MoProViewer: a tool to study proteins from a charge density science perspective

Abstract

Applying the charge density science methods to the structural biology field remains a considerable challenge. Several approaches were followed in the past years, focusing either on multipolar refinement of the rare available subatomic resolution protein structures or on the application of the transferability principle for the evaluation of electrostatic and energetic properties in protein-ligand complexes. However, the usually large size of macromolecules and the consequently large number of multipolar parameters in the Hansen & Coppens formalism [1] obviously complicates the feasibility of such kind of studies. In this presentation, we introduce the tools implemented in the MoProViewer software, part of the MoPro Suite for charge density refinement, especially designed to ease the analysis of a protein structure from a charge density perspective. These tools focus on helping the user in the computation of properties deriving from a refined or transferred [2] protein charge distribution and to manage a large number of atoms described in the multipole formalism in terms for instance of atomic local axis, symmetry or chemical equivalences constraints definitions. Moreover we will present new methods based on the topological analysis of the electrostatic potential [3]. They are designed to allow an original use of the electrostatic properties of a protein-ligand complex structure and rely on the computation and the representation of electrophilic and nucleophilic influence zones of atoms involved in protein-ligand interactions or in a biochemical process. The computational details of these methods as well as application examples on selected protein-ligand complexes will be given.

Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

“…The Hirshfeld surface was computed with software MoProViewer [24] around the four independent organic cations, two CdCl 5 moeities, and two chloride anions (Fig. 4).…”

At the Interface of Isomorphous Behavior in a 3 × 3 Isomer Grid of Monochlorobenzamides: Analyses of the Interaction Landscapes via Contact Enrichment Studies

“…R-factor definitions as R[F 2 > 2(F 2 )], wR(F 2 ). 51 Methods [58][59][60][61][62] Electrostatic energy calculations were performed with the MoProSuite software. 58 The multipolar electron density of the molecules was modelled by transfer of the ELMAM2 charge density database without further refinement.…”

Sev and pcu topological nets in one-pot newly synthesized mixed-ligand imidazole-containing Cu(II) coordination frameworks: Crystal structure, intermolecular interactions, theoretical calculations, magnetic behavior and biological activity

“…It is worth to be noted that this is compensated in (1) In addition, the Hirshfeld surfaces associated to compounds (1) and (2) have been displayed with the MoProViewer software [45] and colored according to the values of the atomic number of the atoms contributing most to the local electron density (Figures 7b and 7e) in order to highlight the chemical type of the closest interacting atoms in the crystal surrounding (Figures 7c and 7f). (1) and (2).…”