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Paromov V, Uversky VN, Cooley A, Liburd LE, Mukherjee S, Na I, Dayhoff GW, Pratap S. The Proteomic Analysis of Cancer-Related Alterations in the Human Unfoldome. Int J Mol Sci 2024; 25:1552. [PMID: 38338831 PMCID: PMC10855131 DOI: 10.3390/ijms25031552] [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: 12/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network.
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Affiliation(s)
- Victor Paromov
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Ayorinde Cooley
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
| | - Lincoln E. Liburd
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Shyamali Mukherjee
- Department of Biochemistry, Cancer Biology, Neuroscience & Pharmacology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA (S.M.)
| | - Insung Na
- Department of Molecular Medicine, USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA; (V.N.U.); (I.N.)
| | - Guy W. Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL 33613, USA;
| | - Siddharth Pratap
- Meharry Proteomics Core, RCMI Research Capacity Core, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
- Meharry Bioinformatics Core, Department of Microbiology, Immunology and Physiology, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA;
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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Lin H, Koren SA, Cvetojevic G, Girardi P, Johnson GV. The role of BAG3 in health and disease: A "Magic BAG of Tricks". J Cell Biochem 2022; 123:4-21. [PMID: 33987872 PMCID: PMC8590707 DOI: 10.1002/jcb.29952] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/25/2021] [Indexed: 01/03/2023]
Abstract
The multi-domain structure of Bcl-2-associated athanogene 3 (BAG3) facilitates its interaction with many different proteins that participate in regulating a variety of biological pathways. After revisiting the BAG3 literature published over the past ten years with Citespace software, we classified the BAG3 research into several clusters, including cancer, cardiomyopathy, neurodegeneration, and viral propagation. We then highlighted recent key findings in each cluster. To gain greater insight into the roles of BAG3, we analyzed five different published mass spectrometry data sets of proteins that co-immunoprecipitate with BAG3. These data gave us insight into universal, as well as cell-type-specific BAG3 interactors in cancer cells, cardiomyocytes, and neurons. Finally, we mapped variable BAG3 SNPs and also mutation data from previous publications to further explore the link between the domains and function of BAG3. We believe this review will provide a better understanding of BAG3 and direct future studies towards understanding BAG3 function in physiological and pathological conditions.
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Affiliation(s)
- Heng Lin
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Shon A. Koren
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Gregor Cvetojevic
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Peter Girardi
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
| | - Gail V.W. Johnson
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester NY 14642 USA
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Suplatov D, Kopylov K, Sharapova Y, Švedas V. Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod. J Biomol Struct Dyn 2018; 37:2049-2060. [PMID: 29749295 DOI: 10.1080/07391102.2018.1475260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the 'out' state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod's binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry Suplatov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Kirill Kopylov
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Yana Sharapova
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
| | - Vytas Švedas
- a Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology , Lomonosov Moscow State University , Vorobjev hills , Moscow , Russia
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Kiselev A, Vaz R, Knyazeva A, Khudiakov A, Tarnovskaya S, Liu J, Sergushichev A, Kazakov S, Frishman D, Smolina N, Pervunina T, Jorholt J, Sjoberg G, Vershinina T, Rudenko D, Arner A, Sejersen T, Lindstrand A, Kostareva A. De novo mutations in FLNC
leading to early-onset restrictive cardiomyopathy and congenital myopathy. Hum Mutat 2018; 39:1161-1172. [DOI: 10.1002/humu.23559] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/22/2018] [Accepted: 05/30/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Artem Kiselev
- Almazov National Medical Research Centre; Saint Petersburg Russia
| | - Raquel Vaz
- Department of Molecular Medicine and Surgery and Center for molecular medicine; Karolinska Institutet; Stockholm Sweden
| | | | | | - Svetlana Tarnovskaya
- Almazov National Medical Research Centre; Saint Petersburg Russia
- Peter the Great St.Petersburg Polytechnic University; Saint Petersburg Russia
| | - Jiao Liu
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | | | | | - Dmitrij Frishman
- Peter the Great St.Petersburg Polytechnic University; Saint Petersburg Russia
- Department of Bioinformatics; Technische Universität München; Wissenschaftszentrum Weihenstephan; Freising Germany
| | - Natalia Smolina
- Almazov National Medical Research Centre; Saint Petersburg Russia
- ITMO University; Saint Petersburg Russia
- Department of Women's and Children's Health and Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
| | | | - John Jorholt
- Department of Women's and Children's Health and Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
| | - Gunnar Sjoberg
- Department of Women's and Children's Health and Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
| | | | | | - Anders Arner
- Department of Physiology and Pharmacology; Karolinska Institutet; Stockholm Sweden
| | - Thomas Sejersen
- Department of Women's and Children's Health and Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for molecular medicine; Karolinska Institutet; Stockholm Sweden
- Clinical Genetics; Karolinska University Laboratory; Karolinska University Hospital; Stockholm Sweden
| | - Anna Kostareva
- Almazov National Medical Research Centre; Saint Petersburg Russia
- Department of Women's and Children's Health and Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
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