Quantum chemical and molecular dynamics modeling of interaction of isomolecular dipeptides of α-l-alanyl-α-l-alanine and β-alanyl-β-alanine with sodium dodecyl sulfate micelles

https://doi.org/10.1016/j.comptc.2020.112844Get rights and content

Highlights

  • Comparative modeling of the interaction of SDS micceles with dipeptides of alanine.

  • DFT modeling with micelle fragment and MD simulation with micelle in water.

  • Energy change and structure evolution of peptides during the complex formation.

  • Most probable localization of peptides atoms relative to SDS micelle.

Abstract

Quantum chemical investigation of α-l-alanyl-α-l-alanine and β-alanyl-β-alanine complexes with SDS dimer as an anion micelle fragment in polarizable continuum has been carried out by using of DFT method with B97-D/6-311++G(3d,3p) level. The variation of peptide structure and the difference in energies of free peptides, SDS dimer and their complexes have been analyzed. Optimized configurations of complexes are stabilized by hydrogen bonds of (H2)Nsingle bondH…O(S) type. The localization of α-l-alanyl-α-l-alanine among the charged groups of SDS dimer is more preferable. The localization of β-alanyl-β-alanine among the charged groups or in the dimer hydrophpbic canal results in close values of the complex formation energy. More favorite change of energy and shorter length of hydrogen bond of (H2)Nsingle bondH…O(S) type have been revealed for complex formation between SDS dimer and β-alanyl-β-alanine as opposed to α-l-alanyl-α-l-alanine. Molecular dynamics simulation of adsorption of the peptides on SDS micelle has been performed in NPT ensemble at 0.1 MPa and 298 K. The cell under study contained 14,678 water molecules, one peptide zwitter-ion, and the micelle including 64 SDS monomers. Most probable localization of peptide atoms relative the micelle has been analyzed. The peptide – SDS micelle interaction is accompanied by diminish of average number of peptide – water H-bonds and the formation of at the mean two H-bonds with SDS. Some peculiarities of adsorption of the isomolecular peptides on SDS micelle are appeared in different values of H-bond lifetimes, different probability of formation of H-bond of NH3+O3Ssingle bondOsingle bond or NH3+single bondOsingle bond(SO3) types, and localization of peptide zwitter-ions outside or within double electrical layer of the micelle.

Introduction

Analysis of changes in the critical micelle concentration (CMC) [1], [2], [3], [4] or registration of changes in the physicochemical properties of micellar solutions with the addition of amino acids or peptides [5], [6], [7] is the subject of many works. To understand the mechanism of interaction of micelles with organic substances, it is necessary to study the structure of the formed micellar aggregates. Structural aspects of interaction with micelles are developed in the studies [8], [9], [10], [11], [12], [13]. The interaction process is often described as the spontaneous absorption of organic molecules onto the micelle surface and the preferential localization of these molecules among the polar head groups of the surfactant [8]. The ability of some organic molecules to penetrate in palisade layer of micelle is also noted in a number of works [9], [10]. The balance of both these processes can be affected by molecular parameters of organic molecules, such as the size, the delocalization and charge density on reaction groups, the structure branching, the hydrophobicity. The influence of the structure of low molecular weight peptides on the energy of interaction with micelles, on the depth of their penetration into micellar aggregates, and on the conformational variation of peptides in complexes with micelles is of interest for predicting the affinity of more complicated peptides for micellar aggregates.

Earlier, an approach to quantum chemical study of the interaction of amino acids/peptides with a surfactant dimer as a micelle model was tested using leucine as an example [13]. In this paper, a comparative quantum chemical and MD investigation of the interaction of α-l-alanyl-α-l-alanine (A) and β-alanyl-β-alanine (B) with sodium dodecyl sulfate micelles in aqueous medium has been performed. The choice of the isomolecular alanine dipeptides provides an opportunity to study the effect of branching structures and side hydrophobic groups on their ability to interact with micelles. The goals of this work are as follows:

  • (1)

    to obtain the most preferred configurations of complexes formed by the most stable conformer of α-l-alanyl-α-l-alanine and β-alanyl-β-alanine with SDS dimer as fragment of anionic micelle by quantum chemical modeling; to examine the energy change and the structure evolution of peptide in process of their interaction for causes of different localization of the peptide: among the polar head groups of the surfactant or in hydrophobic canal of SDS dimer;

  • (2)

    to investigate the binding of the dipeptides with SDS micelle in water by molecular dynamics simulation; to examine the structure of formed complexes and parameters of H-bonds between peptide, SDS and water molecules.

The dimer of SDS with “head to head” and “tail to tail” orientation of molecules was chosen as a model of the micelle fragment for quantum chemical modeling of micelle – peptide complexes in polarizable continuum. This configuration simulates the molecules orientation as in the SDS micelle. In MD simulation the anionic micelle involving 64 SDS monomers and the peptide zwitter-ion in water solvent were considered to investigate the peptide/micelle interaction. The starting structures of the peptides corresponding to their most stable conformers in the crystal were taken for calculation from experimental crystallographic data [14], [15].

Section snippets

Quantum chemical modeling

We studied complex formation of the most stable conformer of peptides with the SDS dimer in which surfactant molecules have “head to head” and “tail to tail” orientation. This configuration simulates the molecules orientation in the SDS micelle. The quantum chemical calculations were carried out using the GAUSSIAN 09 program package [16]. The Density Functional Theory (DFT) approach with B97-D functional [17], including a long-range dispersion correction was used for optimization of structure

The quantum-chemical modeling

Dimer (SDS)2. An optimized dimer structure (SDS)2 [13] with molecules oriented according to “head-to-head” and “tail to tail” pattern has been obtained by us earlier. The pattern reproduces a conical configuration of a micelle pore [11]. The results of NBO analysis suggest the purely ionic character of Na-O bond of the SDS molecule. In the optimized structure Na+ ion is in tridentate coordination towards oxygen atoms of SO4 group. Dispersion interaction between hydrophobic fragments orientates

Conclusion

The results obtained both by quantum chemical modeling with micelle fragment in polarizable continuum and molecular dynamics simulation with micelle at explicitly specified water molecules testify the complex formation of micellar aggregates with zwitterion peptides. The complexes have configuration in which NH3+ group of peptides is oriented to charged head groups of SDS. The formation of H-bonds between NH3+ group of peptides and O3Ssingle bondOsingle bond group of the surfactant was established by both methods

CRediT authorship contribution statement

Vladimir P. Barannikov: Conceptualization, Methodology, Writing - original draft. Marina S. Kurbatova: Software. Darya L. Gurina: Software, Validation. Nina I. Giricheva: Supervision, Writing - review & editing.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgment

The study was financially supported by the Russian Foundation for Basic Research (grant No. 18-03-01032-a).

MD simulation was carried out in the frame of the project No. 01201260481 of G.A. Krestov Institute of Solution Chemistry.

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