The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

Arnold, Konstantin; Bordoli, Lorenza; Kopp, Jürgen; Schwede, Torsten

doi:10.1093/bioinformatics/bti770

Cited by 6,404 publications

(4,058 citation statements)

References 53 publications

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“…We used SwissModel to make a homology model of FLA4 using these two crystal structures as a template. 12–14 The FLA4 sequence has a higher identity with TGFBIp than Drosophila fasciclin I with 21.6% and 17.4%, respectively (the input sequence for the Swissprot query and a list of available structures including sequence identity and GMQE and is presented in the online supplement). Furthermore, although both models do not have a high global model quality estimation score (GMQE: 0.5), the model built with TGFBIp has a better agreement between the model structure and experimental structures.…”

Section: Resultsmentioning

confidence: 99%

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

Turupcu

Almohamed

Oostenbrink

et al. 2018

Plant Signaling & Behavior

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The Arabidopsis thaliana Fasciclin like arabinogalactan protein 4 (FLA4) locus is required for normal root growth in a linear genetic pathway with the FEI1 and FEI2 loci coding for receptor-like kinases. The two Fas1 domains of FLA4 are conserved among angiosperms but only the C-terminal Fas1 domain is required for genetic function. We show that at low salt deletion of the N-terminal Fas1 domain of transgenic FLA4 leads to enhanced root elongation compared to the tandem Fas1 wild type version. Modeling the hypothetical interaction between FLA4 and FEI1 we show that the predicted interaction is predominantly involving the C-terminal Fas1 domain. Relative conformational mobility between the two FLA4 Fas1 domains might regulate the interaction with the FEI receptor kinases. We therefore speculate that the FLA4 FEI complex might be a sensor for environmental conditions in the apoplast.

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Section: Resultsmentioning

confidence: 99%

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

Turupcu

Almohamed

Oostenbrink

et al. 2018

Plant Signaling & Behavior

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“…Using the published structure of human TIMP‐2 (accession code: 1BR9) as a template, predicted structural models were produced using SWISS‐MODEL 49, 50 for TIMP‐2, TIMP‐3, NT2/CT3 and NT3/CT2 fusions (sequence of rat origin). Structures were analysed using reported methods 36, 37, 46 and predictions of protein surface hydrophobicity (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Structural models of TIMP ‐2 and TIMP ‐3 created using SWISS ‐ MODEL 49, 50 and processed through an algorithm developed by the Warwicker group (The University of Manchester). Predictions of the (A–B) hydrophobicity (nonpolar vs. polar regions) and (C–D) electrostatic potential (positive vs. negative charge) of protein surfaces were generated for TIMP ‐2 (A,C) and TIMP ‐3 (B,D).…”

Section: Resultsmentioning

confidence: 99%

“…Predicted structural models of TIMP‐2, TIMP‐3, TIMP‐4 and TIMP fusion/mutant sequences used in this study were generated using SWISS‐MODEL 49, 50, where the published structure of human TIMP‐2 (accession code: 1BR9) was used as a template. Published structures were also analysed for ARTN (accession code: 2GYZ) and PAI‐1 (accession code: 3LW2).…”

Section: Methodsmentioning

confidence: 99%

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A protein chimera strategy supports production of a model “difficult‐to‐express” recombinant target

et al. 2018

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Due in part to the needs of the biopharmaceutical industry, there has been an increased drive to generate high quality recombinant proteins in large amounts. However, achieving high yields can be a challenge as the novelty and increased complexity of new targets often makes them ‘difficult‐to‐express’. This study aimed to define the molecular features that restrict the production of a model ‘difficult‐to‐express’ recombinant protein, Tissue Inhibitor Metalloproteinase‐3 (TIMP‐3). Building from experimental data, computational approaches were used to rationalize the redesign of this recombinant target to generate a chimera with enhanced secretion. The results highlight the importance of early identification of unfavourable sequence attributes, enabling the generation of engineered protein forms that bypass ‘secretory’ bottlenecks and result in efficient recombinant protein production.

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“…We used Swiss Model (Guex & Peitsch, 1997; Arnold et al ., 2006) and PDB entry 2YBP (Chowdhury et al ., 2011) to homology model JMJD‐2 of C. elegans (Wormbase cosmid ID: Y48B6A.11). 2YBP is an X‐ray crystal structure of JMJD2A (αα 7‐355, 2.02 Å), the human ortholog of worm JMJD‐2.…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial metabolites extend lifespan

et al. 2016

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SummaryDisruption of mitochondrial respiration in the nematode Caenorhabditis elegans can extend lifespan. We previously showed that long‐lived respiratory mutants generate elevated amounts of α‐ketoacids. These compounds are structurally related to α‐ketoglutarate, suggesting they may be biologically relevant. Here, we show that provision of several such metabolites to wild‐type worms is sufficient to extend their life. At least one mode of action is through stabilization of hypoxia‐inducible factor‐1 (HIF‐1). We also find that an α‐ketoglutarate mimetic, 2,4‐pyridinedicarboxylic acid (2,4‐PDA), is alone sufficient to increase the lifespan of wild‐type worms and this effect is blocked by removal of HIF‐1. HIF‐1 is constitutively active in isp‐1(qm150) Mit mutants, and accordingly, 2,4‐PDA does not further increase their lifespan. Incubation of mouse 3T3‐L1 fibroblasts with life‐prolonging α‐ketoacids also results in HIF‐1α stabilization. We propose that metabolites that build up following mitochondrial respiratory dysfunction form a novel mode of cell signaling that acts to regulate lifespan.

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The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

Abstract: The SWISS-MODEL workspace can be accessed freely at http://swissmodel.expasy.org/workspace/

Cited by 6,404 publications

References 53 publications

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

A protein chimera strategy supports production of a model “difficult‐to‐express” recombinant target

Mitochondrial metabolites extend lifespan

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