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Peptide Binding to β-Cyclodextrins: Structure, Dynamics, Energetics, and Electronic Effects

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    Peptide Binding to β-Cyclodextrins: Structure, Dynamics, Energetics, and Electronic Effects
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    † Equipe de Chimie et Biochimie Théoriques, SRSMC, Nancy University, CNRS, BP 70239, 54506 Vandœuvre-lès-Nancy, Cedex, France
    ‡ Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería 8, 33006 Oviedo, Spain
    E-mail: [email protected]
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    The Journal of Physical Chemistry A

    Cite this: J. Phys. Chem. A 2011, 115, 42, 11810–11817
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    https://doi.org/10.1021/jp2053037
    Published September 13, 2011
    Copyright © 2011 American Chemical Society
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    Abstract

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    Peptide–cyclodextrin and protein–cyclodextrin host–guest complexes are becoming more and more important for industrial applications, in particular in the fields of pharmaceutical and food chemistry. They have already deserved many experimental investigations although the effect of complex formation in terms of peptide (or protein) structure is not well-known yet. Theoretical calculations represent a unique tool to analyze such effects, and with this aim we have carried out in the present investigation molecular dynamics simulations and combined quantum mechanics–molecular mechanics calculations. We have studied complexes formed between the model Ace-Phe-Nme peptide and the β-cyclodextrin (β-CD) macromolecule, and our analysis focuses on the following points: (1) how is the peptide structure modified in going from bulk water to CD environment (backbone torsion angles), (2) which are the main peptide–CD interactions, in particular in terms of hydrogen bonds, (3) which relative peptide–CD orientation is preferred and which are the structural and energetic differences between them, and (4) how the electronic properties of the peptide changes under complex formation. Overall, our calculations show that in the most stable configuration, the backbone chain lies in the narrow rim of the CD. Strong hydrogen bonds form between the H atoms of the peptidic NH groups and oxygen atoms of the secondary OH groups in the CD. These and other (weaker) hydrogen bonds formed by the carbonyl groups reduce considerably the flexibility of the peptide structure, compared to bulk water, and produce a marked increase of the local dipole moment by favoring configurations in which the two C═O bonds point toward the same direction. This effect might have important consequences in terms of the peptide secondary structure, although this hypothesis needs to be tested using larger peptide models.

    Copyright © 2011 American Chemical Society

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    Full references, refs 49, 50, 62, and 63 This material is available free of charge via the Internet at http://pubs.acs.org.

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    Cited By

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    This article is cited by 19 publications.

    1. Pauline Navals, Anna Kwiatkowska, Nawel Mekdad, Frédéric Couture, Roxane Desjardins, Robert Day, Yves L. Dory. Enhancing the Drug-Like Profile of a Potent Peptide PACE4 Inhibitor by the Formation of a Host–Guest Inclusion Complex with β-Cyclodextrin. Molecular Pharmaceutics 2023, 20 (9) , 4559-4573. https://doi.org/10.1021/acs.molpharmaceut.3c00261
    2. Zhiye Tang and Chia-en A. Chang . Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition. Journal of Chemical Theory and Computation 2018, 14 (1) , 303-318. https://doi.org/10.1021/acs.jctc.7b00899
    3. Masayoshi Takayanagi, Shoko Ito, Kentaro Matsumoto, and Masataka Nagaoka . Formation of Reactant Complex Structure for Initiation Reaction of Lactone Ring-Opening Polymerization by Cooperation of Multiple Cyclodextrin. The Journal of Physical Chemistry B 2016, 120 (29) , 7174-7181. https://doi.org/10.1021/acs.jpcb.6b04372
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    16. Elena Alvira. Influence of valine enantiomer configuration on the molecular dynamics simulation of their separation by β-cyclodextrin. Chemical Physics Letters 2017, 679 , 31-37. https://doi.org/10.1016/j.cplett.2017.04.062
    17. Elena Alvira. Theoretical study of the separation of valine enantiomers by β-cyclodextrin with different solvents: a molecular mechanics and dynamics simulation. Tetrahedron: Asymmetry 2015, 26 (15-16) , 853-860. https://doi.org/10.1016/j.tetasy.2015.06.013
    18. David A. Pink, M. Shajahan G. Razul, T. Gordon, B. Quinn, A. J. MacDonald. Computer Simulation Techniques for Modelling Statics and Dynamics of Nanoscale Structures. 2014, 230-299. https://doi.org/10.1039/BK9781849738958-00230
    19. David A. Pink, M. Shajahan G. Razul. Computer simulation techniques for food science and engineering: Simulating atomic scale and coarse-grained models. Food Structure 2014, 1 (1) , 71-90. https://doi.org/10.1016/j.foostr.2013.11.005
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    The Journal of Physical Chemistry A

    Cite this: J. Phys. Chem. A 2011, 115, 42, 11810–11817
    Click to copy citationCitation copied!
    https://doi.org/10.1021/jp2053037
    Published September 13, 2011
    Copyright © 2011 American Chemical Society
    Request reuse permissions

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