Investigating Alanine-Silica Interaction by Means of First-Principles Molecular-Dynamics Simulations

• Published in: Chemphyschem 2008-02, Vol.9 (3), p.414-421
• Main Authors: Nonella, Marco, Seeger, Stefan
• Format: Article
• Language: English
• Subjects: Alanine - chemistry; Biological and medical sciences; Chemistry; Computer Simulation; density functional calculations; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; General and physical chemistry; hydrogen bonds; Models, Chemical; Molecular biophysics; molecular dynamics; Molecular Structure; peptide-surface-interaction; silica; Silicon Dioxide - chemistry; Surface physical chemistry; Surface properties. Adsorption
• ISSN: 1439-4235; 1439-7641
• DOI: 10.1002/cphc.200700546

In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynamics technique. The simulations are carried out in vacuo as well as in the presence of water molecules. In the case of a negatively charged surface and an alanine cation, an indirect proton transfer from the alanine carboxylic group to the surface takes place. The transfer involves several water molecules revealing an alanine in its zwitterionic state interacting with the neutral surface through indirect hydrogen bonds mediated by water molecules. During the simulation of the zwitterionic state the ammonium group eventually establishes a direct NH⋅⋅⋅OSi interaction, suggesting that the surface–amino group interaction is stronger than the interaction between the surface and the carboxylic group. In vacuum simulations, the amino group exhibits clearly stronger interactions with the surface than the carboxylic group. Sticky surfaces: The microscopic nature of protein–surface interactions in the presence of solvent molecules is investigated using first‐principles molecular‐dynamics techniques (see picture). The two dominant amino acid–surface interactions involve direct and indirect hydrogen bonding.