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Quantitative analysis of atomic polarization and protein-ligand electrostatic interactions via charge density studies in proteins: insights from ultra-high resolution crystallography

Final Report Summary - PROTEINCHARGEDENSITY (Quantitative analysis of atomic polarization and protein-ligand electrostatic interactions via charge density studies in proteins ...)

The protein human aldose reductase (h-AR) is an excellent system to investigate, as X-ray synchrotron diffraction data are available at an exceptional resolution of 0.66 Å at 100K. The laboratory has developed an experimental library of multipolar atom model (ELMAM) database [1] and the unique software MoPro [2] for the charge density analysis of proteins. Recently, these tools have been successfully used to analyze the charge density of h-AR [3]. The electrostatic interactions of two stereoisomers fidarestat inhibitors of h-AR had also been investigated [4].

In this project, the atomic polarisation was further investigated within the protein secondary structures via quantitative analysis of the average electronic distribution of polypeptide backbone C=O and N-H groups. Based on the spherical atom model applied on protein cholesterol oxidase [5], it was claimed that the peptide carbonyl groups are more polarized in a-helices than the ß-sheets.

The project started with an analysis of two crystal polymorphs of a small molecule, namely coumarin 314 to get Dr Munshi extensively acquainted with the software MoPro. The charge density analysis of polymorphs can indeed yield information on atomic polarisation. Dr Munshi, who is an expert in quantum calculations with program CRYSTAL06 [6], was also involved in the validation of our multipolar atoms database on a bioactive molecule, quercetin.

In the present study, we have performed several multipole modeling and refinements of protein h-AR. The observations were also studied from a theoretical point of view with quantum calculations performed on oligo-peptides, notably regular alpha helices. The effect of helix dipole moment on the charge density was observed theoretically. Our analysis points out that it is important to take into account the thermal motion of the protein atoms to avoid artifacts in the experimental observation of atom polarisation. The carbonyl oxygen atoms show stronger population of the electron lone pairs in alpha helices from the multipolar refinements.

[1] Zarychta B., Pichon-Pesme V., Guillot B., Lecomte C., Jelsch C., Acta Cryst. 2007, A63, 108.
[2] Jelsch C., Guillot B., Lagoutte A., Lecomte C., J. Appl. Cryst. 2005, 38, 38.
[3] Guillot B., Jelsch C., Podjarny A., Lecomte C. Acta Cryst. 2008, D64, 567.
[4] Fournier B., ... Jelsch C. (2009). J. Am. Chem. Soc. 131, 10929.
[5] Lario P. I., Vrielink, A., J. Am. Chem. Soc. 2003, 125, 12787.
[6] Dovesi, R.et al. CRYSTAL06 User's Manual, University of Torino, Torino, 2006.