1
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Han J, Jung JH, Lee SY, Park JH. Nanoplasmonic Detection of EGFR Mutations Based on Extracellular Vesicle-Derived EGFR-Drug Interaction. ACS APPLIED MATERIALS & INTERFACES 2024; 16:8266-8274. [PMID: 38335730 DOI: 10.1021/acsami.3c14907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Analysis of membrane proteins from extracellular vesicles (EVs) has emerged as an important strategy for molecular cancer diagnosis. The epidermal growth factor receptor (EGFR) is one of the most well-known oncogenic membrane proteins, particularly in non-small cell lung cancer (NSCLC), where targeted therapies using tyrosine kinase inhibitors (TKIs) are often addressed based on EGFR mutation status. Consequently, several studies aimed at analyzing oncogenic membrane proteins have been proposed for cancer diagnosis. However, conventional protein analysis still faces limitations due to the requirement for large sample quantities and extensive post-labeling processes. Here, we develop a nanoplasmonic detection method for EGFR mutations in the diagnosis of NSCLC based on interactions between EGFR loaded in EVs and TKI. Gefitinib is selected as a model TKI due to its strong signals in the surface-enhanced Raman spectroscopy (SERS) and mutation-dependent binding affinity to EGFR. We demonstrate an SERS signal attributed to gefitinib at a higher value in the EGFR exon 19 deletion, both in cells and EVs, compared to wild-type and exon 19 deletion/T790M variants. Furthermore, we observe a significantly higher gefitinib SERS signal in EGFR obtained from exon 19 deletion NSCLC patient plasma-derived EVs compared with those from wild-type and exon 19 deletion/T790M EVs. Since our approach utilizes an analysis of the SERS signal generated by the interaction between oncogenic membrane proteins within EVs and targeted drugs, its diagnostic applicability could potentially extend to other liquid biopsy methods based on EVs.
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Affiliation(s)
- Junhee Han
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jik-Han Jung
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sung Yong Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Ji-Ho Park
- Department of Bio and Brain Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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2
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Kiouri DP, Ntallis C, Kelaidonis K, Peana M, Tsiodras S, Mavromoustakos T, Giuliani A, Ridgway H, Moore GJ, Matsoukas JM, Chasapis CT. Network-Based Prediction of Side Effects of Repurposed Antihypertensive Sartans against COVID-19 via Proteome and Drug-Target Interactomes. Proteomes 2023; 11:21. [PMID: 37368467 DOI: 10.3390/proteomes11020021] [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: 04/10/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
The potential of targeting the Renin-Angiotensin-Aldosterone System (RAAS) as a treatment for the coronavirus disease 2019 (COVID-19) is currently under investigation. One way to combat this disease involves the repurposing of angiotensin receptor blockers (ARBs), which are antihypertensive drugs, because they bind to angiotensin-converting enzyme 2 (ACE2), which in turn interacts with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. However, there has been no in silico analysis of the potential toxicity risks associated with the use of these drugs for the treatment of COVID-19. To address this, a network-based bioinformatics methodology was used to investigate the potential side effects of known Food and Drug Administration (FDA)-approved antihypertensive drugs, Sartans. This involved identifying the human proteins targeted by these drugs, their first neighbors, and any drugs that bind to them using publicly available experimentally supported data, and subsequently constructing proteomes and protein-drug interactomes. This methodology was also applied to Pfizer's Paxlovid, an antiviral drug approved by the FDA for emergency use in mild-to-moderate COVID-19 treatment. The study compares the results for both drug categories and examines the potential for off-target effects, undesirable involvement in various biological processes and diseases, possible drug interactions, and the potential reduction in drug efficiency resulting from proteoform identification.
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Affiliation(s)
- Despoina P Kiouri
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Charalampos Ntallis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Thomas Mavromoustakos
- Department of Chemistry, Laboratory of Organic Chemistry, National Kapodistrian University of Athens, 15772 Athens, Greece
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Graham J Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V6Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - John M Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
| | - Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
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Sriram N, Mukherjee S, Sah MK. Gene expression profiling and protein-protein interaction analysis reveals the dynamic role of MCM7 in Alzheimer's disorder and breast cancer. 3 Biotech 2022; 12:146. [PMID: 35698583 DOI: 10.1007/s13205-022-03207-1] [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: 02/23/2022] [Accepted: 05/14/2022] [Indexed: 11/01/2022] Open
Abstract
The interrelation of cancer and Alzheimer's disorder (AD)-associated molecular mechanisms, reported last decade, paved the path for drug discoveries. In this direction, while chemotherapy is well established for breast cancer (BC), the detection and targeted therapy for AD is not advanced due to a lack of recognized peripheral biomarkers. The present study aimed to find diagnostic and prognostic molecular signature markers common to both BC and AD for possible drug targeting and repurposing. For these disorders, two corresponding microarray datasets (GSE42568, GSE33000) were used for identifying the differentially expressed genes (DEGs), resulting in recognition of CD209 and MCM7 as the two common players. While the CD209 gene was upregulated in both disorders and has been studied vastly, the MCM7 gene showed a strikingly reverse pattern of expression level, downregulated in the case of BC while upregulated in the case of AD. Thus, the MCM7 gene was further analyzed for expression, predictions, and validations of its structure and protein-protein interaction (PPI) for the possible development of new treatment methods for AD. The study concluded with indicative drug repurposing studies to check the effect of existing clinically approved drugs for BC for rectifying the expression levels of the mutated MCM7 gene in AD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03207-1.
