ESyPred3D: Prediction of proteins 3D structures

Lambert, Christophe; Léonard, Nadia G.; Bolle, Xavier De; Depiereux, Eric

doi:10.1093/bioinformatics/18.9.1250

Cited by 551 publications

(367 citation statements)

References 28 publications

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“…To investigate whether the lack of a C terminus in HAB1 changes the protein's structure, we obtained three-dimensional (3D) structures for both HAB1.1 and HAB1.2 using the ESyPred3D software 30 . As shown in Fig.…”

Section: Hab1 Undergoes Aba-controlled As During Early Developmentmentioning

confidence: 99%

ABA signalling is fine-tuned by antagonistic HAB1 variants

et al. 2015

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Group A protein type 2C phosphatases (PP2Cs) are negative regulators of abscisic acid (ABA) signalling and plant adaptation to stress. However, our knowledge of the regulation of PP2C activity is limited. Here we report that the PP2C HAB1 undergoes alternative splicing to produce two splice variants, which encode HAB1.1 and HAB1.2, that play opposing roles in ABA-mediated seed germination and ABA-mediated post-germination developmental arrest. HAB1.2 is predominately formed in the presence of ABA and prevents seed germination and post-germinative growth. HAB1.2 interacts with OST1, but cannot inhibit OST1 kinase activity; thus, it functions as a positive regulator of ABA signalling. We also identified an RNA-recognition motif-containing protein, RBM25, as a potential regulator of HAB1 alternative splicing and molecular diversity. Our results reveal a mechanism for turning ABA signalling on and off and for plant adaptation to abiotic stress.

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Section: Hab1 Undergoes Aba-controlled As During Early Developmentmentioning

confidence: 99%

ABA signalling is fine-tuned by antagonistic HAB1 variants

et al. 2015

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“…ESyPref3D is based on a strategy using neural networks to evaluate sequence alignments 75 and uses the MODELLER program 76,77 to build the final structural model. Homology models are constructed with MODELLER with a minimal sequence similarity of 50% to the target.…”

Section: Homology Modeling and Mutated Proteinsmentioning

confidence: 99%

A flexible docking scheme to explore the binding selectivity of PDZ domains

Gerek

Ozkan

2010

Protein Science

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Modeling of protein binding site flexibility in molecular docking is still a challenging problem due to the large conformational space that needs sampling. Here, we propose a flexible receptor docking scheme: A dihedral restrained replica exchange molecular dynamics (REMD), where we incorporate the normal modes obtained by the Elastic Network Model (ENM) as dihedral restraints to speed up the search towards correct binding site conformations. To our knowledge, this is the first approach that uses ENM modes to bias REMD simulations towards binding induced fluctuations in docking studies. In our docking scheme, we first obtain the deformed structures of the unbound protein as initial conformations by moving along the binding fluctuation mode, and perform REMD using the ENM modes as dihedral restraints. Then, we generate an ensemble of multiple receptor conformations (MRCs) by clustering the lowest replica trajectory. Using ROSETTALIGAND, we dock ligands to the clustered conformations to predict the binding pose and affinity. We apply this method to postsynaptic density-95/Dlg/ZO-1 (PDZ) domains; whose dynamics govern their binding specificity. Our approach produces the lowest energy bound complexes with an average ligand root mean square deviation of 0.36 Å . We further test our method on (i) homologs and (ii) mutant structures of PDZ where mutations alter the binding selectivity. In both cases, our approach succeeds to predict the correct pose and the affinity of binding peptides. Overall, with this approach, we generate an ensemble of MRCs that leads to predict the binding poses and specificities of a protein complex accurately.

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“…The molecular model of RasGEF1b was built using the homology-modelling program ESyPred3D 40 that is based on a strategy using neural networks to evaluate sequence alignments. ESyPred3D uses the program MODELLER to build the final structural model.…”

Section: Three-dimensional Modelmentioning

confidence: 99%

Early endosome localization and activity of RasGEF1b, a toll-like receptor-inducible Ras guanine-nucleotide exchange factor

et al. 2010

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Guanine-nucleotide exchange factors (GEFs) stimulate the intrinsic GDP/GTP exchange activity of Ras and promote the formation of active Ras-GTP, which in turn controls diverse signalling networks important for the regulation of cell proliferation, survival, differentiation, vesicular trafficking, and gene expression. RasGEF1b is a GEF, whose expression is induced in macrophages on stimulation with toll-like receptor (TLR) agonists. Here, we showed that in vitro RasGEF1b expression by macrophages is mostly induced by TLR3 (poly I:C) and TLR4 (lipopolysaccharyde) through the MyD88-independent pathway. In vivo infection with the protozoan parasites Trypanosoma cruzi and Plasmodium chabaudi induced RasGEF1b in an MyD88-, TRIF-, and IFN-g-dependent manner. Ectopically expressed RasGEF1b was found, mostly, in the heavy membrane fraction of HEK 293T, and by confocal microscopy, it was found to be located at early endosomes. Computational modelling of the RasGEF1b-Ras interaction revealed that RasGEF1b interacts with the binding domain site of Ras, a critical region for interacting with GEFs involved in the activation of Ras-Raf-MEK-ERK pathway. More important, RasGEF1b was found to be closely associated with Ras in live cells and to trigger Ras activity. Altogether, these results indicate that on TLR activation, RasGEF1b may trigger Ras-like proteins and regulate specific biological activities described for this subtype of GTPases.

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ESyPred3D: Prediction of proteins 3D structures

Abstract: christophe.lambert@fundp.ac.be; http://www.fundp.ac.be/~lambertc

Cited by 551 publications

References 28 publications

ABA signalling is fine-tuned by antagonistic HAB1 variants

ABA signalling is fine-tuned by antagonistic HAB1 variants

A flexible docking scheme to explore the binding selectivity of PDZ domains

Early endosome localization and activity of RasGEF1b, a toll-like receptor-inducible Ras guanine-nucleotide exchange factor

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