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Rozano L, Jones DAB, Hane JK, Mancera RL. Template-Based Modelling of the Structure of Fungal Effector Proteins. Mol Biotechnol 2024; 66:784-813. [PMID: 36940017 PMCID: PMC11043172 DOI: 10.1007/s12033-023-00703-4] [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: 08/31/2022] [Accepted: 02/14/2023] [Indexed: 03/21/2023]
Abstract
The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs. The availability of experimentally determined three-dimensional (3D) structures of a number of effector proteins has recently highlighted structural similarities amongst groups of sequence-dissimilar fungal effectors, enabling the search for similar structural folds amongst effector sequence candidates. We have applied template-based modelling to predict the 3D structures of candidate effector sequences obtained from bioinformatics predictions and the PHI-BASE database. Structural matches were found not only with ToxA- and MAX-like effector candidates but also with non-fungal effector-like proteins-including plant defensins and animal venoms-suggesting the broad conservation of ancestral structural folds amongst cytotoxic peptides from a diverse range of distant species. Accurate modelling of fungal effectors were achieved using RaptorX. The utility of predicted structures of effector proteins lies in the prediction of their interactions with plant receptors through molecular docking, which will improve the understanding of effector-plant interactions.
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Affiliation(s)
- Lina Rozano
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Darcy A B Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - James K Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA, 6845, Australia.
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia.
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Barage SH, Deobagkar DD, Baladhye VB. Characterization of structural and functional role of selenocysteine in selenoprotein H and its impact on DNA binding. Amino Acids 2018; 50:593-607. [DOI: 10.1007/s00726-018-2543-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/15/2018] [Indexed: 12/13/2022]
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Adamu A, Shamsir MS, Wahab RA, Parvizpour S, Huyop F. Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1. J Biomol Struct Dyn 2016; 35:3285-3296. [DOI: 10.1080/07391102.2016.1254115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Aliyu Adamu
- Faculty of Biosciences and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
- Faculty of Science, Department of Microbiology, Kaduna State University, Tafawa Balewa way, Kaduna PMB 2339, Nigeria
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
| | - Sepideh Parvizpour
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fahrul Huyop
- Faculty of Biosciences and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
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Structural prediction of a novel laminarinase from the psychrophilic Glaciozyma antarctica PI12 and its temperature adaptation analysis. J Mol Model 2015; 21:63. [PMID: 25721655 DOI: 10.1007/s00894-015-2617-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/09/2015] [Indexed: 12/30/2022]
Abstract
Here, we present a novel psychrophilic β-glucanase from Glaciozyma antarctica PI12 yeast that has been structurally modeled and analyzed in detail. To our knowledge, this is the first attempt to model a psychrophilic laminarinase from yeast. Because of the low sequence identity (<40%), a threading method was applied to predict a 3D structure of the enzyme using the MODELLER9v12 program. The results of a comparative study using other mesophilic, thermophilic, and hyperthermophilic laminarinases indicated several amino acid substitutions on the surface of psychrophilic laminarinase that totally increased the flexibility of its structure for efficient catalytic reactions at low temperatures. Whereas several structural factors in the overall structure can explain the weak thermal stability, this research suggests that the psychrophilic adaptation and catalytic activity at low temperatures were achieved through existence of longer loops and shorter or broken helices and strands, an increase in the number of aromatic and hydrophobic residues, a reduction in the number of hydrogen bonds and salt bridges, a higher total solvent accessible surface area, and an increase in the exposure of the hydrophobic side chains to the solvent. The results of comparative molecular dynamics simulation and principal component analysis confirmed the above strategies adopted by psychrophilic laminarinase to increase its catalytic efficiency and structural flexibility to be active at cold temperature.
