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Edamana S, Login FH, Riishede A, Dam VS, Tramm T, Nejsum LN. The cell polarity protein Scribble is downregulated by the water channel aquaporin-5 in breast cancer cells. Am J Physiol Cell Physiol 2023; 324:C307-C319. [PMID: 36468842 DOI: 10.1152/ajpcell.00311.2022] [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] [Indexed: 12/12/2022]
Abstract
Breast carcinomas originate from cells in the terminal duct-lobular unit. Carcinomas are associated with increased cell proliferation and migration, altered cellular adhesion, as well as loss of epithelial polarity. In breast cancer, aberrant and high levels of aquaporin-5 (AQP5) are associated with increased metastasis, poor prognosis, and cancer recurrence. AQP5 increases the proliferation and migration of cancer cells, and ectopic expression of AQP5 in normal epithelial cells reduces cell-cell adhesion and increases cell detachment and dissemination from migrating cell sheets, the latter via AQP5-mediated activation of the Ras pathway. Here, we investigated if AQP5 also affects cellular polarity by examining the relationship between the essential polarity protein Scribble and AQP5. In tissue samples from invasive lobular and ductal carcinomas, the majority of cells with high AQP5 expression displayed low Scribble levels, indicating an inverse relationship. Probing for interactions via a Glutathione S-transferase pull-down experiment revealed that AQP5 and Scribble interacted. Moreover, overexpression of AQP5 in the breast cancer cell line MCF7 reduced both size and circularity of three-dimensional (3-D) spheroids and induced cell detachment and dissemination from migrating cell sheets. In addition, Scribble levels were reduced. An AQP5 mutant cell line, which cannot activate Ras (AQP5S156A) signaling, displayed unchanged spheroid size and circularity and an intermediate level of Scribble, indicating that the effect of AQP5 on Scribble is, at least in part, dependent on AQP5-mediated activation of Ras. Thus, our results suggest that high AQP5 expression negatively regulates the essential polarity protein Scribble and thus, can affect cellular polarity in breast cancer.
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Affiliation(s)
- Sarannya Edamana
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Frédéric H Login
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Andreas Riishede
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Vibeke S Dam
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Trine Tramm
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Lene N Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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2
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Bousova K, Bednarova L, Zouharova M, Vetyskova V, Postulkova K, Hofbauerová K, Petrvalska O, Vanek O, Tripsianes K, Vondrasek J. The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization. Protein Sci 2021; 30:1653-1666. [PMID: 33969912 DOI: 10.1002/pro.4107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/09/2022]
Abstract
Most of the structural proteins known today are composed of domains that carry their own functions while keeping their structural properties. It is supposed that such domains, when taken out of the context of the whole protein, can retain their original structure and function to a certain extent. Information on the specific functional and structural characteristics of individual domains in a new context of artificial fusion proteins may help to reveal the rules of internal and external domain communication. Moreover, this could also help explain the mechanism of such communication and address how the mutual allosteric effect plays a role in a such multi-domain protein system. The simple model system of the two-domain fusion protein investigated in this work consisted of a well-folded PDZ3 domain and an artificially designed small protein domain called Tryptophan Cage (TrpCage). Two fusion proteins with swapped domain order were designed to study their structural and functional features as well as their biophysical properties. The proteins composed of PDZ3 and TrpCage, both identical in amino acid sequence but different in composition (PDZ3-TrpCage, TrpCage-PDZ3), were studied using circualr dichroism (CD) spectrometry, analytical ultracentrifugation, and molecular dynamic simulations. The biophysical analysis uncovered different structural and denaturation properties of both studied proteins, revealing their different unfolding pathways and dynamics.
