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Molecules 2017, 22(8), 1342; doi:10.3390/molecules22081342

Predicting and Interpreting the Structure of Type IV Pilus of Electricigens by Molecular Dynamics Simulations

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, SoutheastUniversity, Nanjing 210096, China
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Received: 30 June 2017 / Revised: 7 August 2017 / Accepted: 10 August 2017 / Published: 12 August 2017
(This article belongs to the Special Issue Computational Analysis for Protein Structure and Interaction)
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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. View Full-Text
Keywords: electron transfer; electricigen; Geobacter; molecular dynamics simulation; symmetric docking electron transfer; electricigen; Geobacter; molecular dynamics simulation; symmetric docking
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Shu, C.; Xiao, K.; Cao, C.; Ding, D.; Sun, X. Predicting and Interpreting the Structure of Type IV Pilus of Electricigens by Molecular Dynamics Simulations. Molecules 2017, 22, 1342.

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