Abstract
Nanowires that transfer electrons to extracellular acceptors are important in organic matter degradation and nutrient cycling in the environment. Geobacter pili of the group of Type IV pilus are regarded as nanowire-like biological structures. However, determination of the structure of pili remains challenging due to the insolubility of monomers, presence of surface appendages, heterogeneity of the assembly, and low-resolution of electron microscopy techniques. Our previous study provided a method to predict structures for Type IV pili. In this work, we improved on our previous method using molecular dynamics simulations to optimize structures of Neisseria gonorrhoeae (GC), Neisseria meningitidis and Geobacter uraniireducens pilus. Comparison between the predicted structures for GC and Neisseria meningitidis pilus and their native structures revealed that proposed method could predict Type IV pilus successfully. According to the predicted structures, the structural basis for conductivity in G.uraniireducens pili was attributed to the three N-terminal aromatic amino acids. The aromatics were interspersed within the regions of charged amino acids, which may influence the configuration of the aromatic contacts and the rate of electron transfer. These results will supplement experimental research into the mechanism of long-rang electron transport along pili of electricigens.
Highlights
Electricigens that can transfer electrons extracellularly participate widely in geochemical cycling of metals, minerals, and carbon in the environment
As the nuclear magnetic resonance (NMR)/X-ray-derived pilin structure was always derived from pilin monomers immersed in lipid micelles, we refined its structure in solution in molecular dynamics (MD) simulations
The use of molecular dynamics (MD) simulations to improve the docking process has clear advantages: proteins were simulated in a real biological environment and dynamic effects were considered [31]
Summary
Electricigens that can transfer electrons extracellularly participate widely in geochemical cycling of metals, minerals, and carbon in the environment. These microorganisms have been applied to bioremediation of contaminated environments and studied in microbe–electrode interactions [1] Among these electricigens, the Geobacter species produce electrically conductive pili that are thought to play a critical role in long-range electron transfer to extracellular Fe(III) oxides and other electron acceptors [2,3]. The Geobacter species produce electrically conductive pili that are thought to play a critical role in long-range electron transfer to extracellular Fe(III) oxides and other electron acceptors [2,3] These bio-electronic materials, which belong to Type IV pili (T4P), are attractive because they can be obtained from sustainable feedstocks without the need for toxic solvents or harsh chemical processes. A new N-terminal is methylated and the monomers assemble into a pilus [13,14,15]
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