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Affiliation(s)
- Kristyna Bousova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Lucie Bednarova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Monika Zouharova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Second Faculty of Medicine, Charles University, Prague 5, Czech Republic
| | - Veronika Vetyskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague 6, Czech Republic
| | - Klara Postulkova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Second Faculty of Medicine, Charles University, Prague 5, Czech Republic
| | - Kateřina Hofbauerová
- Faculty of Mathematics and Physics, Charles University, Prague 2, Czech Republic.,Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Olivia Petrvalska
- Department of Structural Biology of Signalling Proteins, Division BIOCEV, Institute of Physiology, Vestec, Czech Republic
| | - Ondrej Vanek
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | | | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
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3
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Gpr63 is a modifier of microcephaly in Ttc21b mouse mutants. PLoS Genet 2019; 15:e1008467. [PMID: 31730647 PMCID: PMC6881074 DOI: 10.1371/journal.pgen.1008467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2019] [Accepted: 10/08/2019] [Indexed: 11/19/2022] Open
Abstract
The primary cilium is a signaling center critical for proper embryonic development. Previous studies have demonstrated that mice lacking Ttc21b have impaired retrograde trafficking within the cilium and multiple organogenesis phenotypes, including microcephaly. Interestingly, the severity of the microcephaly in Ttc21baln/aln homozygous null mutants is considerably affected by the genetic background and mutants on an FVB/NJ (FVB) background develop a forebrain significantly smaller than mutants on a C57BL/6J (B6) background. We performed a Quantitative Trait Locus (QTL) analysis to identify potential genetic modifiers and identified two regions linked to differential forebrain size: modifier of alien QTL1 (Moaq1) on chromosome 4 at 27.8 Mb and Moaq2 on chromosome 6 at 93.6 Mb. These QTLs were validated by constructing congenic strains. Further analysis of Moaq1 identified an orphan G-protein coupled receptor (GPCR), Gpr63, as a candidate gene. We identified a SNP that is polymorphic between the FVB and B6 strains in Gpr63 and creates a missense mutation predicted to be deleterious in the FVB protein. We used CRISPR-Cas9 genome editing to create two lines of FVB congenic mice: one with the B6 sequence of Gpr63 and the other with a deletion allele leading to a truncation of the GPR63 C-terminal tail. We then demonstrated that Gpr63 can localize to the cilium in vitro. These alleles affect ciliary localization of GPR63 in vitro and genetically interact with Ttc21baln/aln as Gpr63;Ttc21b double mutants show unique phenotypes including spina bifida aperta and earlier embryonic lethality. This validated Gpr63 as a modifier of multiple Ttc21b neural phenotypes and strongly supports Gpr63 as a causal gene (i.e., a quantitative trait gene, QTG) within the Moaq1 QTL. TTC21B in humans is a known ciliopathy gene and contributes to the pathophysiology of a number of ciliopathies. Mice homozygous for a null allele of Ttc21b also have a spectrum of ciliopathy phenotypes, including microcephaly (small brain). Further work has shown that the severity of the microcephaly significantly depends on the genetic background of the mouse model. The genetic mechanisms of the Ttc21b pathophysiology and the interacting gene network remain far from understood. As an initial attempt to understand the underlying mechanism(s) underlying the variable effects on brain size, we performed a quantitative trait locus (QTL) analysis and found two regions of genomic significance that correlated with smaller brain size. We confirmed both QTLs with congenic lines. One of the two regions was small enough that we considered candidate genes and hypothesized Gpr63 might be a contributing locus for a number of reasons. We evaluated this hypothesis directly with precise variant creation using genome editing and provide evidence that Ttc21b and Gpr63 do indeed genetically interact. Thus, we have been able to combine classical QTL analysis and genome editing to directly test the resulting hypothesis.
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4
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Valgardson J, Cosbey R, Houser P, Rupp M, Van Bronkhorst R, Lee M, Jagodzinski F, Amacher JF. MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Sci 2019; 28:2127-2143. [PMID: 31599029 DOI: 10.1002/pro.3741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
Abstract
Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM-binding domains in the human proteome, the PDZ domain. These domains bind the extreme C-terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer-PDZ, a program that filters and compares all motif-satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C-terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously-relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif-satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer-PDZ is a versatile program to investigate potential PDZ interactions. This proof-of-concept work is poised to enable similar types of analyses for other SLiM-binding domains (e.g., MotifAnalyzer-Kinase). MotifAnalyzer-PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu.
