1
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Schwalbe H, Audergon P, Haley N, Amaro CA, Agirre J, Baldus M, Banci L, Baumeister W, Blackledge M, Carazo JM, Carugo KD, Celie P, Felli I, Hart DJ, Hauß T, Lehtiö L, Lindorff-Larsen K, Márquez J, Matagne A, Pierattelli R, Rosato A, Sobott F, Sreeramulu S, Steyaert J, Sussman JL, Trantirek L, Weiss MS, Wilmanns M. The future of integrated structural biology. Structure 2024; 32:1563-1580. [PMID: 39293444 DOI: 10.1016/j.str.2024.08.014] [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: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/22/2024] [Indexed: 09/20/2024]
Abstract
Instruct-ERIC, "the European Research Infrastructure Consortium for Structural biology research," is a pan-European distributed research infrastructure making high-end technologies and methods in structural biology available to users. Here, we describe the current state-of-the-art of integrated structural biology and discuss potential future scientific developments as an impulse for the scientific community, many of which are located in Europe and are associated with Instruct. We reflect on where to focus scientific and technological initiatives within the distributed Instruct research infrastructure. This review does not intend to make recommendations on funding requirements or initiatives directly, neither at the national nor the European level. However, it addresses future challenges and opportunities for the field, and foresees the need for a stronger coordination within the European and international research field of integrated structural biology to be able to respond timely to thematic topics that are often prioritized by calls for funding addressing societal needs.
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Affiliation(s)
- Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt/M., Germany; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK.
| | - Pauline Audergon
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK
| | - Natalie Haley
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK
| | - Claudia Alen Amaro
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford OX4 2JY, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, UK
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Lucia Banci
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine-CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Martin Blackledge
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS UMR5075, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jose Maria Carazo
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | | | - Patrick Celie
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Isabella Felli
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine-CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Darren J Hart
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS UMR5075, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Thomas Hauß
- Macromolecular Crystallography, Helmholtz-Zentrum, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - José Márquez
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, InBioS Research Unit, University of Liège, Building B6C, Quartier Agora, Allée du 6 Août, 13, 4000 Liège (Sart-Tilman), Belgium
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff", University of Florence and Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine-CIRMMP, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt/M., Germany
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, Brussels, Belgium
| | - Joel L Sussman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lukas Trantirek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL) Hamburg, Hamburg, Germany
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2
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Zhang G, Zhang C, Cai M, Luo C, Zhu F, Liang Z. FuncPhos-STR: An integrated deep neural network for functional phosphosite prediction based on AlphaFold protein structure and dynamics. Int J Biol Macromol 2024; 266:131180. [PMID: 38552697 DOI: 10.1016/j.ijbiomac.2024.131180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Phosphorylation modifications play important regulatory roles in most biological processes. However, the functional assignment for the vast majority of the identified phosphosites remains a major challenge. Here, we provide a deep learning framework named FuncPhos-STR as an online resource, for functional prediction and structural visualization of human proteome-level phosphosites. Based on our reported FuncPhos-SEQ framework, which was built by integrating phosphosite sequence evolution and protein-protein interaction (PPI) information, FuncPhos-STR was developed by further integrating the structural and dynamics information on AlphaFold protein structures. The characterized structural topology and dynamics features underlying functional phosphosites emphasized their molecular mechanism for regulating protein functions. By integrating the structural and dynamics, sequence evolutionary, and PPI network features from protein different dimensions, FuncPhos-STR has advantage over other reported models, with the best AUC value of 0.855. Using FuncPhos-STR, the phosphosites inside the pocket regions are accessible to higher functional scores, theoretically supporting their potential regulatory mechanism. Overall, FuncPhos-STR would accelerate the functional identification of huge unexplored phosphosites, and facilitate the elucidation of their allosteric regulation mechanisms. The web server of FuncPhos-STR is freely available at http://funcptm.jysw.suda.edu.cn/str.
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Affiliation(s)
- Guangyu Zhang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Cai Zhang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Mingyue Cai
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Fei Zhu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China.
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China.
