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Basu S, Hegedűs T, Kurgan L. CoMemMoRFPred: Sequence-based Prediction of MemMoRFs by Combining Predictors of Intrinsic Disorder, MoRFs and Disordered Lipid-binding Regions. J Mol Biol 2023; 435:168272. [PMID: 37709009 DOI: 10.1016/j.jmb.2023.168272] [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: 07/05/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
Molecular recognition features (MoRFs) are a commonly occurring type of intrinsically disordered regions (IDRs) that undergo disorder-to-order transition upon binding to partner molecules. We focus on recently characterized and functionally important membrane-binding MoRFs (MemMoRFs). Motivated by the lack of computational tools that predict MemMoRFs, we use a dataset of experimentally annotated MemMoRFs to conceptualize, design, evaluate and release an accurate sequence-based predictor. We rely on state-of-the-art tools that predict residues that possess key characteristics of MemMoRFs, such as intrinsic disorder, disorder-to-order transition and lipid-binding. We identify and combine results from three tools that include flDPnn for the disorder prediction, DisoLipPred for the prediction of disordered lipid-binding regions, and MoRFCHiBiLight for the prediction of disorder-to-order transitioning protein binding regions. Our empirical analysis demonstrates that combining results produced by these three methods generates accurate predictions of MemMoRFs. We also show that use of a smoothing operator produces predictions that closely mimic the number and sizes of the native MemMoRF regions. The resulting CoMemMoRFPred method is available as an easy-to-use webserver at http://biomine.cs.vcu.edu/servers/CoMemMoRFPred. This tool will aid future studies of MemMoRFs in the context of exploring their abundance, cellular functions, and roles in pathologic phenomena.
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Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, USA
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary; ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, USA.
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Machado Lara Carvalho L, Varella Branco E, Delgado Sarafian R, Shigeru Kobayashi G, Tófoli de Araújo F, Santos Souza L, de Paula Moreira D, Shih Ping Hsia G, Maria Goloni Bertollo E, Barbosa Buck C, Souza da Costa S, Mendes Fialho D, Tadeu Galante Rocha de Vasconcelos F, Abreu Brito L, Elena de Souza Fraga Machado L, Cabreira Ramos I, da Veiga Pereira L, Priszkulnik Koiffmann C, Rita Dos Santos E Passos-Bueno M, Antonio de Oliveira Mendes T, Cristina Victorino Krepischi A, Rosenberg C. Establishment of iPSC lines and zebrafish with loss-of-function AHDC1 variants: models for Xia-Gibbs syndrome. Gene 2023; 871:147424. [PMID: 37054903 DOI: 10.1016/j.gene.2023.147424] [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: 12/12/2022] [Revised: 03/12/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
Xia-Gibbs syndrome (XGS) is a syndromic form of intellectual disability caused by heterozygous AHDC1 variants, but the pathophysiological mechanisms underlying this syndrome are still unclear. In this manuscript, we describe the development of two different functional models: three induced pluripotent stem cell (iPSC) lines with different loss-of-function (LoF) AHDC1 variants, derived by reprogramming peripheral blood mononuclear cells from XGS patients, and a zebrafish strain with a LoF variant in the ortholog gene (ahdc1) obtained through CRISPR/Cas9-mediated editing. The three iPSC lines showed expression of pluripotency factors (SOX2, SSEA-4, OCT3/4, and NANOG). To verify the capacity of iPSC to differentiate into the three germ layers, we obtained embryoid bodies (EBs), induced their differentiation, and confirmed the mRNA expression of ectodermal, mesodermal, and endodermal markers using the TaqMan hPSC Scorecard. The iPSC lines were also approved for the following quality tests: chromosomal microarray analysis (CMA), mycoplasma testing, and short tandem repeat (STR) DNA profiling. The zebrafish model has an insertion of four base pairs in the ahdc1 gene, is fertile, and breeding between heterozygous and wild-type (WT) animals generated offspring in a genotypic proportion in agreement with Mendelian law. The established iPSC and zebrafish lines were deposited on the hpscreg.eu and zfin.org platforms, respectively. These biological models are the first for XGS and will be used in future studies that investigate the pathophysiology of this syndrome, unraveling its underlying molecular mechanisms.