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Casado P, Rodriguez-Prados JC, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, Cutillas PR. Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci Signal 2013; 6:rs6. [PMID: 23532336 DOI: 10.1126/scisignal.2003573] [Citation(s) in RCA: 253] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Kinases determine the phenotypes of many cancer cells, but the frequency with which individual kinases are activated in primary tumors remains largely unknown. We used a computational approach, termed kinase-substrate enrichment analysis (KSEA), to systematically infer the activation of given kinase pathways from mass spectrometry-based phosphoproteomic analysis of acute myeloid leukemia (AML) cells. Experiments conducted in cell lines validated the approach and, furthermore, revealed that DNA-dependent protein kinase (DNA-PK) was activated as a result of inhibiting the phosphoinositide 3-kinase (PI3K)-mammalian target of rapamycin (mTOR) signaling pathway. Application of KSEA to primary AML cells identified PI3K, casein kinases (CKs), cyclin-dependent kinases (CDKs), and p21-activated kinases (PAKs) as the kinase substrate groups most frequently enriched in this cancer type. Substrates phosphorylated by extracellular signal-regulated kinase (ERK) and cell division cycle 7 (CDC7) were enriched in primary AML cells that were resistant to inhibition of PI3K-mTOR signaling, whereas substrates of the kinases Abl, Lck, Src, and CDK1 were increased in abundance in inhibitor-sensitive cells. Modeling based on the abundances of these substrate groups accurately predicted sensitivity to a dual PI3K and mTOR inhibitor in two independent sets of primary AML cells isolated from patients. Thus, our study demonstrates KSEA as an untargeted method for the systematic profiling of kinase pathway activities and for increasing our understanding of diseases caused by the dysregulation of signaling pathways.
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Affiliation(s)
- Pedro Casado
- Analytical Signalling Group, Centre for Cell Signalling, Barts Cancer Institute, Queen Mary University of London, London EC1B 6BQ, UK.
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Ramli ANM, Mahadi NM, Shamsir MS, Rabu A, Joyce-Tan KH, Murad AMA, Illias RM. Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function. J Comput Aided Mol Des 2012; 26:947-61. [DOI: 10.1007/s10822-012-9585-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 06/04/2012] [Indexed: 12/29/2022]
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Aguilar HC, Matreyek KA, Filone CM, Hashimi ST, Levroney EL, Negrete OA, Bertolotti-Ciarlet A, Choi DY, McHardy I, Fulcher JA, Su SV, Wolf MC, Kohatsu L, Baum LG, Lee B. N-glycans on Nipah virus fusion protein protect against neutralization but reduce membrane fusion and viral entry. J Virol 2006; 80:4878-89. [PMID: 16641279 PMCID: PMC1472062 DOI: 10.1128/jvi.80.10.4878-4889.2006] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nipah virus (NiV) is a deadly emerging paramyxovirus. The NiV attachment (NiV-G) and fusion (NiV-F) envelope glycoproteins mediate both syncytium formation and viral entry. Specific N-glycans on paramyxovirus fusion proteins are generally required for proper conformational integrity and biological function. However, removal of individual N-glycans on NiV-F had little negative effect on processing or fusogenicity and has even resulted in slightly increased fusogenicity. Here, we report that in both syncytium formation and viral entry assays, removal of multiple N-glycans on NiV-F resulted in marked increases in fusogenicity (>5-fold) but also resulted in increased sensitivity to neutralization by NiV-F-specific antisera. The mechanism underlying the hyperfusogenicity of these NiV-F N-glycan mutants is likely due to more-robust six-helix bundle formation, as these mutants showed increased fusion kinetics and were more resistant to neutralization by a fusion-inhibitory reagent based on the C-terminal heptad repeat region of NiV-F. Finally, we demonstrate that the fusogenicities of the NiV-F N-glycan mutants were inversely correlated with the relative avidities of NiV-F's interactions with NiV-G, providing support for the attachment protein "displacement" model of paramyxovirus fusion. Our results indicate that N-glycans on NiV-F protect NiV from antibody neutralization, suggest that this "shielding" role comes together with limiting cell-cell fusion and viral entry efficiencies, and point to the mechanisms underlying the hyperfusogenicity of these N-glycan mutants. These features underscore the varied roles that N-glycans on NiV-F play in the pathobiology of NiV entry but also shed light on the general mechanisms of paramyxovirus fusion with host cells.
