Molecular dynamics simulations on the effect of peptide secondary structure and substrate charge on adsorption at silica surface

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Kemian tekniikan korkeakoulu | Master's thesis
Chemical and Process Engineering
Degree programme
Master's Programme in Chemical, Biochemical and Materials Engineering
Polypeptide (PP) adsorption is extensively studied due to the wide range of applications of PP layered surfaces in biotechnology and medical fields. The PP layer on the substrate surface alters interfacial properties and may result in biocompatible or bioactive surfaces. The formation of the adsorbed layer is mainly dependent on the chemistry of the PP and substrate surface. Understanding the subsequent interactions driving adsorption provide the possibility for advanced adjustment of adsorbed layer properties, such as packing density. Studying PPs with ionizable side chain groups is especially interesting as the charge state and consequent electrostatic interactions of the PP can be altered via pH and ionic strength. This makes possible the tuning of the strength of interactions between the PP and substrate. In the present work, all-atom molecular dynamics (MD) simulations were used to study the adsorption of three homopolypeptides, poly-L-glutamic acid (PGA), poly-L-lysine (PLL), and poly-L-arginine (PARG), on α-quartz surface as a function of pH. Changing the pH of the solution alters the charge state of PGA, PLL and the crystal surface, therefore allowing the tuning of electrostatic interactions. PARG is a strong electrolyte fully charged in the studied pH range chosen to study the effect of substrate charge on adsorption. MD simulations allow for the precise control of system variables, such as salt species, ionic strength and ionization degree making it an ideal method for systematically mapping interactions of PP adsorption. The results showed that electrostatic interactions are the main driving force of adsorption on α-quartz while hydrogen bonds facilitated binding when electrostatic interactions were not present. The salt species, in practice counterions of the negatively charged α-quartz surface, were demonstrated to alter the surface characteristics by forming a positively charged ion adlayer. This facilitated the adsorption of the negatively charged PGA on the crystal surface via ion bridging mechanism, while it hindered the adsorption of positively charged PARG due to the shielding of the negatively charged surface. PLL and PARG adsorbed via ion exchange with competitive adsorption with sodium ions. The pH responsive and salt sensitive adsorption phenomena and mechanisms presented in this work provide the possibility to engineering active surfaces with reversible binding.
Laasonen, Kari
Thesis advisor
Sammalkorpi, Maria
macromolecular adsorption, adsorption mechanisms, ion bridging, competitive adsorption, electrostatic interactions, AMBER force field
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