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Affiliation(s)
- Navneeth Sriram
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
| | - Sunny Mukherjee
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
| | - Mahesh Kumar Sah
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
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4
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Zhang H, He J, Hu G, Zhu F, Jiang H, Gao J, Zhou H, Lin H, Wang Y, Chen K, Meng F, Hao M, Zhao K, Luo C, Liang Z. Dynamics of Post-Translational Modification Inspires Drug Design in the Kinase Family. J Med Chem 2021; 64:15111-15125. [PMID: 34668699 DOI: 10.1021/acs.jmedchem.1c01076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Post-translational modification (PTM) on protein plays important roles in the regulation of cellular function and disease pathogenesis. The systematic analysis of PTM dynamics presents great opportunities to enlarge the target space by PTM allosteric regulation. Here, we presented a framework by integrating the sequence, structural topology, and particular dynamics features to characterize the functional context and druggabilities of PTMs in the well-known kinase family. The machine learning models with these biophysical features could successfully predict PTMs. On the other hand, PTMs were identified to be significantly enriched in the reported allosteric pockets and the allosteric potential of PTM pockets were thus proposed through these biophysical features. In the end, the covalent inhibitor DC-Srci-6668 targeting the PTM pocket in c-Src kinase was identified, which inhibited the phosphorylation and locked c-Src in the inactive state. Our findings represent a crucial step toward PTM-inspired drug design in the kinase family.
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Affiliation(s)
- Huimin Zhang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.,Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jixiao He
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Fei Zhu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Hao Jiang
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jing Gao
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hu Zhou
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hua Lin
- Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, 1 Keji Road, Fuzhou 350117, China
| | - Yingjuan Wang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Kaixian Chen
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Fanwang Meng
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Minghong Hao
- Ensem Therapeutics, Inc., 200 Boston Avenue, Medford, Massachusetts 02155, United States
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China.,University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
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5
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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6
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Hirst NL, Nebel JC, Lawton SP, Walker AJ. Deep phosphoproteome analysis of Schistosoma mansoni leads development of a kinomic array that highlights sex-biased differences in adult worm protein phosphorylation. PLoS Negl Trop Dis 2020; 14:e0008115. [PMID: 32203512 PMCID: PMC7089424 DOI: 10.1371/journal.pntd.0008115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
Although helminth parasites cause enormous suffering worldwide we know little of how protein phosphorylation, one of the most important post-translational modifications used for molecular signalling, regulates their homeostasis and function. This is particularly the case for schistosomes. Herein, we report a deep phosphoproteome exploration of adult Schistosoma mansoni, providing one of the richest phosphoprotein resources for any parasite so far, and employ the data to build the first parasite-specific kinomic array. Complementary phosphopeptide enrichment strategies were used to detect 15,844 unique phosphopeptides mapping to 3,176 proteins. The phosphoproteins were predicted to be involved in a wide range of biological processes and phosphoprotein interactome analysis revealed 55 highly interconnected clusters including those enriched with ribosome, proteasome, phagosome, spliceosome, glycolysis, and signalling proteins. 93 distinct phosphorylation motifs were identified, with 67 providing a ‘footprint’ of protein kinase activity; CaMKII, PKA and CK1/2 were highly represented supporting their central importance to schistosome function. Within the kinome, 808 phosphorylation sites were matched to 136 protein kinases, and 68 sites within 37 activation loops were discovered. Analysis of putative protein kinase-phosphoprotein interactions revealed canonical networks but also novel interactions between signalling partners. Kinomic array analysis of male and female adult worm extracts revealed high phosphorylation of transformation:transcription domain associated protein by both sexes, and CDK and AMPK peptides by females. Moreover, eight peptides including protein phosphatase 2C gamma, Akt, Rho2 GTPase, SmTK4, and the insulin receptor were more highly phosphorylated by female extracts, highlighting their possible importance to female worm function. We envision that these findings, tools and methodology will help drive new research into the functional biology of schistosomes and other helminth parasites, and support efforts to develop new therapeutics for their control. Schistosomes are formidable parasites that cause the debilitating and life-threatening disease human schistosomiasis. We need to better understand the cellular biology of these parasites to develop novel strategies for their control. Within cells, a process called protein phosphorylation controls many aspects of molecular communication or ‘signalling’ and is central to cellular function and homeostasis. Here, using complementary strategies, we have performed the first in-depth characterisation and functional annotation of protein phosphorylation events in schistosomes, providing one of the richest phosphoprotein resources for any parasite to date. Using this knowledge, we have developed a novel tool to simultaneously evaluate signalling processes in these worms and highlight sex-biased differences in adult worm protein phosphorylation. Several proteins were found to be more greatly phosphorylated by female worm extracts, suggesting their possible importance to female worm function. This work will help drive new research into the fundamental biology of schistosomes, as well as related parasites, and will support efforts to develop new drug or vaccine-based therapeutics for their control.
