Validation of protein models by a neural network approach

Mereghetti, Paolo; Ganadu, Maria Luisa; Papaleo, Elena; Fantucci, Piercarlo; Gioia, Luca De

doi:10.1186/1471-2105-9-66

Cited by 32 publications

(31 citation statements)

References 49 publications

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“…cgi). 20 The FOX-4 and FOX-4(DGNS) models both have an overall quality considered excellent, with predicted TM scores (which calculate the topological similarity of two protein structures) of 0.74, and respective predicted root mean square deviations (RMSD) of 3.34 and 2.88 Å .…”

Section: Modelling Studiesmentioning

confidence: 99%

A tripeptide deletion in the R2 loop of the class C -lactamase enzyme FOX-4 impairs cefoxitin hydrolysis and slightly increases susceptibility to -lactamase inhibitors

Mallo

Pérez-Llarena

Kerff

et al. 2010

Journal of Antimicrobial Chemotherapy

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Objectives: A natural variant of the AmpC enzyme from Escherichia coli HKY28 with a tripeptide deletion (Gly-286/Ser-287/Asp-288) was recently described. The isolate produced an inhibitor-sensitive AmpC b-lactamase variant that also conferred higher than usual levels of resistance to ceftazidime in the E. coli host. To demonstrate whether this is true in other class C b-lactamase enzymes, we deleted the equivalent tripeptide in the FOX-4 plasmid-mediated class C b-lactamase.Methods: By site-directed mutagenesis, we deleted the tripeptide Gly-306/Asn-307/Ser-308 of FOX-4, thus generating FOX-4(DGNS). The enzymes (FOX-4 wild-type and DGNS) were purified and kinetic parameters (k cat , K m , k cat /K m ) as well as IC 50 values of several b-lactams were assessed. Modelling studies were also performed.Results: FOX-4(DGNS) did not increase the catalytic efficiency towards ceftazidime, although it conferred a slight increase in the susceptibility to b-lactamase inhibitors. There was also a noteworthy decrease in the cefoxitin MIC with the FOX-4(DGNS) mutant (from 512 to 16 mg/L) as well as a 10-fold decrease in k cat /K m towards imipenem, which revealed specific structural features. Conclusions:Although deletions in the R2-loop are able to extend the substrate spectrum of class C enzymes, the present results do not confirm this hypothesis in FOX-4. The FOX-4 R2 site would already be wide enough to accommodate antibiotic molecules, and thus any amino acid replacement or deletion at this location would not affect the hydrolytic efficiency towards b-lactams and would have a less drastic effect on the susceptibility to b-lactamase inhibitors.

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Section: Modelling Studiesmentioning

confidence: 99%

A tripeptide deletion in the R2 loop of the class C -lactamase enzyme FOX-4 impairs cefoxitin hydrolysis and slightly increases susceptibility to -lactamase inhibitors

Mallo

Pérez-Llarena

Kerff

et al. 2010

Journal of Antimicrobial Chemotherapy

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“…2). The protein model quality evaluation scores of the SWISS-MODEL and I-TASSER models, based on root mean square deviation (RMSD), TM, LG score, and MaxSub, using ProQ (27) and AIDE (28), pinpointed the best-ranked model generated by I-TASSER as the most suitable candidate to reconstruct the homodimer. Indeed, the I-TASSER model showed a predicted RMSD of 0.69 Å instead of 2.35 Å, a predicted TM score of 0.69 instead of 0.62, a predicted LG score of 4.161 instead of 2.820, and a predicted MaxSub score of 0.396 instead of 0.217 if compared to the model obtained by SWISS-MODEL.…”

Section: )-By Internalizationmentioning

confidence: 99%

“…The top-scored models generated were then ranked and validated by the protein model quality predictors ProQ (27) and AIDE (28).…”

Section: Mccb17mentioning

confidence: 99%

Functional and Structural Study of the Dimeric Inner Membrane Protein SbmA

Corbalán

Runti

Adler

et al. 2013

Journal of Bacteriology

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g SbmA protein has been proposed as a dimeric secondary transporter. The protein is involved in the transport of microcins B17 and J25, bleomycin, proline-rich antimicrobial peptides, antisense peptide phosphorodiamidate morpholino oligomers, and peptide nucleic acids into the Escherichia coli cytoplasm. The sbmA homologue is found in a variety of bacteria, though the physiological role of the protein is hitherto unknown. In this work, we carried out a functional and structural analysis to determine which amino acids are critical for the transport properties of SbmA. We created a set of 15 site-directed sbmA mutants in which single conserved amino acids were replaced by glycine residues. Our work demonstrated that strains carrying the site-directed mutants V102G, F219G, and E276G had a null phenotype for SbmA transport functions. In contrast, strains carrying the single point mutants W19G, W53G, F60G, S69G, N155G, R190, L233G, A344G, T255G, N308G, and R385G showed transport capacities indistinguishable from those of strains harboring a wild-type sbmA. The strain carrying the Y116G mutant exhibited mixed phenotypic characteristics. We also demonstrated that those sbmA mutants with severely impaired transport capacity showed a dominant negative phenotype. Electron microscopy data and in silico three-dimensional (3D) homology modeling support the idea that SbmA forms a homodimeric complex, closely resembling the membrane-spanning region of the ATP-binding cassette transporter family. Direct mapping of the sbmA single point mutants on the protein surface allowed us to explain the observed phenotypic differences in transport ability.

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“…In this context, we are presently developing a computational tool in which several structural and physical parameters that can be computed on a protein structure are weighted by a neural network, with the aim of obtaining an empirical energy function suited to discriminate among correct and incorrect protein models [78].…”

Section: Towards the Combined Use Of Molecular Dynamics And Structuramentioning

confidence: 99%

Computational approaches to shed light on molecular mechanisms in biological processes

et al. 2006

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Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.

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Validation of protein models by a neural network approach

Cited by 32 publications

References 49 publications

A tripeptide deletion in the R2 loop of the class C -lactamase enzyme FOX-4 impairs cefoxitin hydrolysis and slightly increases susceptibility to -lactamase inhibitors

A tripeptide deletion in the R2 loop of the class C -lactamase enzyme FOX-4 impairs cefoxitin hydrolysis and slightly increases susceptibility to -lactamase inhibitors

Functional and Structural Study of the Dimeric Inner Membrane Protein SbmA

Computational approaches to shed light on molecular mechanisms in biological processes

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