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Affiliation(s)
- Hector C Aguilar
- Department of MIMG, David Geffen Schoo; of Medicine at UCLA, Los Angeles, CA 90095, USA
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Wallace IS, Roberts DM. Homology modeling of representative subfamilies of Arabidopsis major intrinsic proteins. Classification based on the aromatic/arginine selectivity filter. PLANT PHYSIOLOGY 2004; 135:1059-68. [PMID: 15181215 PMCID: PMC514140 DOI: 10.1104/pp.103.033415] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Revised: 11/24/2003] [Accepted: 12/02/2003] [Indexed: 05/18/2023]
Abstract
Major intrinsic proteins (MIPs) are a family of membrane channels that facilitate the bidirectional transport of water and small uncharged solutes such as glycerol. The 35 full-length members of the MIP family in Arabidopsis are segregated into four structurally homologous subfamilies: plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), nodulin 26-like intrinsic membrane proteins (NIPs), and small basic intrinsic proteins (SIPs). Computational methods were used to construct structural models of the putative pore regions of various plant MIPs based on homology modeling with the atomic resolution crystal structures of mammalian aquaporin 1 and the bacterial glycerol permease GlpF. Based on comparisons of the narrow selectivity filter regions (the aromatic/Arg [ar/R] filter), the members of the four phylogenetic subfamilies of Arabidopsis MIPs can be classified into eight groups. PIPs possess a uniform ar/R signature characteristic of high water transport aquaporins, whereas TIPs are highly diverse with three separate conserved ar/R regions. NIPs possess two separate conserved ar/R regions, one that is similar to the archetype, soybean (Glycine max) nodulin 26, and another that is characteristic of Arabidopsis NIP6;1. The SIP subfamily possesses two ar/R subgroups, characteristic of either SIP1 or SIP2. Both SIP ar/R residues are divergent from all other MIPs in plants and other kingdoms. Overall, these findings suggest that higher plant MIPs have a common fold but show distinct differences in proposed pore apertures, potential to form hydrogen bonds with transported molecules, and amphiphilicity that likely results in divergent transport selectivities.
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Affiliation(s)
- Ian S Wallace
- Department of Biochemistry, Cellular, and Molecular Biology and Center of Excellence in Structural Biology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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Hickox DM, Gibbs G, Morrison JR, Sebire K, Edgar K, Keah HH, Alter K, Loveland KL, Hearn MTW, de Kretser DM, O'Bryan MK. Identification of a novel testis-specific member of the phosphatidylethanolamine binding protein family, pebp-2. Biol Reprod 2002; 67:917-27. [PMID: 12193403 DOI: 10.1095/biolreprod.101.001446] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The phosphatidylethanolamine binding proteins (pebps) are an evolutionarily conserved family of proteins recently implicated in mitogen-activated protein (MAP) kinase pathway regulation, where they are called raf kinase inhibitory proteins. Here, we describe the cloning, cellular localization, and partial characterization of a new member, pebp-2, with potential roles in male fertility. Expression data show that pebp-2 is a testis-specific 21-kDa protein found within late meiotic and haploid germ cells in a stage-specific pattern that is temporally distinct from that of pebp-1. Sequence analyses suggest that pebp-2 forms a distinct subset of the pebp family within mammals. Database analyses revealed the existence of a third subset. Analysis suggests that the specificity/regulation of the distinct pebps subsets is likely to be determined by the amino terminal 40 amino acids or the 3' untranslated region, where the majority of sequence differences occur. Protein homology modeling suggests that pebp-2 protein is, however, topologically similar to other pebps and composed of Greek key fold motifs, a dominant beta-sheet formed from five anti-parallel beta strands forming a shallow groove associated with a putative phosphatidylethanolamine binding site. The pebp-2 gene is intronless and data suggest that it is a retrogene derived from pebp-1. Further, pebp-2 colocalizes with members of the MAP kinase pathway in late spermatocytes and spermatids and on the midpiece of epididymal sperm. These data raise the possibility that pebp-2 is a novel participant in the MAP kinase signaling pathway, with a role in spermatogenesis or posttesticular sperm maturation.