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3
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Zhang S, Cheng Y, Guan Y, Wen J, Chen Z. Hydrogen Sulfide Exerted a Pro-Angiogenic Role by Promoting the Phosphorylation of VEGFR2 at Tyr797 and Ser799 Sites in Hypoxia-Reoxygenation Injury. Int J Mol Sci 2024; 25:4340. [PMID: 38673925 PMCID: PMC11050214 DOI: 10.3390/ijms25084340] [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: 03/05/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The protective effects of hydrogen sulfide (H2S) against ischemic brain injury and its role in promoting angiogenesis have been established. However, the specific mechanism underlying these effects remains unclear. This study is designed to investigate the regulatory impact and mechanism of H2S on VEGFR2 phosphorylation. Following expression and purification, the recombinant His-VEGFR2 protein was subjected to LC-PRM/MS analysis to identify the phosphorylation sites of VEGFR2 upon NaHS treatment. Adenovirus infection was used to transfect primary rat brain artery endothelial cells (BAECs) with the Ad-VEGFR2WT, Ad-VEGFR2Y797F, and Ad-VEGFR2S799A plasmids. The expression of VEGFR2 and recombinant Flag-VEGFR2, along with Akt phosphorylation, cell proliferation, and LDH levels, was assessed. The migratory capacity and tube-forming potential of BAECs were assessed using wound healing, transwell, and tube formation assays. NaHS notably enhanced the phosphorylation of VEGFR2 at Tyr797 and Ser799 sites. These phosphorylation sites were identified as crucial for mediating the protective effects of NaHS against hypoxia-reoxygenation (H/R) injury. NaHS significantly enhanced the Akt phosphorylation, migratory capacity, and tube formation of BAECs and upregulated the expression of VEGFR2 and recombinant proteins. These findings suggest that Tyr797 and Ser799 sites of VEGFR2 serve as crucial mediators of H2S-induced pro-angiogenic effects and protection against H/R injury.
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Affiliation(s)
- Sen Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Yongfeng Cheng
- Clinical Medical College, Anhui Medical University, Hefei 230012, China;
| | - Yining Guan
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Jiyue Wen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Zhiwu Chen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
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Yang YH, Yang JT, Liu JF. Lactylation prediction models based on protein sequence and structural feature fusion. Brief Bioinform 2024; 25:bbad539. [PMID: 38385873 PMCID: PMC10939394 DOI: 10.1093/bib/bbad539] [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: 09/05/2023] [Revised: 11/14/2023] [Accepted: 12/27/2023] [Indexed: 02/23/2024] Open
Abstract
Lysine lactylation (Kla) is a newly discovered posttranslational modification that is involved in important life activities, such as glycolysis-related cell function, macrophage polarization and nervous system regulation, and has received widespread attention due to the Warburg effect in tumor cells. In this work, we first design a natural language processing method to automatically extract the 3D structural features of Kla sites, avoiding potential biases caused by manually designed structural features. Then, we establish two Kla prediction frameworks, Attention-based feature fusion Kla model (ABFF-Kla) and EBFF-Kla, to integrate the sequence features and the structure features based on the attention layer and embedding layer, respectively. The results indicate that ABFF-Kla and Embedding-based feature fusion Kla model (EBFF-Kla), which fuse features from protein sequences and spatial structures, have better predictive performance than that of models that use only sequence features. Our work provides an approach for the automatic extraction of protein structural features, as well as a flexible framework for Kla prediction. The source code and the training data of the ABFF-Kla and the EBFF-Kla are publicly deposited at: https://github.com/ispotato/Lactylation_model.
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Affiliation(s)
- Ye-Hong Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, No.5, Dongdan 3, Dongcheng District Municipality of Beijing, Beijing 100005, China
| | - Jun-Tao Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, No.5, Dongdan 3, Dongcheng District Municipality of Beijing, Beijing 100005, China
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100144, PR China
| | - Jiang-Feng Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, No.5, Dongdan 3, Dongcheng District Municipality of Beijing, Beijing 100005, China
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100144, PR China
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5
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Liang Z, Liu T, Li Q, Zhang G, Zhang B, Du X, Liu J, Chen Z, Ding H, Hu G, Lin H, Zhu F, Luo C. Deciphering the functional landscape of phosphosites with deep neural network. Cell Rep 2023; 42:113048. [PMID: 37659078 DOI: 10.1016/j.celrep.2023.113048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/11/2023] [Accepted: 08/11/2023] [Indexed: 09/04/2023] Open
Abstract
Current biochemical approaches have only identified the most well-characterized kinases for a tiny fraction of the phosphoproteome, and the functional assignments of phosphosites are almost negligible. Herein, we analyze the substrate preference catalyzed by a specific kinase and present a novel integrated deep neural network model named FuncPhos-SEQ for functional assignment of human proteome-level phosphosites. FuncPhos-SEQ incorporates phosphosite motif information from a protein sequence using multiple convolutional neural network (CNN) channels and network features from protein-protein interactions (PPIs) using network embedding and deep neural network (DNN) channels. These concatenated features are jointly fed into a heterogeneous feature network to prioritize functional phosphosites. Combined with a series of in vitro and cellular biochemical assays, we confirm that NADK-S48/50 phosphorylation could activate its enzymatic activity. In addition, ERK1/2 are discovered as the primary kinases responsible for NADK-S48/50 phosphorylation. Moreover, FuncPhos-SEQ is developed as an online server.
