�-Lactoglobulin is a protein found in bovine milk that makes an interesting subject for the analysis of protein folding because of a transient helix not present in the native structure.  It has been suggested that the purpose of this transient structure is to help guide the protein to its native conformation and avoid time-consuming folding pathways. The fact that this helix forms in a portion of the protein that is not involved in long-range intramolecular interactions in the native structure makes it suitable for a small-scale study of the local three-dimensional structure.  While proteins are often studied in aqueous environments that mimic the environment of a cell, a lot can be learned from taking the unconventional approach of studying isolated peptides.  This not only allows inherent intramolecular interactions to be discovered, it also makes possible the comparison of high-level calculations with well-resolved experimental spectra resulting in precise conformational assignments. The goal of this work is to compare a sequence of increasingly longer peptides that correspond to this unique section of �-lactoglobulin.  The segment studied includes adjacent tryptophan and tyrosine residues, and it has been previously determined that in the dipeptide the aromatic rings interact both with one another and a backbone NH group.  In this work, molecular dynamics simulations followed by optimization using density functional theory have been used to identify low-energy backbone configurations and aromatic ring interactions in larger peptide segments in which up to three additional amino acids from the �-lactoglobulin sequence have been added to the C-terminus.  The additional amino acids, serine, leucine, and alanine, represent both hydrophilic and hydrophobic residues and make possible additional intramolecular interactions that could either stabilize or destabilize the dipeptide configuration.

Effect of additional amino acids on the conformation of a short peptide

246th National Meeting (2013)

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