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Affiliation(s)
- Natasha L. Hirst
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Jean-Christophe Nebel
- School of Computer Science and Mathematics, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Scott P. Lawton
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
| | - Anthony J. Walker
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames, United Kingdom
- * E-mail:
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7
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D K, C S. Comparative analysis of human and mouse transcriptional cofactors (TcoFs) with special emphasis on intrinsically disordered regions and their associated regulating post‐translational modifications. J Cell Biochem 2018; 119:8531-8546. [DOI: 10.1002/jcb.27083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/26/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Kamalesh D
- Department of Integrative Biology School of Bioscience and Technology, VIT University Vellore India
| | - Sudandiradoss C
- Department of Biotechnology School of Bioscience and Technology, VIT University Vellore India
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8
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Su MG, Weng JTY, Hsu JBK, Huang KY, Chi YH, Lee TY. Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. BMC SYSTEMS BIOLOGY 2017; 11:132. [PMID: 29322920 PMCID: PMC5763307 DOI: 10.1186/s12918-017-0506-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins. The improved throughput of mass spectrometry (MS) or MS/MS technology has not only brought about a surge in proteome-scale studies, but also contributed to a fruitful list of identified PTMs. However, with the increase in the number of identified PTMs, perhaps the more crucial question is what kind of biological mechanisms these PTMs are involved in. This is particularly important in light of the fact that most protein-based pharmaceuticals deliver their therapeutic effects through some form of PTM. Yet, our understanding is still limited with respect to the local effects and frequency of PTM sites near pharmaceutical binding sites and the interfaces of protein-protein interaction (PPI). Understanding PTM’s function is critical to our ability to manipulate the biological mechanisms of protein. Results In this study, to understand the regulation of protein functions by PTMs, we mapped 25,835 PTM sites to proteins with available three-dimensional (3D) structural information in the Protein Data Bank (PDB), including 1785 modified PTM sites on the 3D structure. Based on the acquired structural PTM sites, we proposed to use five properties for the structural characterization of PTM substrate sites: the spatial composition of amino acids, residues and side-chain orientations surrounding the PTM substrate sites, as well as the secondary structure, division of acidity and alkaline residues, and solvent-accessible surface area. We further mapped the structural PTM sites to the structures of drug binding and PPI sites, identifying a total of 1917 PTM sites that may affect PPI and 3951 PTM sites associated with drug-target binding. An integrated analytical platform (CruxPTM), with a variety of methods and online molecular docking tools for exploring the structural characteristics of PTMs, is presented. In addition, all tertiary structures of PTM sites on proteins can be visualized using the JSmol program. Conclusion Resolving the function of PTM sites is important for understanding the role that proteins play in biological mechanisms. Our work attempted to delineate the structural correlation between PTM sites and PPI or drug-target binding. CurxPTM could help scientists narrow the scope of their PTM research and enhance the efficiency of PTM identification in the face of big proteome data. CruxPTM is now available at http://csb.cse.yzu.edu.tw/CruxPTM/. Electronic supplementary material The online version of this article (10.1186/s12918-017-0506-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Min-Gang Su
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan
| | - Julia Tzu-Ya Weng
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan
| | - Justin Bo-Kai Hsu
- Department of Medical Research, Taipei Medical University Hospital, Taipei, 110, Taiwan
| | - Kai-Yao Huang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan.,Department of Medical Research, Hsinchu Mackay Memorial Hospital, Hsinchu City, 300, Taiwan
| | - Yu-Hsiang Chi
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan
| | - Tzong-Yi Lee
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, 320, Taiwan. .,Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan, 320, Taiwan.
