MetaMQAP: A meta-server for the quality assessment of protein models

Pawłowski, Marcin; Gajda, Michał J.; Matlak, Ryszard; Bujnicki, Janusz M.

doi:10.1186/1471-2105-9-403

Cited by 158 publications

(126 citation statements)

References 59 publications

(69 reference statements)

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“…First, MetaMQAPII, an updated version of a method described in [35]. In particular, we used the values of predicted global distance test total score (GDT_TS) for the evaluation of the global accuracy of the models (the higher GDT_TS, the better) and the predicted deviation of individual residues as a measure of predicted local accuracy (the lower the predicted deviation the better).…”

Section: Protein Model Quality Assessmentmentioning

confidence: 99%

Structure and intrinsic disorder of the proteins of theTrypanosoma brucei editosome

et al. 2015

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a b s t r a c tMitochondrial pre-mRNAs in trypanosomatids undergo RNA editing to be converted into translatable mRNAs. The reaction is characterized by the insertion and deletion of uridine residues and is catalyzed by a macromolecular protein complex called the editosome. Despite intensive research, structural information for the majority of editosome proteins is still missing and no high resolution structure for the editosome exists. Here we present a comprehensive structural bioinformatics analysis of all proteins of the Trypanosoma brucei editosome. We specifically focus on the interplay between intrinsic order and disorder. According to computational predictions, editosome proteins involved in the basal reaction steps of the processing cycle are mostly ordered. By contrast, thirty percent of the amino acid content of the editosome is intrinsically disordered, which includes most prominently proteins with OB-fold domains. Based on the data we suggest a functional model, in which the structurally disordered domains of the complex are correlated with the RNA binding and RNA unfolding activity of the T. brucei editosome.

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Section: Protein Model Quality Assessmentmentioning

confidence: 99%

Structure and intrinsic disorder of the proteins of theTrypanosoma brucei editosome

et al. 2015

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“…Model quality assessment was performed iteratively using MetaMQAP (Pawlowski et al, 2008). Stability tests were done by molecular dynamics simulations with NAMD (Phillips et al, 2005) using a Charmm27 force field on a high-performance computing facility.…”

Section: Internal Model Assessmentmentioning

confidence: 99%

Structural Determinants at the Interface of the ARC2 and Leucine-Rich Repeat Domains Control the Activation of the Plant Immune Receptors Rx1 and Gpa2

et al. 2013

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Many plant and animal immune receptors have a modular nucleotide-binding-leucine-rich repeat (NB-LRR) architecture in which a nucleotide-binding switch domain, NB-ARC, is tethered to a LRR sensor domain. The cooperation between the switch and sensor domains, which regulates the activation of these proteins, is poorly understood. Here, we report structural determinants governing the interaction between the NB-ARC and LRR in the highly homologous plant immune receptors Gpa2 and Rx1, which recognize the potato cyst nematode Globodera pallida and Potato virus X, respectively. Systematic shuffling of polymorphic sites between Gpa2 and Rx1 showed that a minimal region in the ARC2 and N-terminal repeats of the LRR domain coordinate the activation state of the protein. We identified two closely spaced amino acid residues in this region of the ARC2 (positions 401 and 403) that distinguish between autoactivation and effector-triggered activation. Furthermore, a highly acidic loop region in the ARC2 domain and basic patches in the N-terminal end of the LRR domain were demonstrated to be required for the physical interaction between the ARC2 and LRR. The NB-ARC and LRR domains dissociate upon effector-dependent activation, and the complementary-charged regions are predicted to mediate a fast reassociation, enabling multiple rounds of activation. Finally, we present a mechanistic model showing how the ARC2, NB, and N-terminal half of the LRR form a clamp, which regulates the dissociation and reassociation of the switch and sensor domains in NB-LRR proteins.Resistance (R) proteins play a central role in the recognition-based immune system of plants. Unlike vertebrates, plants lack an adaptive immune system with highly specialized immune cells. Instead, they rely on an innate immune system in which each cell is autonomous. Two types of immune receptors can be distinguished in plants, pathogen-associated molecular patterns recognition receptors that detect conserved molecular patterns in plant pathogens and intracellular R proteins that recognize specific effectors employed by pathogens as modifiers of host metabolism or defense mechanisms (Jones and Dangl, 2006). Effector-triggered activation of R proteins leads to an array of protective responses, often culminating in programmed cell death at the site of infection (Greenberg and Yao, 2004), thereby preventing further ingress of the pathogen. Pathogens have evolved mechanisms to evade recognition by R proteins and to regain their virulence (Dodds and Rathjen, 2010). This continuous coevolutionary process between host and pathogen has resulted in a reservoir of highly diverse R proteins in plants, enabling them to counteract a wide range of pathogens and pests.The most common class of R proteins consists of nucleotide-binding (NB)-leucine-rich repeat (LRR) proteins with a tripartite domain architecture, which roughly corresponds to an N-terminal response domain (a coiled coil [CC] or Toll/Interleukin-1 receptor [TIR] domain) involved in downstream signaling, a central molecula...

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“…The homology models were assessed using DOPE Z score (Shen and Sali 2006) and model evaluation algorithms provided by the MetaMQAPII server (Pawlowski et al 2008). Generally, models with a DOPE Z score lower than -1 are likely to be native like.…”

Section: Homology Models Of Chemotaxis Proteinsmentioning

confidence: 99%

“…When needed, problematic loops were refined using MODELLER. The models were evaluated based on their Discrete Optimized Protein Energy (DOPE Z) scores and MetaMQAPII results (Pawlowski et al 2008). …”

Section: Homology Modelling and Validationmentioning

confidence: 99%

Comparative structural bioinformatics analysis of Bacillus amyloliquefaciens chemotaxis proteins within Bacillus subtilis group

Yssel

Reva

Bishop

2011

Appl Microbiol Biotechnol

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Chemotaxis is a process in which bacteria sense their chemical environment and move towards more favourable conditions. Since plant colonization by bacteria is a multifaceted process which requires a response to the complex chemical environment, a finely tuned and sensitive chemotaxis system is needed. Members of the Bacillus subtilis group including Bacillus amyloliquefaciens are industrially important, for example in bio-pesticides. The group exhibits plant growth promoting characteristics, with different specificity towards certain host plants. Therefore, we hypothesize that while the principal molecular mechanisms of bacterial chemotaxis may be conserved, the bacterial chemotaxis system may need an evolutionary tweaking to adapt it to specific requirements, particularly in the process of evolution of free-living soil organisms, towards plant colonization behaviour. To date almost nothing is known about what parts of the chemotaxis proteins are subjected to positive amino acid substitutions, involved in adjusting the chemotaxis system of bacteria during speciation.In this novel study, positively selected and purified sites of chemotaxis proteins were calculated and these residues were mapped onto homology models that were built for the chemotaxis proteins, in an attempt to understand the spatial evolution of the chemotaxis proteins. Various positively selected amino acids were identified in semi-conserved regions of the proteins away from the known active sites.

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MetaMQAP: A meta-server for the quality assessment of protein models

Cited by 158 publications

References 59 publications

Structure and intrinsic disorder of the proteins of theTrypanosoma brucei editosome

Structure and intrinsic disorder of the proteins of theTrypanosoma brucei editosome

Structural Determinants at the Interface of the ARC2 and Leucine-Rich Repeat Domains Control the Activation of the Plant Immune Receptors Rx1 and Gpa2

Comparative structural bioinformatics analysis of Bacillus amyloliquefaciens chemotaxis proteins within Bacillus subtilis group

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