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Conformational landscape of isolated capped amino acids: on the nature of non-covalent interactions

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Abstract

The intramolecular interactions for isolated capped amino acids were investigated computationally by characterizing the conformers for selected amino acids with charged (arginine), polar (asparagine and glutamine), non-polar (alanine, valine and isoleucine), and aromatic (phenylalanine, tryptophan and tyrosine) side chains. The computational method applied combined a molecular mechanics conformational search (with an MMFFs forced field) followed by structural and vibrational density-functional calculations (M06-2X with a triple-ζ Pople’s basis set). The intramolecular forces in each amino acid were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 15 most stable conformers studied showed that the structure of isolated capped amino acids resembles those found in proteins. In particular, the two most stable conformers of the nine amino acids investigated exhibit γ L and β L conformations with 7- and 5-membered rings, respectively, as a result of the balance between non-covalent interactions (hydrogen bonds and van der Waals).

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Authors and Affiliations

  1. Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco-UPV/EHU, Barrio Sarriena s/n, 48940, Leioa, Spain

    Jorge González & José A. Fernández

  2. Departamento de Química, Facultad de Ciencia y Tecnología, Universidad de La Rioja, Madre de Dios, 53, 26006, Logroño, Spain

    Rodrigo Martínez & Judith Millan

Authors
  1. Jorge González
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  2. Rodrigo Martínez
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  3. José A. Fernández
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  4. Judith Millan
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Correspondence to Judith Millan.

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Contribution to the Topical Issue “Dynamics of Molecular Systems (MOLEC 2016) ”, edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

Supplementary material in the form of one pdf file available from the Journal web page at https://doi.org/10.1140/epjd/e2017-80187-5

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González, J., Martínez, R., Fernández, J.A. et al. Conformational landscape of isolated capped amino acids: on the nature of non-covalent interactions. Eur. Phys. J. D 71, 203 (2017). https://doi.org/10.1140/epjd/e2017-80187-5

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  • DOI: https://doi.org/10.1140/epjd/e2017-80187-5

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