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Affiliation(s)
- Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| | - Tonghai Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qi Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Guangyu Zhang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Bei Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xikun Du
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Jingqiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| | - Hao Lin
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Fei Zhu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China.
| | - Cheng Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China; School of Pharmacy, Fujian Medical University, Fuzhou 350122, China.
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6
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Pergu R, Shoba VM, Chaudhary SK, Munkanatta Godage DNP, Deb A, Singha S, Dhawa U, Singh P, Anokhina V, Singh S, Siriwardena SU, Choudhary A. Development and Applications of Chimera Platforms for Tyrosine Phosphorylation. ACS CENTRAL SCIENCE 2023; 9:1558-1566. [PMID: 37637727 PMCID: PMC10450875 DOI: 10.1021/acscentsci.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 08/29/2023]
Abstract
Chimeric small molecules that induce post-translational modification (PTM) on a target protein by bringing it into proximity to a PTM-inducing enzyme are furnishing novel modalities to perturb protein function. Despite recent advances, such molecules are unavailable for a critical PTM, tyrosine phosphorylation. Furthermore, the contemporary design paradigm of chimeric molecules, formed by joining a noninhibitory binder of the PTM-inducing enzyme with the binder of the target protein, prohibits the recruitment of most PTM-inducing enzymes as their noninhibitory binders are unavailable. Here, we report two platforms to generate phosphorylation-inducing chimeric small molecules (PHICS) for tyrosine phosphorylation. We generate PHICS from both noninhibitory binders (scantily available, platform 1) and kinase inhibitors (abundantly available, platform 2) using cysteine-based group transfer chemistry. PHICS triggered phosphorylation on tyrosine residues in diverse sequence contexts and target proteins (e.g., membrane-associated, cytosolic) and displayed multiple bioactivities, including the initiation of a growth receptor signaling cascade and the death of drug-resistant cancer cells. These studies provide an approach to induce biologically relevant PTM and lay the foundation for pharmacologic PTM editing (i.e., induction or removal) of target proteins using abundantly available inhibitors of PTM-inducing or -erasing enzymes.
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Affiliation(s)
- Rajaiah Pergu
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Veronika M. Shoba
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Santosh K. Chaudhary
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | | | - Arghya Deb
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Santanu Singha
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Uttam Dhawa
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Prashant Singh
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Viktoriya Anokhina
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Sameek Singh
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Sachini U. Siriwardena
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Amit Choudhary
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions
of Renal Medicine and Engineering, Brigham
and Women’s Hospital, Boston, Massachusetts 02115, United States
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7
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Chen X, Ma L, Zhao J, Pan X, Chen S. Effect of empagliflozin on cytoskeletal repair in the hippocampus of obese mice. Front Neurosci 2022; 16:1000839. [PMID: 36408417 PMCID: PMC9667058 DOI: 10.3389/fnins.2022.1000839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/22/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE We aimed to investigate the effect of empagliflozin on hippocampal phosphorylated protein levels in obese mice. MATERIALS AND METHODS Sixteen obese mice successfully modeled on high-fat diet were randomly divided into high-fat feeding group (group H) and empagliflozin group (group H + empagliflozin, group E), eight mice in each group, and eight C57BL/6J male normal mice were selected as the control group (normal control, group C). Group E was treated with empagliflozin 10 mg/kg/d for 12 weeks, while mice in groups H and C were treated with equal amounts of saline. The spatial learning memory ability of the mice was determined by the Morris water maze experiment. Further, their body weights and serological indices were measured. Finally, total proteins were extracted from hippocampal tissues for functional analysis by the phosphorylated proteomics method. RESULTS The results showed that escape latency was prolonged, retention time in the target quadrant was shortened, and the number of loop penetrations was reduced in the obese mice induced by a high-calorie diet compared with normal controls, whereas escape latency was shortened, retention time in the target quadrant was increased, and the number of loop penetrations was increased after empagliflozin treatment. Phosphoproteomics in the high-fat/control (H/C), empagliflozin/high-fat (E/H), and E/C groups showed 844, 1,552, and 1,512 differentially significant phosphorylation sites, respectively. The proteins corresponding to these differentially phosphorylated sites were mainly involved in neurodegenerative pathways and actin cytoskeleton regulation. Notably, myosin heavy chain 10 (MYH10), p21 protein-activated kinase 4 (PAK4), phosphatidylinositol 3 -phosphate 5-kinase (PIKfyve), and other differentially phosphorylated proteins were involved in actin cytoskeleton regulation. CONCLUSION We concluded that empagliflozin protects cognitive functions by inducing serine phosphorylation in MYH10, PAK4, and PIKfyve in the hippocampal tissue of obese mice.