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Affiliation(s)
- Laura Machado Lara Carvalho
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Elisa Varella Branco
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Raquel Delgado Sarafian
- National Embryonic Stem Cell Laboratory Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gerson Shigeru Kobayashi
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Fabiano Tófoli de Araújo
- National Embryonic Stem Cell Laboratory Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lucas Santos Souza
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Danielle de Paula Moreira
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gabriella Shih Ping Hsia
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | - Silvia Souza da Costa
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Davi Mendes Fialho
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Luciano Abreu Brito
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Igor Cabreira Ramos
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lygia da Veiga Pereira
- National Embryonic Stem Cell Laboratory Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Celia Priszkulnik Koiffmann
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | - Carla Rosenberg
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
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Liquid-liquid phase separation in tumor biology. Signal Transduct Target Ther 2022; 7:221. [PMID: 35803926 PMCID: PMC9270353 DOI: 10.1038/s41392-022-01076-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) is a novel principle for explaining the precise spatial and temporal regulation in living cells. LLPS compartmentalizes proteins and nucleic acids into micron-scale, liquid-like, membraneless bodies with specific functions, which were recently termed biomolecular condensates. Biomolecular condensates are executors underlying the intracellular spatiotemporal coordination of various biological activities, including chromatin organization, genomic stability, DNA damage response and repair, transcription, and signal transduction. Dysregulation of these cellular processes is a key event in the initiation and/or evolution of cancer, and emerging evidence has linked the formation and regulation of LLPS to malignant transformations in tumor biology. In this review, we comprehensively summarize the detailed mechanisms of biomolecular condensate formation and biophysical function and review the recent major advances toward elucidating the multiple mechanisms involved in cancer cell pathology driven by aberrant LLPS. In addition, we discuss the therapeutic perspectives of LLPS in cancer research and the most recently developed drug candidates targeting LLPS modulation that can be used to combat tumorigenesis.
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Mitić NS, Malkov SN, Kovačević JJ, Pavlović-Lažetić GM, Beljanski MV. Structural disorder of plasmid-encoded proteins in Bacteria and Archaea. BMC Bioinformatics 2018; 19:158. [PMID: 29699482 PMCID: PMC5922023 DOI: 10.1186/s12859-018-2158-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/16/2018] [Indexed: 01/30/2023] Open
Abstract
Background In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered proteins (IDPs) and intrinsically disordered (protein) regions (IDRs) are involved in essential cell processes through two basic mechanisms: the entropic chain mechanism which is responsible for rapid fluctuations among many alternative conformations, and molecular recognition via short recognition elements that bind to other molecules. IDPs possess a high adaptive potential and there is special interest in investigating their involvement in organism evolution. Results We analyzed 2554 Bacterial and 139 Archaeal proteomes, with a total of 8,455,194 proteins for disorder content and its implications for adaptation of organisms, using three disorder predictors and three measures. Along with other findings, we revealed that for all three predictors and all three measures (1) Bacteria exhibit significantly more disorder than Archaea; (2) plasmid-encoded proteins contain considerably more IDRs than proteins encoded on chromosomes (or whole genomes) in both prokaryote superkingdoms; (3) plasmid proteins are significantly more disordered than chromosomal proteins only in the group of proteins with no COG category assigned; (4) antitoxin proteins in comparison to other proteins, are the most disordered (almost double) in both Bacterial and Archaeal proteomes; (5) plasmidal proteins are more disordered than chromosomal proteins in Bacterial antitoxins and toxin-unclassified proteins, but have almost the same disorder content in toxin proteins. Conclusion Our results suggest that while disorder content depends on genome and proteome characteristics, it is more influenced by functional engagements than by gene location (on chromosome or plasmid). Electronic supplementary material The online version of this article (10.1186/s12859-018-2158-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nenad S Mitić
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia.
