title: Quantum-Chemical Electron Densities of Proteins and of Selected Protein Sites from Subsystem Density Functional Theory.
abstract: The ability to calculate accurate electron densities of full proteins or of selected sites in proteins is a prerequisite for a fully quantum-mechanical calculation of protein-protein and protein-ligand interaction energies. Quantum-chemical subsystem methods capable of treating proteins and other biomolecular systems provide a route to calculate the electron densities of proteins efficiently and further make it possible to focus on specific parts. Here, we evaluate and extend the 3-partition frozen-density embedding (3-FDE) scheme [Jacob, C. R.; Visscher, L. J. Chem. Phys.2008, 128, 155102] for this purpose. In particular, we have extended this scheme to allow for the treatment of disulfide bridges and charged amino acid residues and have introduced the possibility to employ more general partitioning schemes. These extensions are tested both for the prediction of full protein electron densities and for focusing on the electron densities of a selected protein site. Our results demonstrate that 3-FDE is a promising tool for the fully quantum-chemical treatment of proteins.
authors.affiliation: Amsterdam Center for Multiscale Modeling, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
authors.forename: Karin
authors.initials: K
authors.lastname: Kiewisch
authors.affiliation: Center for Functional Nanostructures and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany.
authors.forename: Christoph R
authors.initials: CR
authors.lastname: Jacob
authors.affiliation: Amsterdam Center for Multiscale Modeling, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
authors.forename: Lucas
authors.initials: L
authors.lastname: Visscher