Project Description

Figure: Density of states around the HOMO and LUMO of the lowest energy conformer of the GS pilin generated by QM optimization in vacuum (944 atoms) and in solution (4580 atoms).

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.

Model system/Software:

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.