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Affiliation(s)
- Jordan Valgardson
- Department of Computer Science, Western Washington University, Bellingham, Washington.,Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Robin Cosbey
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Paul Houser
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Milo Rupp
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Raiden Van Bronkhorst
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Michael Lee
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, Washington
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5
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Enogieru OJ, Ung PMU, Yee SW, Schlessinger A, Giacomini KM. Functional and structural analysis of rare SLC2A2 variants associated with Fanconi-Bickel syndrome and metabolic traits. Hum Mutat 2019; 40:983-995. [PMID: 30950137 DOI: 10.1002/humu.23758] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/01/2019] [Accepted: 03/23/2019] [Indexed: 02/06/2023]
Abstract
Deleterious variants in SLC2A2 cause Fanconi-Bickel Syndrome (FBS), a glycogen storage disorder, whereas less common variants in SLC2A2 associate with numerous metabolic diseases. Phenotypic heterogeneity in FBS has been observed, but its causes remain unknown. Our goal was to functionally characterize rare SLC2A2 variants found in FBS and metabolic disease-associated variants to understand the impact of these variants on GLUT2 activity and expression and establish genotype-phenotype correlations. Complementary RNA-injected Xenopus laevis oocytes were used to study mutant transporter activity and membrane expression. GLUT2 homology models were constructed for mutation analysis using GLUT1, GLUT3, and XylE as templates. Seventeen FBS variants were characterized. Only c.457_462delCTTATA (p.Leu153_Ile154del) exhibited residual glucose uptake. Functional characterization revealed that only half of the variants were expressed on the plasma membrane. Most less common variants (except c.593 C>A (p.Thr198Lys) and c.1087 G>T (p.Ala363Ser)) exhibited similar GLUT2 transport activity as the wild type. Structural analysis of GLUT2 revealed that variants affect substrate-binding, steric hindrance, or overall transporter structure. The mutant transporter that is associated with a milder FBS phenotype, p.Leu153_Ile154del, retained transport activity. These results improve our overall understanding of the underlying causes of FBS and impact of GLUT2 function on various clinical phenotypes ranging from rare to common disease.
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Affiliation(s)
- Osatohanmwen J Enogieru
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California
| | - Peter M U Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California.,Institute for Human Genetics, University of California, San Francisco, San Francisco, California
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6
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Pryce KD, Powell R, Agwa D, Evely KM, Sheehan GD, Nip A, Tomasello DL, Gururaj S, Bhattacharjee A. Magi-1 scaffolds Na V1.8 and Slack K Na channels in dorsal root ganglion neurons regulating excitability and pain. FASEB J 2019; 33:7315-7330. [PMID: 30860870 DOI: 10.1096/fj.201802454rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Voltage-dependent sodium (NaV) 1.8 channels regulate action potential generation in nociceptive neurons, identifying them as putative analgesic targets. Here, we show that NaV1.8 channel plasma membrane localization, retention, and stability occur through a direct interaction with the postsynaptic density-95/discs large/zonula occludens-1-and WW domain-containing scaffold protein called membrane-associated guanylate kinase with inverted orientation (Magi)-1. The neurophysiological roles of Magi-1 are largely unknown, but we found that dorsal root ganglion (DRG)-specific knockdown of Magi-1 attenuated thermal nociception and acute inflammatory pain and produced deficits in NaV1.8 protein expression. A competing cell-penetrating peptide mimetic derived from the NaV1.8 WW binding motif decreased sodium currents, reduced NaV1.8 protein expression, and produced hypoexcitability. Remarkably, a phosphorylated variant of the very same peptide caused an opposing increase in NaV1.8 surface expression and repetitive firing. Likewise, in vivo, the peptides produced diverging effects on nocifensive behavior. Additionally, we found that Magi-1 bound to sequence like a calcium-activated potassium channel sodium-activated (Slack) potassium channels, demonstrating macrocomplexing with NaV1.8 channels. Taken together, these findings emphasize Magi-1 as an essential scaffold for ion transport in DRG neurons and a central player in pain.-Pryce, K. D., Powell, R., Agwa, D., Evely, K. M., Sheehan, G. D., Nip, A., Tomasello, D. L., Gururaj, S., Bhattacharjee, A. Magi-1 scaffolds NaV1.8 and Slack KNa channels in dorsal root ganglion neurons regulating excitability and pain.
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Affiliation(s)
- Kerri D Pryce
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Rasheen Powell
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Dalia Agwa
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Katherine M Evely
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Garrett D Sheehan
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Allan Nip
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Danielle L Tomasello
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Sushmitha Gururaj
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
| | - Arin Bhattacharjee
- Department of Pharmacology and Toxicology, University at Buffalo-The State University of New York, Buffalo, New York, USA
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7
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Sarkar D, Jana T, Saha S. LMDIPred: A web-server for prediction of linear peptide sequences binding to SH3, WW and PDZ domains. PLoS One 2018; 13:e0200430. [PMID: 30001346 PMCID: PMC6042728 DOI: 10.1371/journal.pone.0200430] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/26/2018] [Indexed: 12/29/2022] Open
Abstract
Protein-peptide interactions form an important subset of the total protein interaction network in the cell and play key roles in signaling and regulatory networks, and in major biological processes like cellular localization, protein degradation, and immune response. In this work, we have described the LMDIPred web server, an online resource for generalized prediction of linear peptide sequences that may bind to three most prevalent and well-studied peptide recognition modules (PRMs)—SH3, WW and PDZ. We have developed support vector machine (SVM)-based prediction models that achieved maximum Matthews Correlation Coefficient (MCC) of 0.85 with an accuracy of 94.55% for SH3, MCC of 0.90 with an accuracy of 95.82% for WW, and MCC of 0.83 with an accuracy of 92.29% for PDZ binding peptides. LMDIPred output combines predictions from these SVM models with predictions using Position-Specific Scoring Matrices (PSSMs) and string-matching methods using known domain-binding motif instances and regular expressions. All of these methods were evaluated using a five-fold cross-validation technique on both balanced and unbalanced datasets, and also validated on independent datasets. LMDIPred aims to provide a preliminary bioinformatics platform for sequence-based prediction of probable binding sites for SH3, WW or PDZ domains.
