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Garg A, Dabburu GR, Singhal N, Kumar M. Investigating the disordered regions (MoRFs, SLiMs and LCRs) and functions of mimicry proteins/peptides in silico. PLoS One 2022; 17:e0265657. [PMID: 35421114 PMCID: PMC9009644 DOI: 10.1371/journal.pone.0265657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/24/2022] Open
Abstract
Microbial mimicry of the host proteins/peptides can elicit host auto-reactive T- or B-cells resulting in autoimmune disease(s). Since intrinsically disordered protein regions (IDPRs) are involved in several host cell signaling and PPI networks, molecular mimicry of the IDPRs can help the pathogens in substituting their own proteins in the host cell-signaling and PPI networks and, ultimately hijacking the host cellular machinery. Thus, the present study was conducted to discern the structural disorder and intrinsically disordered protein regions (IDPRs) like, molecular recognition features (MoRFs), short linear motifs (SLiMs), and low complexity regions (LCRs) in the experimentally verified mimicry proteins and peptides (mimitopes) of bacteria, viruses and host. Also, functional characteristics of the mimicry proteins were studied in silico. Our results indicated that 78% of the bacterial host mimicry proteins and 45% of the bacterial host mimitopes were moderately/highly disordered while, 73% of the viral host mimicry proteins and 31% of the viral host mimitopes were moderately/highly disordered. Among the pathogens, 27% of the bacterial mimicry proteins and 13% of the bacterial mimitopes were moderately/highly disordered while, 53% of the viral mimicry proteins and 21% of the viral mimitopes were moderately/highly disordered. Though IDPR were frequent in host, bacterial and viral mimicry proteins, only a few mimitopes overlapped with the IDPRs like, MoRFs, SLiMs and LCRs. This suggests that most of the microbes cannot use molecular mimicry to modulate the host PPIs and hijack the host cell machinery. Functional analyses indicated that most of the pathogens exhibited mimicry with the host proteins involved in ion binding and signaling pathways. This is the first report on the disordered regions and functional aspects of experimentally proven host and microbial mimicry proteins.
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Affiliation(s)
- Anjali Garg
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Govinda Rao Dabburu
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail: (MK); (NS)
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail: (MK); (NS)
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DeForte S, Uversky VN. Quarterly intrinsic disorder digest (April-May-June, 2014). INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1287505. [PMID: 28321370 DOI: 10.1080/21690707.2017.1287505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This is the 6th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Département De Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute of Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol 2015; 35:49-59. [PMID: 26402567 DOI: 10.1016/j.sbi.2015.08.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium; Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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Cato L, Neeb A, Brown M, Cato ACB. Control of steroid receptor dynamics and function by genomic actions of the cochaperones p23 and Bag-1L. NUCLEAR RECEPTOR SIGNALING 2014; 12:e005. [PMID: 25422595 PMCID: PMC4242288 DOI: 10.1621/nrs.12005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/20/2014] [Indexed: 01/23/2023]
Abstract
Molecular chaperones encompass a group of unrelated proteins that facilitate the
correct assembly and disassembly of other macromolecular structures, which they
themselves do not remain a part of. They associate with a large and diverse set
of coregulators termed cochaperones that regulate their function and
specificity. Amongst others, chaperones and cochaperones regulate the activity
of several signaling molecules including steroid receptors, which upon ligand
binding interact with discrete nucleotide sequences within the nucleus to
control the expression of diverse physiological and developmental genes.
Molecular chaperones and cochaperones are typically known to provide the correct
conformation for ligand binding by the steroid receptors. While this
contribution is widely accepted, recent studies have reported that they further
modulate steroid receptor action outside ligand binding. They are thought to
contribute to receptor turnover, transport of the receptor to different
subcellular localizations, recycling of the receptor on chromatin and even
stabilization of the DNA-binding properties of the receptor. In addition to
these combined effects with molecular chaperones, cochaperones are reported to
have additional functions that are independent of molecular chaperones. Some of
these functions also impact on steroid receptor action. Two well-studied
examples are the cochaperones p23 and Bag-1L, which have been identified as
modulators of steroid receptor activity in nuclei. Understanding details of
their regulatory action will provide new therapeutic opportunities of
controlling steroid receptor action independent of the widespread effects of
molecular chaperones.
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Affiliation(s)
- Laura Cato
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
| | - Antje Neeb
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
| | - Myles Brown
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
| | - Andrew C B Cato
- Division of Molecular and Cellular Oncology, Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA (LC, MB) and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany (AN, ACBC)
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