Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations

• Published in: Molecules (Basel, Switzerland) Vol. 27; no. 23; p. 8417
• Main Authors: Soltani, Sepideh, Sowlati-Hashjin, Shahin, Tetsassi Feugmo, Conrard Giresse, Karttunen, Mikko
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01-12-2022; MDPI
• Subjects: 5,6-dihydroxyindole-2-carboxylic acid (DHICA); Acids; Anions; Aqueous solutions; Binary mixtures; Binding; Carboxylic acids; Chemical properties; Chemical research; Chemical structure; Density Functional Theory; density functional theory (DFT); eumelanin; Experiments; Geometry; Hair - chemistry; Inner ear; Ions; Melanins - metabolism; Molecular dynamics; Molecular Dynamics (MD) simulations; Molecular Dynamics Simulation; Optimization; Physiology; Pigments; Polymers; Polymers - analysis; Pyrroles - analysis; Quinones; Scanning electron microscopy; Self-assembly; Simulation; Canada; density functional theory (DFT); 5,6-dihydroxyindole-2-carboxylic acid (DHICA); Molecular Dynamics (MD) simulations; eumelanin
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules27238417

Eumelanin is an important pigment, for example, in skin, hair, eyes, and the inner ear. It is a highly heterogeneous polymer with 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and 5,6-dihydroxyindole (DHI) building blocks, of which DHICA is reported as the more abundant in natural eumelanin. The DHICA-eumelanin protomolecule consists of three building blocks, indole-2-carboxylic acid-5,6-quinone (ICAQ), DHICA and pyrrole-2,3,5-tricarboxylic acid (PTCA). Here, we focus on the self-assembly of DHICA-eumelanin using multi-microsecond molecular dynamics (MD) simulations at various concentrations in aqueous solutions. The molecule was first parameterized using density functional theory (DFT) calculations. Three types of systems were studied: (1) uncharged DHICA-eumelanin, (2) charged DHICA-eumelanin corresponding to physiological pH, and (3) a binary mixture of both of the above protomolecules. In the case of uncharged DHICA-eumelanin, spontaneous aggregation occurred and water molecules were present inside the aggregates. In the systems corresponding to physiological pH, all the carboxyl groups are negatively charged and the DHICA-eumelanin model has a net charge of -4. The effect of K+ ions as counterions was investigated. The results show high probability of binding to the deprotonated oxygens of the carboxylate anions in the PTCA moiety. Furthermore, the K+ counterions increased the solubility of DHICA-eumelanin in its charged form. A possible explanation is that the charged protomolecules favor binding to the K+ ions rather than aggregating and binding to other protomolecules. The binary mixtures show aggregation of uncharged DHICA-eumelanins; unlike the charged systems with no aggregation, a few charged DHICA-eumelanins are present on the surface of the uncharged aggregation, binding to the K+ ions.