Computational protocol: Structural Basis for Metallic-Like Conductivity in Microbial Nanowires

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Protocol publication

[…] For the modeling using the NMR structure, the clash score and MolProbity score (MPscore) were calculated for all 18 conformers to determine the best conformer () (see in the supplemental material). The clash score is defined as the number of unfavorable all-atom steric overlaps of ≥0.4 Å per 1,000 atoms (), whereas the MolProbity score is defined as 0.426 × ln(1 + clash score) + 0.33 × ln[1 + max(0,rota_out | −1)] + 0.25 × ln(1 + max[0,rama_iffy | −2)] + 0.5, where rota_out is the percentage of side-chain conformations classed as rotamer outliers from those side chains that can be evaluated, and Rama_iffy is the percentage of backbone Ramachandran conformations outside the favored region from those residues that can be evaluated. The coefficients were derived from a log-linear fit to crystallographic resolution on a filtered set of PDB structures, so that a model’s MPscore is the resolution at which its individual scores would be the expected values (). Thus, lower MPscores are better. The conformer no. 5 () yielded the best clash score and also the best overall MolProbity score (see ). Therefore, this conformer was used in addition to our homology model for modeling the G. sulfurreducens pilus filament assembly.A homology model for the full pilus filament () was built using the Swiss-Pdb Viewer (DeepView) software (http://spdbv.vital-it.ch). The modeling was templated against the model of the Pseudomonas aeruginosa strain K pilus filament (). The P. aeruginosa pilus filament model was computationally assembled using the X-ray fiber diffraction data and the X-ray crystal structure of pilin (). In this model, pilin subunits are assembled as a right-handed one-start helix (a helical path that connects every subunit in the filament with the smallest axial rotation) with a 41-Å pitch and four subunits per turn or as a left-handed three-start helix (a set of three identical helices with the same pitch and number of subunits per turn, which together connect all subunits in the filament) with a 123-Å pitch and four submits per turn (). The spacing between the three-start strands is 41 Å, consistent with the fiber diffraction data (). The model does not account for side-chain flexibility that might allow tighter packing. Therefore, the structure-based model of the P. aeruginosa pilus filament is slightly thicker than the dimensions obtained from the fiber diffraction data ().To construct the pilus model of G. sulfurreducens using the NMR structure of the pilin monomer, 19 copies of the conformer no. 5 were superimposed, using DeepView’s “magic fit” (sequence-guided structural alignment, backbone root mean square deviation [RMSD] of 2.08 Å), onto the 19 pilin monomers of Pseudomonas aeruginosa strain K () to obtain a full pilus filament assembly model ().A homology model of the G. sulfurreducens pilin monomer was built using the Swiss-Model server (http://swissmodel.expasy.org) (). ConSurf (http://consurf.tau.ac.il) was used for calculation of the evolutionary conservation of amino acids presented in ().To construct the pilus model of G. sulfurreducens using the homology model of the pilin monomer, 19 copies of the pilin monomer homology model of G. sulfurreducens were superimposed, using DeepView’s “magic fit” (sequence-guided structural alignment, backbone RMSD of 1.52 Å), onto the 19 pilin monomers of Pseudomonas aeruginosa strain K () to obtain a full pilus filament assembly model ().FirstGlance in Jmol (http://firstglance.jmol.org) and the Jmol application (http://jmol.org) () were used to generate the images shown in . Aromatic amino acids in G. sulfurreducens PilA are highlighted in yellow in , and the aromatic ring atoms are displayed at their van der Waals radii (carbon, 1.7 Å) (). Models and animations can be visualized or downloaded as described below.The Protein Calculator tool (http://protcalc.sourceforge.net) was used to estimate protonation-induced charges in pilus filaments (). […]

Pipeline specifications

Software tools MolProbity, Swiss-PdbViewer, SWISS-MODEL, ConSurf, FirstGlance, Jmol
Databases ExPASy
Applications Drug design, Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma, Geobacter sulfurreducens, Pseudomonas aeruginosa, Neisseria gonorrhoeae