DISULFIND: a disulfide bonding state and cysteine connectivity prediction server

Ceroni, Alessio; Passerini, Andrea; Vullo, Alessandro; Frasconi, Paolo

doi:10.1093/nar/gkl266

Cited by 299 publications

(231 citation statements)

References 19 publications

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“…4). The disulphide linkage prediction performed using the DISULFIND web server further confirmed the possibility of these two disulfide bonds in EAP (Ceroni et al 2006). …”

Section: Homology Modelling Of Eapmentioning

confidence: 55%

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

Corso

Chellappan

Sukumaran

et al. 2010

World J Microbiol Biotechnol

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An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca 2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.Keywords Engyodontium album Á Alkaline serine protease Á Subtilases Á Homology modelling Abbreviations E. album Engyodontium album EAPEngyodontium album protease (deduced protein) Eap Engyodontium album protease (gene)

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“…4). The disulphide linkage prediction performed using the DISULFIND web server further confirmed the possibility of these two disulfide bonds in EAP (Ceroni et al 2006). …”

Section: Homology Modelling Of Eapmentioning

confidence: 55%

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

Corso

Chellappan

Sukumaran

et al. 2010

World J Microbiol Biotechnol

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“…Therefore, the predicted protein structure of LTPG was modeled. Both the four amphipathic a-helices (Jpred; Cole et al, 2008) and eight Cys residues capable of forming four disulfide bonds (DISUL-FIND; Ceroni et al, 2006) were predicted (see Supplemental Figure 2 online), leading to the question of whether the structure of LTPG supports lipid binding.…”

Section: Ltpg Displays Lipid Binding Activitymentioning

confidence: 99%

Arabidopsis LTPG Is a Glycosylphosphatidylinositol-Anchored Lipid Transfer Protein Required for Export of Lipids to the Plant Surface

et al. 2009

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Plant epidermal cells dedicate more than half of their lipid metabolism to the synthesis of cuticular lipids, which seal and protect the plant shoot. The cuticle is made up of a cutin polymer and waxes, diverse hydrophobic compounds including very-long-chain fatty acids and their derivatives. How such hydrophobic compounds are exported to the cuticle, especially through the hydrophilic plant cell wall, is not known. By performing a reverse genetic screen, we have identified LTPG, a glycosylphosphatidylinositol-anchored lipid transfer protein that is highly expressed in the epidermis during cuticle biosynthesis in Arabidopsis thaliana inflorescence stems. Mutant plant lines with decreased LTPG expression had reduced wax load on the stem surface, showing that LTPG is involved either directly or indirectly in cuticular lipid deposition. In vitro 2-p-toluidinonaphthalene-6-sulfonate assays showed that recombinant LTPG has the capacity to bind to this lipid probe. LTPG was primarily localized to the plasma membrane on all faces of stem epidermal cells in the growing regions of inflorescence stems where wax is actively secreted. These data suggest that LTPG may function as a component of the cuticular lipid export machinery.

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“…The signal peptide was predicted using the SignalP program (http://www.cbs.dtu.dk/services/SignalP/) (34). Disulfide bonds were predicted using the DISULFIND program (http:// disulfind.dsi.unifi.it/) (38). Global sequence comparisons were performed using the MatGAT program (39) using the BLOSUM60 scoring matrix.…”

Section: Sequence Analysismentioning

confidence: 99%

Functional Characterization of a Nonmammalian IL-21: Rainbow Trout Oncorhynchus mykiss IL-21 Upregulates the Expression of the Th Cell Signature Cytokines IFN-γ, IL-10, and IL-22

Wang

Díaz‐Rosales

Costa

et al. 2011

The Journal of Immunology

151

169

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In mammals, IL-21 is a common γ chain cytokine produced by activated CD4+ T cells and NKT cells that acts on multiple lineages of cells. Although IL-21 has also been discovered in birds, amphibians, and fish, to date, no functional studies have been reported for any nonmammalian IL-21 molecule. We have sequenced an IL-21 gene (tIL-21) in rainbow trout, which has a six-exon/five-intron structure, is expressed in immune tissues, and is induced by bacterial and viral infection and the T cell stimulant PHA. In contrast to mammals, calcium ionophore and PMA act synergistically to induce tIL-21. Recombinant tIL-21 (rtIL-21) induced a rapid and long-lasting (4–72 h) induction of expression of IFN-γ, IL-10, and IL-22, signature cytokines for Th1-, Th2-, and Th17-type responses, respectively, in head kidney leukocytes. However, rtIL-21 had little effects on the expression of other cytokines studied. rtIL-21 maintained the expression of CD8α, CD8β, and IgM at a late stage of stimulation when their expression was significantly decreased in controls and increased the expression of the Th cell markers CD4, T-bet, and GATA3. Intraperitoneal injection of rtIL-21 confirmed the in vitro bioactivity and increased the expression of IFN-γ, IL-10, IL-21, IL-22, CD8, and IgM. Inhibition experiments revealed that the activation of JAK/STAT3, Akt1/2, and PI3K pathways were responsible for rtIL-21 action. This study helps to clarify the role of IL-21 in lower vertebrates for the first time, to our knowledge, and suggests IL-21 is a likely key regulator of T and B cell function in fish.

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DISULFIND: a disulfide bonding state and cysteine connectivity prediction server

Cited by 299 publications

References 19 publications

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

Arabidopsis LTPG Is a Glycosylphosphatidylinositol-Anchored Lipid Transfer Protein Required for Export of Lipids to the Plant Surface

Functional Characterization of a Nonmammalian IL-21: Rainbow Trout Oncorhynchus mykiss IL-21 Upregulates the Expression of the Th Cell Signature Cytokines IFN-γ, IL-10, and IL-22

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