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Affiliation(s)
- Xiaoyi Chen
- Graduate School of Hebei North University, Zhangjiakou, China,Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China
| | - Liang Ma
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Jingyu Zhao
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China,Graduate School of North China University of Science and Technology, Tangshan, China
| | - Xiaoyu Pan
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China
| | - Shuchun Chen
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China,*Correspondence: Shuchun Chen,
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8
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Senturk A, Sahin AT, Armutlu A, Kiremit MC, Acar O, Erdem S, Bagbudar S, Esen T, Ozlu N. Quantitative Phosphoproteomics Analysis Uncovers PAK2- and CDK1-Mediated Malignant Signaling Pathways in Clear Cell Renal Cell Carcinoma. Mol Cell Proteomics 2022; 21:100417. [PMID: 36152754 PMCID: PMC9637947 DOI: 10.1016/j.mcpro.2022.100417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 08/23/2022] [Accepted: 09/19/2022] [Indexed: 01/18/2023] Open
Abstract
Clear cell Renal Cell Carcinoma (ccRCC) is among the 10 most common cancers in both men and women and causes more than 140,000 deaths worldwide every year. In order to elucidate the underlying molecular mechanisms orchestrated by phosphorylation modifications, we performed a comprehensive quantitative phosphoproteomics characterization of ccRCC tumor and normal adjacent tissues. Here, we identified 16,253 phosphopeptides, of which more than 9000 were singly quantified. Our in-depth analysis revealed 600 phosphopeptides to be significantly differentially regulated between tumor and normal tissues. Moreover, our data revealed that significantly up-regulated phosphoproteins are associated with protein synthesis and cytoskeletal re-organization which suggests proliferative and migratory behavior of renal tumors. This is supported by a mesenchymal profile of ccRCC phosphorylation events. Our rigorous characterization of the renal phosphoproteome also suggests that both epidermal growth factor receptor and vascular endothelial growth factor receptor are important mediators of phospho signaling in RCC pathogenesis. Furthermore, we determined the kinases p21-activated kinase 2, cyclin-dependent kinase 1 and c-Jun N-terminal kinase 1 to be master kinases that are responsible for phosphorylation of many substrates associated with cell proliferation, inflammation and migration. Moreover, high expression of p21-activated kinase 2 is associated with worse survival outcome of ccRCC patients. These master kinases are targetable by inhibitory drugs such as fostamatinib, minocycline, tamoxifen and bosutinib which can serve as novel therapeutic agents for ccRCC treatment.
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Affiliation(s)
- Aydanur Senturk
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Ayse T. Sahin
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Ayse Armutlu
- Department of Pathology, Koc University School of Medicine, Istanbul, Turkey
| | - Murat Can Kiremit
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
| | - Omer Acar
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
| | - Selcuk Erdem
- Department of Urology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Sidar Bagbudar
- Department of Pathology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Tarik Esen
- Department of Urology, Koc University School of Medicine, Istanbul, Turkey
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey,Koc University Research Center for Translational Medicine (KUTTAM), Omics Laboratory, Istanbul, Turkey,For correspondence: Nurhan Ozlu
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9
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Bludau I, Willems S, Zeng WF, Strauss MT, Hansen FM, Tanzer MC, Karayel O, Schulman BA, Mann M. The structural context of posttranslational modifications at a proteome-wide scale. PLoS Biol 2022; 20:e3001636. [PMID: 35576205 PMCID: PMC9135334 DOI: 10.1371/journal.pbio.3001636] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/26/2022] [Accepted: 04/19/2022] [Indexed: 01/01/2023] Open
Abstract
The recent revolution in computational protein structure prediction provides folding models for entire proteomes, which can now be integrated with large-scale experimental data. Mass spectrometry (MS)-based proteomics has identified and quantified tens of thousands of posttranslational modifications (PTMs), most of them of uncertain functional relevance. In this study, we determine the structural context of these PTMs and investigate how this information can be leveraged to pinpoint potential regulatory sites. Our analysis uncovers global patterns of PTM occurrence across folded and intrinsically disordered regions. We found that this information can help to distinguish regulatory PTMs from those marking improperly folded proteins. Interestingly, the human proteome contains thousands of proteins that have large folded domains linked by short, disordered regions that are strongly enriched in regulatory phosphosites. These include well-known kinase activation loops that induce protein conformational changes upon phosphorylation. This regulatory mechanism appears to be widespread in kinases but also occurs in other protein families such as solute carriers. It is not limited to phosphorylation but includes ubiquitination and acetylation sites as well. Furthermore, we performed three-dimensional proximity analysis, which revealed examples of spatial coregulation of different PTM types and potential PTM crosstalk. To enable the community to build upon these first analyses, we provide tools for 3D visualization of proteomics data and PTMs as well as python libraries for data accession and processing.
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Affiliation(s)
- Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sander Willems
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wen-Feng Zeng
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian T. Strauss
- Proteomics Program, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fynn M. Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria C. Tanzer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Proteomics Program, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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