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Structure and dynamics of the peptide strand KRFK from the thrombospondin TSP-1 in water

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Abstract

Theoretical investigations of a solute in liquid water at normal temperature and pressure can be performed at different levels of theory. Static quantum calculations as well as classical and ab initio molecular dynamics are used to completely explore the conformational space for large solvated molecular systems. In the classical approach, it is essential to describe all of the interactions of the solute and the solvent in detail. Water molecules are very often described as rigid bodies when the most commonly used interaction potentials, such as the SPCE and the TIP4P models, are employed. Recently, a physical model based upon a cluster of rigid water molecules with a tetrahedral architecture (AB4) was proposed that describes liquid water as a mixture of both TIP4P and SPCE molecular species that occur in the proportions implied by the tetrahedral architecture (one central molecule versus four outer molecules; i.e., 20% TIP4P versus 80% SPCE molecules). In this work, theoretical spectroscopic data for a peptide strand were correlated with the structural properties of the peptide strand solvated in water, based on data calculated using different theoretical approaches and physical models. We focused on a particular peptide strand, KRFK (lysine-arginine-phenylalanine-lysine), found in the thrombospondin TSP-1, due to its interesting properties. As the activity and electronic structure of this system is strongly linked to its structure, we correlated its structure with charge-density maps obtained using different semi-empirical charge Qeq equations. The structural and thermodynamic properties obtained from classical simulations were correlated with ab initio molecular dynamics (AIMD) data. Structural changes in the peptide strand were rationalized in terms of the motions of atoms and groups of atoms. To achieve this, conformational changes were investigated using calculated infrared spectra for the peptide in the gas phase and in water solvent. The calculated AIMD infrared spectrum for the peptide was correlated with static quantum calculations of the molecular system based on a harmonic approach as well as the VDOS (vibrational density of states) spectra obtained using various classical solvent models (SPCE, TIP4P, and AB4) and charge maps.

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Acknowledgements

The authors are deeply grateful to the University of Reims Champagne Ardennes (URCA, France) for providing us with computational resources and time on the Romeo cluster. We are equally grateful to the University of Oran (Algeria) for assigning us computational resources and time on Haytham at the UCI (Unité de Calcul Intensif).

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Authors and Affiliations

  1. LCPM, Dpt of Chemistry, Faculty of Sciences, University Oran 1 Ahmed Benbella, 31000, Oran, Algeria

    W. Taleb Bendiab, B. Benomrane, B. Bounaceur & A. M. Krallafa

  2. SirMa CNRS UMR 7369, MEDyC, University of Reims Champagne Ardenne, Reims, France

    M. Dauchez

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  1. W. Taleb Bendiab
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  2. B. Benomrane
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  5. A. M. Krallafa
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Correspondence to A. M. Krallafa.

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Taleb Bendiab, W., Benomrane, B., Bounaceur, B. et al. Structure and dynamics of the peptide strand KRFK from the thrombospondin TSP-1 in water. J Mol Model 24, 54 (2018). https://doi.org/10.1007/s00894-018-3583-1

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