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Affiliation(s)
- Deborah M Hickox
- Monash Institute of Reproduction and Development, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Clayton, Victoria 3168, Australia
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Schafferhans A, Klebe G. Docking ligands onto binding site representations derived from proteins built by homology modelling. J Mol Biol 2001; 307:407-27. [PMID: 11243828 DOI: 10.1006/jmbi.2000.4453] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Due to the abundant sequence information available from genome projects, an increasing number of structurally unknown proteins, homologous to examples of known 3D structure, will be discovered as new targets for drug design. Since homology models do not provide sufficient accuracy to apply common drug design tools, a new approach, DragHome, has been developed to dock ligands into such approximate protein models. DragHome combines information from homology modelling with ligand data, used by and derived from 3D quantitative structure-activity relationships (QSAR). The binding-site of a model-built protein is analysed in terms of putative ligand interaction sites and translated via Gaussian functions into a functional binding-site description represented by physico-chemical properties. Ligands to be docked onto these binding-site representations are similarly translated into a description based on Gaussian functions. The docking is computed by optimising the overlap between the functional description of the binding site and the ligand, generating multiple solutions. For a set of different ligands, these solutions are ranked according to the internal similarity consistance among the various ligands in the binding modes obtained from docking. DragHome has been validated at examples for which crystal structures are available: structurally distinct thrombin inhibitors were docked onto models of thrombin generated from serine proteases of 28 to 40 % sequence identity, yielding ligand binding modes with an average RMS deviation of 1.4 A. Mostly the near-native solutions are ranked best. Molecular flexibility of ligands can be considered in terms of pre-calculated multiple conformers. DragHome has been used to automatically generate an alignment of 88 thrombin inhibitors, for which a significant 3D QSAR model could be derived. The contribution maps resulting from this analysis can be interpreted with respect to the surrounding protein model. They highlight inconsistencies and deficiencies present in the model. In future developments, this information could be fed back into a subsequent modelling step to improve the protein model.
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Affiliation(s)
- A Schafferhans
- Department of Pharmaceutical Chemistry, Philipps-University of Marburg, D-35032 Marburg, Germany
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Yuan C, Selby TL, Li J, Byeon IJ, Tsai MD. Tumor suppressor INK4: refinement of p16INK4A structure and determination of p15INK4B structure by comparative modeling and NMR data. Protein Sci 2000; 9:1120-8. [PMID: 10892805 PMCID: PMC2144649 DOI: 10.1110/ps.9.6.1120] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Within the tumor suppressor protein INK4 (inhibitor of cyclin-dependent kinase 4) family, p15INK4B is the smallest and the only one whose structure has not been determined previously, probably due to the protein's conformational flexibility and instability. In this work, multidimensional NMR studies were performed on this protein. The first tertiary structure was built by comparative modeling with p16INK4A as the template, followed by restrained energy minimization with NMR constraints (NOE and H-bonds). For this purpose, the solution structure of pl6INK4A, whose quality was also limited by similar problems, was refined with additional NMR experiments conducted on an 800 MHz spectrometer and by structure-based iterative NOE assignments. The nonhelical regions showed major improvement with root-mean-square deviation (RMSD) improved from 1.23 to 0.68 A for backbone heavy atoms. The completion of p15INK4B coupled with refinement of p16INK4A made it possible to compare the structures of the four INK4 members in depth, and to compare the structures of p16INK4A in the free form and in the p16INK4A-CDK6 complex. This is an important step toward a comprehensive understanding of the precise functional roles of each INK4 member.
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Affiliation(s)
- C Yuan
- Department of Chemistry, The Ohio State University, Columbus 43210-1185, USA
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Fraternali F, Pastore A. Modularity and homology: modelling of the type II module family from titin. J Mol Biol 1999; 290:581-93. [PMID: 10390355 DOI: 10.1006/jmbi.1999.2876] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report the homology modelling of the structures of the 162 type II modules from the giant multi-domain protein titin (also known as connectin). The package MODELLER was used and implemented in an automated fashion using four experimentally determined structures as templates. Validation of the models was assessed in terms of divergence from the templates and consensus of the alignments. The homology within the whole family of type II modules as well as with the templates is relatively high (20-35% identity and ca 50% similarity). Comparison between the models of domains for which an NMR structure has been solved and the experimental solution gives an estimate of the quality of the modelling. Our results allow us to distinguish between a set of structurally relevant residues, which are conserved throughout the whole family and buried in the hydrophobic core, from the residues that are conserved and exposed. These latter residues are potentially functionally important. Comparison of exposed conserved patches for modules in different regions of the titin molecule suggests potential interaction surfaces. Our results may be tested directly for those modules whose binding partner is known.
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