Structural and functional insights into the conductive pili of Geobacter sulfurreducens revealed in molecular dynamics simulations

Abstract

Geobacter sulfurreducens (GS) electronically connects with extracellular electron acceptors using conductive protein filaments or pili. To gain insights into their role as biological nanowires, we investigated the structural dynamics of the GS pilus in solution via molecular dynamics simulations. In the model, all of the pilin's aromatics clustered as a right-handed helical band along the pilus, maintaining inter-aromatic distances and dimer configurations optimal for multistep hopping. The aromatics were interspersed within the regions of highest negative potential, which influenced the type and configuration of the aromatic contacts and the rates of electron transfer. Small foci of positive potential were also present but were neutralized within uncharged regions, thus minimizing charge trapping. Consistent with the model predictions, mutant strains with reduced aromatic contacts or negative potentials had defects in pili functions such as the reduction of Fe(III) oxides and electrodes. The results therefore support the notion of a pilus fiber evolved to function as an electronic conduit between the cell and extracellular electron acceptors.

Harnessing the power of microbial nanowires

“…Although these conditions preserved the structural and electronic signatures described for cell‐associated pili (Veazey et al ., 2011), the assay was performed with T4P immobilized on a surface. This contrasts with the in‐vivo conditions, where the fibres undergo antagonistic cycles of protrusion and retraction and experience motions that are predicted to promote electronic coupling and charge transport (Feliciano et al ., 2015). Thus, the charge transport rates estimated in vitro (Lampa‐Pastirk et al ., 2016) may in fact underestimate the true transport capacity of the T4P in vivo .…”

“…The GS α1 domain also retains a phenylalanine in position +1 (F1) and a glutamic acid residue in position +5 (E5), which interact in neighbouring pilins to align the peptides during assembly (Feliciano et al ., 2015; Steidl et al ., 2016). Thus, the GS pilin retains the conserved structure (α1 domain) and amino acids (F1 and E5 residues) needed for pilin assembly (Feliciano et al ., 2015). But it lacks the globular head that neutralizes the natural dipole of the α1 domain in other pilins.…”

“…Conflicting interpretations about the nature of DNA conductivity have been linked to the sensitivity of transport measurements to the purity of the samples, intrinsic properties of the DNA molecule (such as conformation and length), and extrinsic parameters that modulate these properties (e.g., humidity) (Yamahata et al ., 2008). Evidence is also emerging in support for a mechanism of GS T4P conductance dominated by multistep hopping (Feliciano et al ., 2015). Single molecule conductivity measurements have been particularly useful to investigate how the GS T4P protein matrix permits long‐range electron transfer in the absence of inorganic and organic cofactors (Lampa‐Pastirk et al ., 2016).…”

“…In the absence of experimental verification of the T4P structure, insights into interaromatic distances and the configuration of the aromatic side‐chains have been gained from computational models built using homologous T4P structures (Bonanni et al ., 2013; Reardon and Mueller, 2013; Feliciano et al ., 2015; Malvankar et al ., 2015; Xiao et al ., 2016). Although the distribution of aromatic residues in these models varies, none have the sandwich‐type dimer geometries that are needed to allow for π‐π orbital stacking and metallic conductivity.…”

“…Although the distribution of aromatic residues in these models varies, none have the sandwich‐type dimer geometries that are needed to allow for π‐π orbital stacking and metallic conductivity. Only one of these models has been optimized in molecular dynamics (MD) to improve the accuracy of the structural predictions (Feliciano et al ., 2015). Structural assumptions in this model were minimized using experimentally validated structures of the GS pilin (Reardon and Mueller, 2013) and the T4P template (the Neisseria ghonorrhoeae T4P) (Craig et al ., 2006).…”