Molecular and Electronic Structure of the Peptide Subunit from First Principles
Feliciano G.T , da Silva A., Reguera G. E and Artacho, E. J. Phys. Chem. A 2012, 116, 8023−8030
Motivation of the modeling:
Relevant study to provide fundamental knowledge for the engineering of protein nanowires with custom properties
Achievements of the model:
The structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction at both the structural and amino acid sequence level.
Statistically independent snapshots of MM simulations (GROMACS code) of a small α –helical peptide belonging to the bacterium Geobacter sulfurreducens (GS-pilin) were extracted for SIESTA single-point calculations and used to calculate statistical averages of the electronic structure and electrostatics from first principles.
The SIESTA simulations provided the following main information:
- Energies of the different conformers
- Spatial charge distribution. HOMO-LUMO gaps
- Average electrostatic potential along the GS pilin
Emilio Artacho, part of the SIMUNE´s board of experts and member of the core development team of the SIESTA code, is one of the authors of this work.