| | - Saša N Malkov
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia
| | - Jovana J Kovačević
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia
| | - Gordana M Pavlović-Lažetić
- Department of Computer Science, Faculty of Mathematics, University of Belgrade, P.O.B. 550 Studentski trg 16, Belgrade, 11001, Serbia
| | - Miloš V Beljanski
- Bio-lab, Institute of General and Physical Chemistry, P.O.B. 45, Studentski trg 12/V, Belgrade, 11001, Serbia
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Dosztányi Z. Prediction of protein disorder based on IUPred. Protein Sci 2017; 27:331-340. [PMID: 29076577 DOI: 10.1002/pro.3334] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Many proteins contain intrinsically disordered regions (IDRs), functional polypeptide segments that in isolation adopt a highly flexible conformational ensemble instead of a single, well-defined structure. Disorder prediction methods, which can discriminate ordered and disordered regions from the amino acid sequence, have contributed significantly to our current understanding of the distinct properties of intrinsically disordered proteins by enabling the characterization of individual examples as well as large-scale analyses of these protein regions. One popular method, IUPred provides a robust prediction of protein disorder based on an energy estimation approach that captures the fundamental difference between the biophysical properties of ordered and disordered regions. This paper reviews the energy estimation method underlying IUPred and the basic properties of the web server. Through an example, it also illustrates how the prediction output can be interpreted in a more complex case by taking into account the heterogeneous nature of IDRs. Various applications that benefited from IUPred to provide improved disorder predictions, complementing domain annotations and aiding the identification of functional short linear motifs are also described here. IUPred is freely available for noncommercial users through the web server (http://iupred.enzim.hu and http://iupred.elte.hu) . The program can also be downloaded and installed locally for large-scale analyses.
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Affiliation(s)
- Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
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DeForte S, Uversky VN. Order, Disorder, and Everything in Between. Molecules 2016; 21:molecules21081090. [PMID: 27548131 PMCID: PMC6274243 DOI: 10.3390/molecules21081090] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 02/04/2023] Open
Abstract
In addition to the “traditional” proteins characterized by the unique crystal-like structures needed for unique functions, it is increasingly recognized that many proteins or protein regions (collectively known as intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs)), being biologically active, do not have a specific 3D-structure in their unbound states under physiological conditions. There are also subtler categories of disorder, such as conditional (or dormant) disorder and partial disorder. Both the ability of a protein/region to fold into a well-ordered functional unit or to stay intrinsically disordered but functional are encoded in the amino acid sequence. Structurally, IDPs/IDPRs are characterized by high spatiotemporal heterogeneity and exist as dynamic structural ensembles. It is important to remember, however, that although structure and disorder are often treated as binary states, they actually sit on a structural continuum.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
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Functional Interaction between the Cytoplasmic ABC Protein LptB and the Inner Membrane LptC Protein, Components of the Lipopolysaccharide Transport Machinery in Escherichia coli. J Bacteriol 2016; 198:2192-203. [PMID: 27246575 DOI: 10.1128/jb.00329-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/24/2016] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED The assembly of lipopolysaccharide (LPS) in the outer leaflet of the outer membrane (OM) requires the transenvelope Lpt (lipopolysaccharide transport) complex, made in Escherichia coli of seven essential proteins located in the inner membrane (IM) (LptBCFG), periplasm (LptA), and OM (LptDE). At the IM, LptBFG constitute an unusual ATP binding cassette (ABC) transporter, composed by the transmembrane LptFG proteins and the cytoplasmic LptB ATPase, which is thought to extract LPS from the IM and to provide the energy for its export across the periplasm to the cell surface. LptC is a small IM bitopic protein that binds to LptBFG and recruits LptA via its N- and C-terminal regions, and its role in LPS export is not completely understood. Here, we show that the expression level of lptB is a critical factor for suppressing lethality of deletions in the C-terminal region of LptC and the functioning of a hybrid Lpt machinery that carries Pa-LptC, the highly divergent LptC orthologue from Pseudomonas aeruginosa We found that LptB overexpression stabilizes C-terminally truncated LptC mutant proteins, thereby allowing the formation of a sufficient amount of stable IM complexes to support growth. Moreover, the LptB level seems also critical for the assembly of IM complexes carrying Pa-LptC which is otherwise defective in interactions with the E. coli LptFG components. Overall, our data suggest that LptB and LptC functionally interact and support a model whereby LptB plays a key role in the assembly of the Lpt machinery. IMPORTANCE The asymmetric outer membrane (OM) of Gram-negative bacteria contains in its outer leaflet an unusual glycolipid, the lipopolysaccharide (LPS). LPS largely contributes to the peculiar permeability barrier properties of the OM that prevent the entry of many antibiotics, thus making Gram-negative pathogens difficult to treat. In Escherichia coli the LPS transporter (the Lpt machine) is made of seven essential proteins (LptABCDEFG) that form a transenvelope complex. Here, we show that increased expression of the membrane-associated ABC protein LptB can suppress defects of LptC, which participates in the formation of the periplasmic bridge. This reveals functional interactions between these two components and supports a role of LptB in the assembly of the Lpt machine.
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