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Liu Y, Xu Y, Xu Y, Zhao Z, Cheng GJ, Ren R, Chiang YC. Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations. Int J Mol Sci 2024; 25:3729. [PMID: 38612541 PMCID: PMC11011501 DOI: 10.3390/ijms25073729] [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: 01/25/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step in triacylglycerol synthesis. Understanding its substrate recognition mechanism may help to design drugs to regulate the production of glycerol lipids in cells. In this work, we investigate how the native substrate, glycerol-3-phosphate (G3P), and palmitoyl-coenzyme A (CoA) bind to the human GPAT isoform GPAT4 via molecular dynamics simulations (MD). As no experimentally resolved GPAT4 structure is available, the AlphaFold model is employed to construct the GPAT4-substrate complex model. Using another isoform, GPAT1, we demonstrate that once the ligand binding is properly addressed, the AlphaFold complex model can deliver similar results to the experimentally resolved structure in MD simulations. Following the validated protocol of complex construction, we perform MD simulations using the GPAT4-substrate complex. Our simulations reveal that R427 is an important residue in recognizing G3P via a stable salt bridge, but its motion can bring the ligand to different binding hotspots on GPAT4. Such high flexibility can be attributed to the flexible region that exists only on GPAT4 and not on GPAT1. Our study reveals the substrate recognition mechanism of GPAT4 and hence paves the way towards designing GPAT4 inhibitors.
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Affiliation(s)
- Yulan Liu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yunong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yinuo Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Zhihao Zhao
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Gui-Juan Cheng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200438, China
- Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - Ying-Chih Chiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
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Zhao X, Vogirala VK, Liu M, Zhou Y, Rhodes D, Sandin S, Yan J. Exploring TRF2-Dependent DNA Distortion Through Single-DNA Manipulation Studies. Commun Biol 2024; 7:148. [PMID: 38310140 PMCID: PMC10838314 DOI: 10.1038/s42003-024-05838-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/20/2024] [Indexed: 02/05/2024] Open
Abstract
TRF2 is a component of shelterin, a telomere-specific protein complex that protects the ends of mammalian chromosomes from DNA damage signaling and improper repair. TRF2 functions as a homodimer and its interaction with telomeric DNA has been studied, but its full-length DNA-binding properties are unknown. This study examines TRF2's interaction with single-DNA strands and focuses on the conformation of the TRF2-DNA complex and TRF2's preference for DNA chirality. The results show that TRF2-DNA can switch between extended and compact conformations, indicating multiple DNA-binding modes, and TRF2's binding does not have a strong preference for DNA supercoiling chirality when DNA is under low tension. Instead, TRF2 induces DNA bending under tension. Furthermore, both the N-terminal domain of TRF2 and the Myb domain enhance its affinity for the telomere sequence, highlighting the crucial role of multivalent DNA binding in enhancing its affinity and specificity for telomere sequence. These discoveries offer unique insights into TRF2's interaction with telomeric DNA.
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Affiliation(s)
- Xiaodan Zhao
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore
| | - Vinod Kumar Vogirala
- School of Biological Sciences, Nanyang Technology University, 637551, Singapore, Singapore
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Meihan Liu
- Mechanobiology Institute, National University of Singapore, 117411, Singapore, Singapore
| | - Yu Zhou
- Mechanobiology Institute, National University of Singapore, 117411, Singapore, Singapore
| | - Daniela Rhodes
- School of Biological Sciences, Nanyang Technology University, 637551, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technology University, 636921, Singapore, Singapore
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technology University, 637551, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technology University, 636921, Singapore, Singapore.
- Umeå university, KBC-huset (KB), Linnaeus väg 10, Umeå, 90187, Sweden.
| | - Jie Yan
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore.
- Mechanobiology Institute, National University of Singapore, 117411, Singapore, Singapore.
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou, 350207, China.
