < 10−5). rs6578890, which is located on chromosome 11 in the intronic region of the gene encoding tyrosine phosphatase receptor type F polypeptide-interacting protein-binding protein 2 (PPFIBP2), showed the strongest association with ILD occurrence (odds ratio 4.32, P = 10−7.93). Conclusion PPFIBP2 could be a useful genetic marker for occurrence of interstitial pneumonia in RA patients and might help to identify the risk of ILD occurrence before RA treatment, thereby improving patient outcomes.
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Affiliation(s)
- Shinya Hayashi
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
| | - Tsukasa Matsubara
- Department of Orthopaedic Surgery, Matsubara Mayflower Hospital , Kato, Japan
| | - Koji Fukuda
- Department of Orthopaedic Surgery, Matsubara Mayflower Hospital , Kato, Japan
| | - Toshihisa Maeda
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
| | | | | | - Yoshinori Takashima
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
| | - Kenichi Kikuchi
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
| | - Masahiro Fujita
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
| | - Tomoyuki Matsumoto
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
| | - Ryosuke Kuroda
- Department of Orthopaedic Surgery, Kobe University Graduate School of Medicine , Kobe, Japan
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Bagnéris C, Rogala KB, Baratchian M, Zamfir V, Kunze MBA, Dagless S, Pirker KF, Collins MK, Hall BA, Barrett TE, Kay CWM. Probing the Solution Structure of IκB Kinase (IKK) Subunit γ and Its Interaction with Kaposi Sarcoma-associated Herpes Virus Flice-interacting Protein and IKK Subunit β by EPR Spectroscopy. J Biol Chem 2015; 290:16539-49. [PMID: 25979343 PMCID: PMC4505408 DOI: 10.1074/jbc.m114.622928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/13/2015] [Indexed: 01/04/2023] Open
Abstract
Viral flice-interacting protein (vFLIP), encoded by the oncogenic Kaposi sarcoma-associated herpes virus (KSHV), constitutively activates the canonical nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) pathway. This is achieved through subversion of the IκB kinase (IKK) complex (or signalosome), which involves a physical interaction between vFLIP and the modulatory subunit IKKγ. Although this interaction has been examined both in vivo and in vitro, the mechanism by which vFLIP activates the kinase remains to be determined. Because IKKγ functions as a scaffold, recruiting both vFLIP and the IKKα/β subunits, it has been proposed that binding of vFLIP could trigger a structural rearrangement in IKKγ conducive to activation. To investigate this hypothesis we engineered a series of mutants along the length of the IKKγ molecule that could be individually modified with nitroxide spin labels. Subsequent distance measurements using electron paramagnetic resonance spectroscopy combined with molecular modeling and molecular dynamics simulations revealed that IKKγ is a parallel coiled-coil whose response to binding of vFLIP or IKKβ is localized twisting/stiffening and not large-scale rearrangements. The coiled-coil comprises N- and C-terminal regions with distinct registers accommodated by a twist: this structural motif is exploited by vFLIP, allowing it to bind and subsequently activate the NF-κB pathway. In vivo assays confirm that NF-κB activation by vFLIP only requires the N-terminal region up to the transition between the registers, which is located directly C-terminal of the vFLIP binding site.
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Affiliation(s)
- Claire Bagnéris
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Kacper B Rogala
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom, Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Mehdi Baratchian
- MRC Centre for Medical Molecular Virology, UCL Cancer Institute and National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom
| | - Vlad Zamfir
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom, Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Micha B A Kunze
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Selina Dagless
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Katharina F Pirker
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Mary K Collins
- MRC Centre for Medical Molecular Virology, UCL Cancer Institute and National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom
| | - Benjamin A Hall
- MRC Cancer Unit, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XZ, United Kingdom, and
| | - Tracey E Barrett
- From the Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom,
| | - Christopher W M Kay
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, United Kingdom, London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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The Liprin homology domain is essential for the homomeric interaction of SYD-2/Liprin-α protein in presynaptic assembly. J Neurosci 2012; 31:16261-8. [PMID: 22072677 DOI: 10.1523/jneurosci.0002-11.2011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synapses are asymmetric structures that are specialized for neuronal signal transduction. A unique set of proteins is present at the presynaptic active zone, which is a core structure essential for neurotransmitter release. In Caenorhabditis elegans HSN neurons, SYD-2, a Liprin-α family protein, acts together with a GAP protein SYD-1 to promote presynaptic assembly. Previous studies have shown that elevating the activity of syd-2 can bypass the requirement of syd-1. Liprin-α proteins are composed of coiled-coil-rich regions in the N-terminal half, which mediate interactions with adapter proteins at the presynaptic active zone, and three SAM domains in the C terminus, which bind proteins such as LAR receptor tyrosine phosphatase. To address the molecular mechanism by which SYD-2 activity is regulated, we performed structure-function studies. By monitoring the ability of SYD-2 transgenes to rescue syd-2(lf) and to suppress syd-1(lf) phenotypes in HSN neuron synapses, we identified the N-terminal half of SYD-2 as minimally required for rescuing syd-2(lf) phenotypes. A highly conserved short coiled-coil segment named Liprin Homology 1 (LH1) domain is both necessary and sufficient to suppress syd-1(lf) defects. We show that the LH1 domain forms a dimer and promotes further oligomerization and/or complex formation of SYD-2/Liprin-α proteins. The role of the LH1 domain in presynaptic assembly can be partially complemented by artificial dimerization. These findings suggest a model by which the self-assembly of SYD-2/Liprin-α proteins mediated by the coiled-coil LH1 domain is one of the key steps to the accumulation of presynaptic components at nascent synaptic junctions.
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