First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach

Stefano Pantaleone, Albert Rimola, Piero Ugliengo, Mariona Sodupe

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2∗ theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, β-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C=O groups form Ti-O=C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the β-sheet because in the former, more Ti-O=C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed β-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the β-sheet.

Original languageEnglish
Article number11
Pages (from-to)5484-5498
Number of pages15
JournalJournal of Chemical Information and Modeling
Volume61
Issue number11
DOIs
Publication statusPublished - 22 Nov 2021

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