Conformational Changes and Flexibility for ArkA Binding to Abp1-SH3

Abstract

SH3 domains are the most common protein interaction domains and are found across all forms of life. However, little is known about how flexible peptides bind to these domains. These flexible peptides are often intrinsically disordered proteins (IDPs) which are difficult to model using only experimental methods. One SH3 domain found in yeast, Abp1SH3, has a binding site for the ArkA IDP. Molecular dynamics simulations were used to model the Abp1SH3 domain and the Abp1SH3-ArkA complex. SH3 domains are believed to have a two-step binding process in which part of the peptide binds to Surface I (SI) and afterwards, the rest of the protein binds to Surface II (SII). It was found that there is a greater amount of flexibility in the residues located in SI and SII compared to other residues in the SH3 domain. Also, several side chain dihedral angles in SI and SII have different angle preferences between the free and bound states. Mutations to the ArkA peptide were made including several residues mutated to alanine and a K-3R mutation. It was found that although lysine and arginine are similar in structure, this mutation resulted in fewer contacts between ArkA and Abp1.The mutations to alanine gave insight to the specificity SII has for binding the ArkA peptide, shown by a change in binding pattern between the proteins. Simulations were also run with a linker between Abp1 and ArkA, to mimic experimental procedures. It was found that there are similar contacts between Abp1 and ArkA with and without the linker, however, there is an increased flexibility in Abp1 in the presence of the linker compared to the normal bound structure. This increased flexibility may be compensating for the reduction of entropy caused by the linker.