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9
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Bickel KG, Mann BJ, Waitzman JS, Poor TA, Rice SE, Wadsworth P. Src family kinase phosphorylation of the motor domain of the human kinesin-5, Eg5. Cytoskeleton (Hoboken) 2017. [PMID: 28646493 DOI: 10.1002/cm.21380] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Spindle formation in mammalian cells requires precise spatial and temporal regulation of the kinesin-5, Eg5, which generates outward force to establish spindle bipolarity. Our results demonstrate that Eg5 is phosphorylated in cultured cells by Src family kinases (SFKs) at three sites in the motor head: Y125, Y211, and Y231. Mutation of these sites diminishes motor activity in vitro, and replacement of endogenous Eg5 with phosphomimetic Y211 in LLC-Pk1 cells results in monopolar spindles, consistent with loss of Eg5 activity. Cells treated with SFK inhibitors show defects in spindle formation, similar to those in cells expressing the nonphosphorylatable Y211 mutant, and distinct from inhibition of other mitotic kinases. We propose that this phosphoregulatory mechanism tunes Eg5 enzymatic activity for optimal spindle morphology.
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Affiliation(s)
- Kathleen G Bickel
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Barbara J Mann
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Joshua S Waitzman
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Taylor A Poor
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Sarah E Rice
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611
| | - Patricia Wadsworth
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
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10
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Ahmad S, Ytterberg AJ, Thulasingam M, Tholander F, Bergman T, Zubarev R, Wetterholm A, Rinaldo-Matthis A, Haeggström JZ. Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity. J Biol Chem 2016; 291:18410-8. [PMID: 27365393 DOI: 10.1074/jbc.m116.735647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 01/07/2023] Open
Abstract
Leukotriene C4 synthase (LTC4S) catalyzes the formation of the proinflammatory lipid mediator leukotriene C4 (LTC4). LTC4 is the parent molecule of the cysteinyl leukotrienes, which are recognized for their pathogenic role in asthma and allergic diseases. Cellular LTC4S activity is suppressed by PKC-mediated phosphorylation, and recently a downstream p70S6k was shown to play an important role in this process. Here, we identified Ser(36) as the major p70S6k phosphorylation site, along with a low frequency site at Thr(40), using an in vitro phosphorylation assay combined with mass spectrometry. The functional consequences of p70S6k phosphorylation were tested with the phosphomimetic mutant S36E, which displayed only about 20% (20 μmol/min/mg) of the activity of WT enzyme (95 μmol/min/mg), whereas the enzyme activity of T40E was not significantly affected. The enzyme activity of S36E increased linearly with increasing LTA4 concentrations during the steady-state kinetics analysis, indicating poor lipid substrate binding. The Ser(36) is located in a loop region close to the entrance of the proposed substrate binding pocket. Comparative molecular dynamics indicated that Ser(36) upon phosphorylation will pull the first luminal loop of LTC4S toward the neighboring subunit of the functional homotrimer, thereby forming hydrogen bonds with Arg(104) in the adjacent subunit. Because Arg(104) is a key catalytic residue responsible for stabilization of the glutathione thiolate anion, this phosphorylation-induced interaction leads to a reduction of the catalytic activity. In addition, the positional shift of the loop and its interaction with the neighboring subunit affect active site access. Thus, our mutational and kinetic data, together with molecular simulations, suggest that phosphorylation of Ser(36) inhibits the catalytic function of LTC4S by interference with the catalytic machinery.
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Affiliation(s)
| | - A Jimmy Ytterberg
- Chemistry I, and Department of Medicine, Solna, Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | | | - Fredrik Tholander
- Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden and
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11
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Korkuć P, Walther D. Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding. Proteins 2016; 84:565-79. [PMID: 26817627 DOI: 10.1002/prot.25001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 01/07/2023]
Abstract
Phosphorylation is an important post-translational modification that regulates protein function by the attachment of negatively charged phosphate groups to phosphorylatable amino acid residues. As a mode of action, an influence of phosphorylation on the binding of compounds to proteins has been discussed and described for a number of proteins in the literature. However, a systematic statistical survey probing for enriched phosphorylation sites close to compound binding sites in support of this notion and with properly chosen random reference distributions has not been presented yet. Using high-resolution protein structures from the Protein Data Bank including their co-crystallized non-covalently bound compounds and experimentally determined phosphorylation sites, we analyzed the pairwise distance distributions of phosphorylation and compound binding sites on protein surfaces. We found that phosphorylation sites are indeed located at significantly closer distances to compounds than expected by chance holding true specifically also for the subset of compound binding sites serving as catalytic sites of metabolic reactions. This tendency was particularly evident when treating phosphorylation sites as collective sets supporting the relevance of phosphorylation hotspots. Interestingly, phosphorylation sites were found to be closer to negatively charged than to positively charged compounds suggesting a stronger modulation of the binding of negatively charged compounds in dependence on phosphorylation status than on positively charged compounds. The enrichment of phosphorylation sites near compound binding sites confirms a regulatory role of phosphorylation in compound binding and provides a solid statistical basis for the literature-reported selected events.