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Affiliation(s)
| | - Tanmoy Jana
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata, India
- * E-mail: ,
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8
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Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R. Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res 2018; 46:W25-W29. [PMID: 29788132 PMCID: PMC6030932 DOI: 10.1093/nar/gky329] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/03/2018] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.
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Affiliation(s)
- Martin Raden
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Syed M Ali
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Omer S Alkhnbashi
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Fabrizio Costa
- Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK
| | - Jason A Davis
- Coreva Scientific, Kaiser-Joseph-Str 198-200, 79098 Freiburg, Germany
| | - Florian Eggenhofer
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rick Gelhausen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1HH, UK
| | - Robert Kleinkauf
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Steffen C Lott
- Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Mostafa M Mohamed
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Alexander Mattheis
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Milad Miladi
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | | | - Sebastian Will
- Theoretical Biochemistry Group, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
| | - Joachim Wolff
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Patrick R Wright
- Department of Clinical Research, Clinical Trial Unit, University of Basel Hospital, Schanzenstrasse 55, 4031 Basel, Switzerland
| | - Rolf Backofen
- Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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9
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Qi Z, Holland JW, Jiang Y, Secombes CJ, Nie P, Wang T. Molecular characterization and expression analysis of four fish-specific CC chemokine receptors CCR4La, CCR4Lc1, CCR4Lc2 and CCR11 in rainbow trout (Oncorhynchus mykiss). FISH & SHELLFISH IMMUNOLOGY 2017; 68:411-427. [PMID: 28732768 DOI: 10.1016/j.fsi.2017.07.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/08/2017] [Accepted: 07/16/2017] [Indexed: 06/07/2023]
Abstract
The chemokine and chemokine receptor networks regulate leukocyte trafficking, inflammation, immune cell differentiation, cancer and other biological processes. Comparative immunological studies have revealed that both chemokines and their receptors have expanded greatly in a species/lineage specific way. Of the 10 human CC chemokine receptors (CCR1-10) that bind CC chemokines, orthologues only to CCR6, 7, 9 and 10 are present in teleost fish. In this study, four fish-specific CCRs, termed as CCR4La, CCR4Lc1, CCR4Lc2 and CCR11, with a close link to human CCR1-5 and 8, in terms of amino acid homology and syntenic conservation, have been identified and characterized in rainbow trout (Oncorhynchus mykiss). These CCRs were found to possess the conserved features of the G protein-linked receptor family, including an extracellular N-terminal, seven TM domains, three extracellular loops and three intracellular loops, and a cytoplasmic carboxyl tail with multiple potential serine/threonine phosphorylation sites. Four cysteine residues known to be involved in forming two disulfide bonds are present in the extracellular domains and a DRY motif is present in the second intracellular loop. Signaling mediated by these receptors might be regulated by N-glycosylation, tyrosine sulfation, S-palmitoylation, a PDZ ligand motif and di-leucine motifs. Studies of intron/exon structure revealed distinct fish-specific CCR gene organization in different fish species/lineages that might contribute to the diversification of the chemokine ligand-receptor networks in different fish lineages. Fish-specific trout CCRs are highly expressed in immune tissues/organs, such as thymus, spleen, head kidney and gills. Their expression can be induced by the pro-inflammatory cytokines, IL-1β, IL-6 and IFNγ, by the pathogen associated molecular patterns, PolyIC and peptidoglycan, and by bacterial infection. These data suggest that fish-specific CCRs are likely to have an important role in immune regulation in fish.
