Transferability and reproducibility in electron-density studies – bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine

Grabowsky, Simon; Kalinowski, Roman; Weber, Manuela; Förster, Diana; Paulmann, Carsten; Luger, Peter (2009). Transferability and reproducibility in electron-density studies – bond-topological and atomic properties of tripeptides of the type L-alanyl-X-L-alanine. Acta crystallographica. Section B - Structural science, 65(4), pp. 488-501. Wiley-Blackwell 10.1107/S0108768109016966

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In the last decade three different data bank approaches have been developed that are intended to make electron-density examinations of large biologically important molecules possible. They rely on Bader's concept of transferability of submolecular fragments with retention of their electronic properties. Therefore, elaborate studies on the quantification of transferability in experiment and theory are still very important. Tripeptides of the type L-alanyl-X-L-alanine (X being any of the 20 naturally encoded amino acids) serve as a model case between amino acids and proteins. The two experimental electron-density determinations (L-alanyl-L-histidinyl-L-alanine and L-alanyl-L-phenylalanyl-L-alanine, highly resolved synchrotron X-ray diffraction data sets) performed in this study and theoretical calculations on all 20 different L-alanyl-X-L-alanine molecules contribute to a better estimation of transferability in the peptide case. As a measure of reproducibility and transferability, standard deviations from averaging over bond-topological and atomic properties of atoms or bonds that are considered equal in their chemical environments were calculated. This way, transferability and reproducibility indices were introduced. It can be shown that experimental transferability indices generally slightly exceed experimental reproducibility indices and that these larger deviations can be attributed to chemical effects such as changes in the geometry (bond lengths and angles), the polarization pattern and the neighboring sphere due to crystal packing. These effects can partly be separated from each other and quantified with the help of gas-phase calculations at optimized and experimental geometries. Thus, the degree of transferability can be quantified in very narrow limits taking into account experimental errors and chemical effects.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Grabowsky, Simon

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry

ISSN:

0108-7681

Publisher:

Wiley-Blackwell

Language:

English

Submitter:

Simon Grabowsky

Date Deposited:

05 Feb 2020 16:22

Last Modified:

05 Feb 2020 16:22

Publisher DOI:

10.1107/S0108768109016966

BORIS DOI:

10.7892/boris.138497

URI:

https://boris.unibe.ch/id/eprint/138497

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