TopPred II: an improved software for membrane protein structure predictions

Claros, M. Gonzalo; Heijne, Gunnar von

doi:10.1093/bioinformatics/10.6.685

Cited by 730 publications

(709 citation statements)

References 10 publications

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“…S2;von Heijne, 1992;Claros and von Heijne, 1994). To confirm that the approximately 200-kD band in the SYP41 precipitate corresponds to TNO1, SYP41 and preimmune immunoprecipitates were analyzed by immunoblotting using antibodies against SYP41 or TNO1 (see below).…”

Section: Identification Of Tno1mentioning

confidence: 99%

TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis

Kim

Bassham

2011

Plant Physiology

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The Arabidopsis (Arabidopsis thaliana) soluble N-ethylmaleimide-sensitive factor attachment protein receptor SYP41 is involved in vesicle fusion at the trans-Golgi network (TGN) and interacts with AtVPS45, SYP61, and VTI12. These proteins are involved in diverse cellular processes, including vacuole biogenesis and stress tolerance. A previously uncharacterized protein, named TNO1 (for TGN-localized SYP41-interacting protein), was identified by coimmunoprecipitation as a SYP41-interacting protein.TNO1 was found to localize to the TGN by immunofluorescence microscopy. A tno1 mutant showed increased sensitivity to high concentrations of NaCl, KCl, and LiCl and also to mannitol-induced osmotic stress. Localization of SYP61, which is involved in the salt stress response, was disrupted in the tno1 mutant. Vacuolar proteins were partially secreted to the apoplast in the tno1 mutant, suggesting that TNO1 is required for efficient protein trafficking to the vacuole. The tno1 mutant had delayed formation of the brefeldin A (BFA) compartment in cotyledons upon application of BFA, suggesting less efficient membrane fusion processes in the mutant. Unlike most TGN proteins, TNO1 does not relocate to the BFA compartment upon BFA treatment. These data demonstrate that TNO1 is involved in vacuolar trafficking and salt tolerance, potentially via roles in vesicle fusion and in maintaining TGN structure or identity.

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Section: Identification Of Tno1mentioning

confidence: 99%

TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis

Kim

Bassham

2011

Plant Physiology

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“…Conserved domains were determined from BLAST analysis ( Table 3). The transmembrane helical regions of Pheromone Receptor Pre-A protein topology prediction and validation were done by using various servers like TMHMM (Krogh et al 2001), HMMTOP (Tusnady and Simon 1998), TMpred (Claros and von Heijne 1994), MEMSAT (Jones, Taylor, and Thornton 1994) and TopPred (Hofman 1993), that predicted the nature of the query sequence (Sahoo et al 2013). …”

Section: Sequence Analysis and Secondary Structure Predictionmentioning

confidence: 99%

Computational, structural and functional aspects of hypothetical protein of Aspergillus flavus Pheromone Receptor Pre-A (PRP-A)

Kumar¹,

Rana²,

Kumar³

et al. 2017

J App Pharm Sci

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Pheromone Receptor Pre-A (PRP-A) is a G Protein-coupled receptor (G-PCR protein with seven transmembrane helices) in Aspergillus flavus, a filamentous fungus known for its aflatoxin production, germination and quorum sensing. It causes an aspergillosis in human beings and domestic animals. With an aim to find a better inhibitor against biosynthesis of aflatoxin, the integral protein structure was effectively engineered, designed, screening against various antifungal compound databases. The LibDock protein-ligand interaction of DSv3.5 study suggests that blasticidin S, pipernonaline and piperin, inhibit PRP-A protein with highest binding affinity. The amino acids frequently involved in binding with the ligand blasticidin S of O2 and H33 and H234 at Arg 40 0 and Tyr 394 respectively. Our in silico prediction may lead to establish better therapeutic approaches for the treatment against aspergillosis.

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“…This process was repeated iteratively until most of the amino acids were below 95% cutoff value and residue which lies above 95% cutoff value were subjected to loop modeling in MODELLER. Finally, GPR87 model showing the best PROCHECK and ERRAT plot was then subjected to native protein folding energy evaluation using ProSA server (Wiederstein et al, 2007 DOI:http://dx.doi.org/10.7314/APJCP.2013.14.12.7473 Computational 3-D Analysis of Human GPR87 Protein of: Implications for Structure-Based Drug Design Transmembrane helices prediction and function assignment of GPR87 protein Different servers like DAS, TMHMM, HMMTOP, TMpred, TopPred, SOSUI, SPLIT, and Predictprotein (PHD) servers were accessed to predict and validate the transmembrane helical region (TM region) of GPR87 protein (Hofmann et al, 1993;Claros et al, 1994;Cserzo et al, 1994;Hirokawa et al, 1998;Tusnády et al, 1998;Krogh et al, 2001;Juretic et al, 2002;Jones et al, 2004;Rost et al, 2004). To know the novel functions of GPR87 protein by using a SVMProt server with the aim of support vector machine learning techniques (SVM) which classifies protein into functional families from its primary sequences i.e.…”

Section: Model Validationmentioning

confidence: 99%

Computational Analysis of the 3-D structure of Human GPR87 Protein: Implications for Structure-Based Drug Design

Rani

Nischal²,

Sahoo³

et al. 2013

Asian Pacific Journal of Cancer Prevention

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The G-protein coupled receptor 87 (GPR87) is a recently discovered orphan GPCR which means that the search of their endogenous ligands has been a novel challenge. GPR87 has been shown to be overexpressed in squamous cell carcinomas (SCCs) or adenocarcinomas in lungs and bladder. The 3D structure of GPR87 was here modeled using two templates (2VT4 and 2ZIY) by a threading method. Functional assignment of GPR87 by SVM revealed that along with transporter activity, various novel functions were predicted. The 3D structure was further validated by comparison with structural features of the templates through Verify-3D, ProSA and ERRAT for determining correct stereochemical parameters. The resulting model was evaluated by Ramachandran plot and good 3D structure compatibility was evidenced by DOPE score. Molecular dynamics simulation and solvation of protein were studied through explicit spherical boundaries with a harmonic restraint membrane water system. A DRY-motif (Asp-Arg-Tyr sequence) was found at the end of transmembrane helix3, where GPCR binds and thus activation of signals is transduced. In a search for better inhibitors of GPR87, in silico modification of some substrate ligands was carried out to form polar interactions with Arg115 and Lys296. Thus, this study provides early insights into the structure of a major drug target for SCCs.

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TopPred II: an improved software for membrane protein structure predictions

Cited by 730 publications

References 10 publications

TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis

TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis

Computational, structural and functional aspects of hypothetical protein of Aspergillus flavus Pheromone Receptor Pre-A (PRP-A)

Computational Analysis of the 3-D structure of Human GPR87 Protein: Implications for Structure-Based Drug Design

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