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3
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Pradhan AK, Modi J, Maji S, Kumar A, Bhoopathi P, Mannangatti P, Guo C, Afosah DK, Mochel MC, Mukhopadhyay ND, Kirkwood JM, Wang XY, Desai UR, Sarkar D, Emdad L, Das SK, Fisher PB. Dual Targeting of the PDZ1 and PDZ2 Domains of MDA-9/Syntenin Inhibits Melanoma Metastasis. Mol Cancer Ther 2023; 22:1115-1127. [PMID: 37721536 DOI: 10.1158/1535-7163.mct-22-0653] [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: 10/07/2022] [Revised: 04/14/2023] [Accepted: 06/27/2023] [Indexed: 09/19/2023]
Abstract
Genome-wide gene expression analysis and animal modeling indicate that melanoma differentiation associated gene-9 (mda-9, Syntenin, Syndecan binding protein, referred to as MDA-9/Syntenin) positively regulates melanoma metastasis. The MDA-9/Syntenin protein contains two tandem PDZ domains serving as a nexus for interactions with multiple proteins that initiate transcription of metastasis-associated genes. Although targeting either PDZ domain abrogates signaling and prometastatic phenotypes, the integrity of both domains is critical for full biological function. Fragment-based drug discovery and NMR identified PDZ1i, an inhibitor of the PDZ1 domain that effectively blocks cancer invasion in vitro and in vivo in multiple experimental animal models. To maximize disruption of MDA-9/Syntenin signaling, an inhibitor has now been developed that simultaneously binds and blocks activity of both PDZ domains. PDZ1i was joined to the second PDZ binding peptide (TNYYFV) with a PEG linker, resulting in PDZ1i/2i (IVMT-Rx-3) that engages both PDZ domains of MDA-9/Syntenin. IVMT-Rx-3 blocks MDA-9/Syntenin interaction with Src, reduces NF-κB activation, and inhibits MMP-2/MMP-9 expression, culminating in repression of melanoma metastasis. The in vivo antimetastatic properties of IVMT-Rx-3 are enhanced when combined with an immune-checkpoint inhibitor. Collectively, our results support the feasibility of engineering MDA-9 dual-PDZ inhibitors with enhanced antimetastatic activities and applications of IVMT-Rx-3 for developing novel therapeutic strategies effectively targeting melanoma and in principle, a broad spectrum of human cancers that also overexpress MDA-9/Syntenin.
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Affiliation(s)
- Anjan K Pradhan
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Jinkal Modi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Santanu Maji
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Amit Kumar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Praveen Bhoopathi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Padmanabhan Mannangatti
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Chunqing Guo
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Daniel K Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Mark C Mochel
- Department of Pathology, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Nitai D Mukhopadhyay
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - John M Kirkwood
- Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Xiang-Yang Wang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- VCU Institute of Molecular Medicine, Massey Comprehensive Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
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Sheehan CT, Hampton TH, Madden DR. Tryptophan mutations in G3BP1 tune the stability of a cellular signaling hub by weakening transient interactions with Caprin1 and USP10. J Biol Chem 2022; 298:102552. [PMID: 36183834 PMCID: PMC9723946 DOI: 10.1016/j.jbc.2022.102552] [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: 03/11/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) often coordinate transient interactions with multiple proteins to mediate complex signals within large protein networks. Among these, the IDP hub protein G3BP1 can form complexes with cytoplasmic phosphoprotein Caprin1 and ubiquitin peptidase USP10; the resulting control of USP10 activity contributes to a pathogenic virulence system that targets endocytic recycling of the ion channel CFTR. However, while the identities of protein interactors are known for many IDP hub proteins, the relationship between pairwise affinities and the extent of protein recruitment and activity is not well understood. Here, we describe in vitro analysis of these G3BP1 affinities and show tryptophan substitutions of specific G3BP1 residues reduce its affinity for both USP10 and Caprin1. We show that these same mutations reduce the stability of complexes between the full-length proteins, suggesting that copurification can serve as a surrogate measure of interaction strength. The crystal structure of G3BP1 TripleW (F15W/F33W/F124W) mutant reveals a clear reorientation of the side chain of W33, creating a steric clash with USP10 and Caprin1. Furthermore, an amino-acid scan of USP10 and Caprin1 peptides reveals similarities and differences in the ability to substitute residues in the core motifs as well as specific substitutions with the potential to create higher affinity peptides. Taken together, these data show that small changes in component binding affinities can have significant effects on the composition of cellular interaction hubs. These specific protein mutations can be harnessed to manipulate complex protein networks, informing future investigations into roles of these networks in cellular processes.
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Affiliation(s)
- Colin T Sheehan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Dean R Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
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