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Affiliation(s)
- Paula Korkuć
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Dirk Walther
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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12
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Huang KY, Su MG, Kao HJ, Hsieh YC, Jhong JH, Cheng KH, Huang HD, Lee TY. dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Nucleic Acids Res 2015; 44:D435-46. [PMID: 26578568 PMCID: PMC4702878 DOI: 10.1093/nar/gkv1240] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/02/2015] [Indexed: 01/23/2023] Open
Abstract
Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM (http://dbPTM.mbc.nctu.edu.tw/) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S-nitrosylation, S-glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein-protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.
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Affiliation(s)
- Kai-Yao Huang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Min-Gang Su
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Hui-Ju Kao
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Yun-Chung Hsieh
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Jhih-Hua Jhong
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Kuang-Hao Cheng
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan
| | - Hsien-Da Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Tzong-Yi Lee
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan Innovation Center for Big Data and Digital Convergence, Yuan Ze University, Taoyuan 320, Taiwan
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13
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Gianazza E, Parravicini C, Primi R, Miller I, Eberini I. In silico prediction and characterization of protein post-translational modifications. J Proteomics 2015; 134:65-75. [PMID: 26436211 DOI: 10.1016/j.jprot.2015.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/17/2015] [Accepted: 09/23/2015] [Indexed: 01/06/2023]
Abstract
This review outlines the computational approaches and procedures for predicting post translational modification (PTM)-induced changes in protein conformation and their influence on protein function(s), the latter being assessed as differential affinity in interaction with either low (ligands for receptors or transporters, substrates for enzymes) or high molecular mass molecules (proteins or nucleic acids in supramolecular assemblies). The scope for an in silico approach is discussed against a summary of the in vitro evidence on the structural and functional outcome of protein PTM.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Sezione di Scienze Farmacologiche, Via Balzaretti 9, I-20133 Milan, Italy.
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
| | - Roberto Primi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
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Sehnal D, Pravda L, Svobodová Vařeková R, Ionescu CM, Koča J. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res 2015; 43:W383-8. [PMID: 26013810 PMCID: PMC4489247 DOI: 10.1093/nar/gkv561] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/17/2015] [Indexed: 01/10/2023] Open
Abstract
Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
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Affiliation(s)
- David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Crina-Maria Ionescu
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 2014; 43:D512-20. [PMID: 25514926 PMCID: PMC4383998 DOI: 10.1093/nar/gku1267] [Citation(s) in RCA: 2056] [Impact Index Per Article: 205.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PhosphoSitePlus® (PSP, http://www.phosphosite.org/), a knowledgebase dedicated to mammalian post-translational modifications (PTMs), contains over 330 000 non-redundant PTMs, including phospho, acetyl, ubiquityl and methyl groups. Over 95% of the sites are from mass spectrometry (MS) experiments. In order to improve data reliability, early MS data have been reanalyzed, applying a common standard of analysis across over 1 000 000 spectra. Site assignments with P > 0.05 were filtered out. Two new downloads are available from PSP. The ‘Regulatory sites’ dataset includes curated information about modification sites that regulate downstream cellular processes, molecular functions and protein-protein interactions. The ‘PTMVar’ dataset, an intersect of missense mutations and PTMs from PSP, identifies over 25 000 PTMVars (PTMs Impacted by Variants) that can rewire signaling pathways. The PTMVar data include missense mutations from UniPROTKB, TCGA and other sources that cause over 2000 diseases or syndromes (MIM) and polymorphisms, or are associated with hundreds of cancers. PTMVars include 18 548 phosphorlyation sites, 3412 ubiquitylation sites, 2316 acetylation sites, 685 methylation sites and 245 succinylation sites.
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Affiliation(s)
| | - Bin Zhang
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA
| | - Beth Murray
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA
| | | | - Vaughan Latham
- Cell Signaling Technology, 3 Trask Lane, Danvers, MA 01923, USA
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