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Affiliation(s)
- Zhitao Qi
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK; Key Laboratory of Biochemistry and Biotechnology of Marine Wetland of Jiangsu Province, Yancheng Institute of Technology, Jiangsu, Yancheng, 224051, China
| | - Jason W Holland
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Yousheng Jiang
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK; College of Fishery and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Christopher J Secombes
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei province 430072, China
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK.
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10
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An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions. Methods Mol Biol 2017. [PMID: 28092029 DOI: 10.1007/978-1-4939-6762-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data. However, these high-throughput data are often affected by a low signal to noise ratio. Furthermore, the prediction methods have several additional shortcomings, such as linearity problem, high computational complexity, etc. Thus, computational identification of SH2-peptide interactions using high-throughput data remains challenging. Here, we propose a machine learning approach based on an efficient semi-supervised learning technique for the prediction of 51 SH2 domain mediated interactions in the human proteome. In our study, we have successfully employed several strategies to tackle the major problems in computational identification of SH2-peptide interactions.
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Sain N, Mohanty D. modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks. Biol Direct 2016; 11:48. [PMID: 27655048 PMCID: PMC5031328 DOI: 10.1186/s13062-016-0151-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/14/2016] [Indexed: 11/27/2022] Open
Abstract
Background PDZ domains recognize short sequence stretches usually present in C-terminal of their interaction partners. Because of the involvement of PDZ domains in many important biological processes, several attempts have been made for developing bioinformatics tools for genome-wide identification of PDZ interaction networks. Currently available tools for prediction of interaction partners of PDZ domains utilize machine learning approach. Since, they have been trained using experimental substrate specificity data for specific PDZ families, their applicability is limited to PDZ families closely related to the training set. These tools also do not allow analysis of PDZ-peptide interaction interfaces. Results We have used a structure based approach to develop modPDZpep, a program to predict the interaction partners of human PDZ domains and analyze structural details of PDZ interaction interfaces. modPDZpep predicts interaction partners by using structural models of PDZ-peptide complexes and evaluating binding energy scores using residue based statistical pair potentials. Since, it does not require training using experimental data on peptide binding affinity, it can predict substrates for diverse PDZ families. Because of the use of simple scoring function for binding energy, it is also fast enough for genome scale structure based analysis of PDZ interaction networks. Benchmarking using artificial as well as real negative datasets indicates good predictive power with ROC-AUC values in the range of 0.7 to 0.9 for a large number of human PDZ domains. Another novel feature of modPDZpep is its ability to map novel PDZ mediated interactions in human protein-protein interaction networks, either by utilizing available experimental phage display data or by structure based predictions. Conclusions In summary, we have developed modPDZpep, a web-server for structure based analysis of human PDZ domains. It is freely available at http://www.nii.ac.in/modPDZpep.html or http://202.54.226.235/modPDZpep.html. Reviewers This article was reviewed by Michael Gromiha and Zoltán Gáspári. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0151-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Neetu Sain
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Debasisa Mohanty
- Bioinformatics Center, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Li L, Li J, Xiao W, Li Y, Qin Y, Zhou S, Yang H. Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:947-953. [PMID: 26571537 DOI: 10.1109/tcbb.2015.2495140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Kundu K, Mann M, Costa F, Backofen R. MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. ACTA ACUST UNITED AC 2014; 30:2668-9. [PMID: 24872426 PMCID: PMC4155253 DOI: 10.1093/bioinformatics/btu350] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Summary: MoDPepInt (Modular Domain Peptide Interaction) is a new easy-to-use web server for the prediction of binding partners for modular protein domains. Currently, we offer models for SH2, SH3 and PDZ domains via the tools SH2PepInt, SH3PepInt and PDZPepInt, respectively. More specifically, our server offers predictions for 51 SH2 human domains and 69 SH3 human domains via single domain models, and predictions for 226 PDZ domains across several species, via 43 multidomain models. All models are based on support vector machines with different kernel functions ranging from polynomial, to Gaussian, to advanced graph kernels. In this way, we model non-linear interactions between amino acid residues. Results were validated on manually curated datasets achieving competitive performance against various state-of-the-art approaches. Availability and implementation: The MoDPepInt server is available under the URL http://modpepint.informatik.uni-freiburg.de/ Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kousik Kundu
- Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany
| | - Martin Mann
- Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany
| | - Fabrizio Costa
- Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany Bioinformatics Group, Department of Computer Science, 79110 Freiburg and Centre for Biological Signalling Studies (BIOSS), 79104 Freiburg, University of Freiburg, Germany
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