Model quality assessment for membrane proteins

A, Ray; Lindahl, Erik; Wallner, Björn

doi:10.1093/bioinformatics/btq581

Cited by 75 publications

(86 citation statements)

References 44 publications

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“…We then ran two "loop refinement" protocols on each of the initial models and chose the "best" on the basis of the force field energy calculated by CHARMM. To check on the validity of the best model, we separated the first (NR1) and second (NR2) subunits and submitted them to the ProQM server, a server trained on quality of membrane proteins (Ray et al, 2010). As a further improvement, the model was then optimized with CHARMM to a gradient of 0.0001 kcal/mol-Å in the presence of harmonic restraints on the backbone atoms of 10 kcal/Å 2 .…”

Section: Methodsmentioning

confidence: 99%

Ethanol Inhibition of Constitutively Open N-Methyl-d-Aspartate Receptors

Smothers²,

Trudell³

et al. 2011

J Pharmacol Exp Ther

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N-Methyl-D-aspartate (NMDA) receptors gate a slow and calciumrich component of the postsynaptic glutamate response. Like all ionotropic glutamate receptors, NMDA subunits contain a highly conserved motif (SYTANLAAF) in the transmembrane (TM) 3 domain that is critically involved in channel gating. Mutation of an alanine in this domain (A7; underlined above) results in constitutively open receptors that show reduced sensitivity to several allosteric modulators. In this study, we examined the effects of ethanol, a substance that inhibits NMDA currents via an unknown mechanism, on tonically active NMDA receptors expressed in human embryonic kidney 293 cells. Ethanol (100 mM) inhibited currents from GluN1(A7R)/GluN2A and GluN1(A7R)/GluN2B receptors by approximately 50%, whereas those from GluN1/ GluN2B(A7R) receptors were reduced by less than 10%. In cysteine-substituted GluN1 and GluN2 A7 mutants, estimated ethanol IC 50 values for agonist-gated currents were 101, 117, 103, and 69 mM for GluN1(A7C)/GluN2A, GluN1(A7C)/GluN2B, GluN1/ GluN2A(A7C), and GluN1/GluN2B(A7C) receptors, respectively. After exposure to the thiol-modifying reagent 2-(trimethylammonium)ethyl methanethiosulfonate (MTSET), A7C mutants showed robust agonist-independent currents and reduced sensitivity to ethanol (IC 50 values of 371, 256, 715, and 958 mM, respectively, as above). In contrast, cysteine modification of the ligand-binding domain resulted in constitutively open receptors that showed robust ethanol inhibition. Ethanol inhibition of MTSET-treated GluN1(A7C) receptors was further reduced by TM3/TM4 mutations previously shown to reduce ethanol sensitivity of agonistgated receptors. Overall, these results show that ethanol affects NMDA receptor function at a site distal from agonist binding and appears to exert greater effects via perturbation of GluN2 subunits.

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Section: Methodsmentioning

confidence: 99%

Ethanol Inhibition of Constitutively Open N-Methyl-d-Aspartate Receptors

Smothers²,

Trudell³

et al. 2011

J Pharmacol Exp Ther

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“…This library was constructed using each amino acid sequence underlying the PDB structures and clustering over their sequences was done using CD-HIT (Li et al, 2001) to admit at least 95% sequence identity between them. MODELLER (Sali and Blundell, 1993) was used to produce several models based on this alignment and the best model was chosen using ProQM Server (Ray et al, 2010) for model quality assessment.…”

Section: Template Alignment and Model Building For S17 Acr3mentioning

confidence: 99%

Genome comparison of two Exiguobacterium strains from high altitude andean lakes with different arsenic resistance: identification and 3D modeling of the Acr3 efflux pump

Ordoñez

Lanzarotti

Kurth

et al. 2015

Front. Environ. Sci.

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Arsenic exists in natural systems in a variety of chemical forms, including inorganic arsenite (As [III]) and arsenate (As [V]). The majority of living organisms have evolved various mechanisms to avoid occurrence of arsenic inside the cell due to its toxicity. Common core genes include a transcriptional repressor ArsR, an arsenate reductase ArsC, and arsenite efflux pumps ArsB and Acr3. To understand arsenic resistance we have performed arsenic tolerance studies, genomic and bioinformatic analysis of two Exiguobacterium strains, S17 and N139, from the high-altitude Andean Lakes. In these environments high concentrations of arsenic were described in the water due to a natural geochemical phenomenon, therefore, these strains represent an attractive model system for the study of environmental stress and can be readily cultivated. Our experiments show that S17 has a greater tolerance to arsenite (10 mM) than N139, but similar growth in arsenate (150 mM). We sequenced the genome of the two Exiguobacterium and identified an acr3 gene in S17 as the only difference between both species regarding known arsenic resistance genes. To further understand the Acr3 we modeled the 3D structure and identified the location of relevant residues of this protein. Our model is in agreement with previous experiments and allowed us to identify a region where a relevant cysteine lies. This Acr3 membrane efflux pump, present only in S17, may explain its increased tolerance to As(III) and is the first Acr3-family protein described in Exiguobacterium genus.

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“…The 20 best-ranked structures were visually checked, resulting in the selection of four models, one for each possible TM-10 fold in both subtypes. Geometrical quality assessment was performed with PROCHECK, 27 followed by in-depth investigation using ProQM, 28 which is optimized for membrane proteins. The estimated model error was in the range of the template resolution, and significantly higher in loop regions remote from the binding event (see supporting Figure 1).…”

Section: Molecular Modelingmentioning

confidence: 99%