Conformation and Aggregation of LKα14 Peptide in Bulk Water and at the Air/Water Interface
| Autor: | Mehmet Sayar, Cahit Dalgicdir |
|---|---|
| Rok vydání: | 2015 |
| Předmět: |
Protein Conformation
Thermodynamic equilibrium Stereochemistry Molecular Sequence Data Peptide 010402 general chemistry 01 natural sciences Protein structure 0103 physical sciences Materials Chemistry Side chain Amino Acid Sequence Physical and Theoretical Chemistry Potential of mean force Peptide sequence chemistry.chemical_classification 010304 chemical physics Chemistry Air Water 0104 chemical sciences Surfaces Coatings and Films Chemical physics Protein folding Umbrella sampling Peptides |
| Zdroj: | The Journal of Physical Chemistry B. 119:15164-15175 |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.5b08871 |
| Popis: | Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly depend on the environmental conditions. Here, we study the aggregation behavior of the model peptide LKα14 (with amino acid sequence LKKLLKLLKKLLKL) in bulk water and at the air/water interface. We start by a quantitative analysis of the conformational space of a single LKα14 in bulk water. Next, in order to analyze the aggregation tendency of LKα14, by using the umbrella sampling technique we calculate the potential of mean force for pulling a single peptide from an n-molecule aggregate. In agreement with the experimental results, our calculations yield the optimal aggregate size as four. This equilibrium state is achieved by two opposing forces: Coulomb repulsion between the lysine side chains and the reduction of solvent accessible hydrophobic surface area upon aggregation. At the vacuum/water interface, however, even dimers of LKα14 become marginally stable, and any larger aggregate falls apart instantaneously. Our results indicate that even though the interface is highly influential in stabilizing the α-helix conformation for a single molecule, it significantly reduces the attraction between two LKα14 peptides, along with their aggregation tendency. |
| Databáze: | OpenAIRE |
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