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
Graphical abstract
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 −O3SO 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.
References (32)
- et al.
Effect of biologically active amino acids on the surface activity and micellar properties of industrially important ionic surfactants
Colloids Surf. A: Physicochem. Eng. Aspects
(2014) - et al.
Thermodynamic insights into drug–surfactant interactions: Study of the interactions of naporxen, diclofenac sodium, neomycin, andlincomycin with hexadecytrimethylammonium bromide by usingisothermal titration calorimetry
Colloids Surf., B
(2015) - et al.
Molecular dynamics simulation study of sodium dodecyl sulfate micelle: Water penetration and sodium dodecyl sulfate dissociation
Colloids Surf. A: Physicochem. Eng. Aspects
(2015) - et al.
A coarse-grained molecular dynamics simulation of a sodium dodecyl sulfate micelle in aqueous solution
Colloid Surface A : Physicochem. Eng. Asp.
(2009) - et al.
Interaction of glycine with cationic, anionic, and nonionic surfactants at different temperatures: a volumetric, viscometric, refractive index, conductometric, and fluorescence probe study
Colloid Polym. Sci.
(2008) - et al.
Effect of temperature on the interactions of glycyl dipeptides with sodium dodecyl sulfate in aqueous solution: a volumetric, conductometric, and fluorescence probe study
J. Chem. Eng. Data.
(2010) - et al.
Conductometric studies on micellization of cationic surfactants in the presence of glycine
J. Solution Chem.
(2015) - et al.
Studies on the effect of amino acids/peptide on micellization of SDS at different temperatures
J. Surfact. Deterg.
(2010) - et al.
Conductometric and fluorometric studies of sodium dodecyl sulphate in aqueous solution and in the presence of amino acids
Mol. Phys.
(2014) - et al.
Study of mixed micellar aqueous solutions of sodium dodecyl sulfate and amino acids
Colloid J.
(2013)
Amphiphilic a-helical antimicrobial peptides and their structure/function relationships
Protein Pept. Lett.
Complex formation and aggregate transitions of sodium dodecyl sulfate with an oligomeric connecting molecule in aqueous solution
Langmuir
A quantum chemical simulation of the interaction between leucine and sodium dodecyl sulfate dimmer
J. Struct. Chem.
The crystal and Molecular Structure of β-Alanine
Acta Cryst.
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