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Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters

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Summary

Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.

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Acknowledgements

Authors are indebted to the “Centre de Supercomputació de Catalunya” (CESCA) and the “Centre Europeu de Paral lelisme de Barcelona” (CEPBA) for computational facilities.

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Authors and Affiliations

  1. Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, E-08028, Barcelona, Spain

    David Curcó

  2. Departament d’Enginyeria Química, E.T.S. d’Enginyers Industrials de Barcelona, Universitat Politécnica de Catalunya, Diagonal 647, E-08028, Barcelona, Spain

    Francisco Rodríguez-Ropero & Carlos Alemán

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  1. David Curcó
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  2. Francisco Rodríguez-Ropero
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  3. Carlos Alemán
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Correspondence to Carlos Alemán.

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Curcó, D., Rodríguez-Ropero, F. & Alemán, C. Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters. J Comput Aided Mol Des 20, 13–25 (2006). https://doi.org/10.1007/s10822-005-9032-0

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  • DOI: https://doi.org/10.1007/s10822-005-9032-0

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