Proline Isomerization In Arka12 In Silico

ArkA12 is a proline rich intrinsically disordered protein (IDP) region of a larger ArkA protein which interacts with an AbpSH3 domain. SH3 domains are numerous in the human genome and largely responsible for cytoskeleton regulation and signal transduction. They also have an affinity for binding proline rich IDPs making them a good model for studying ArkA12 binding dynamics. Specifically, SH3 binds to a conserved PxxP motif on the IDP with a polyproline II helix conformation via a step wise mechanism and intermediate complex. There are five prolines in ArkA12 that are capable of isomerizing between the cis and trans states at the peptide bond. Proline is the only amino acid capable of achieving a sizeable stability in the cis state; many proteins use this mechanism as a kind of “proline-switch” frequently used in gene regulation. Previous molecular dynamics (MD) simulation on ArkA12-SH3 binding have postulated a binding pathway, however the prolines in ArkA12 do not isomerize. There is currently no data in the literature showing proline peptide bond isomerization in proteins of lengths larger than ∼5 residues, even with enhanced methods. It's important to sample a complete conformational ensemble of the peptide to create a model that will more likely resemble the experimental structural data. The current work uses the gaussian accelerated molecular dynamics (GaMD) algorithm along with a modified Amberff14SB force field with a lowered peptide bond transition height to observe if the prolines in ArkA12 sampled cis. Simulations showed cis-trans isomerization for all five prolines in ArkA12 starting from an extended structure, suggesting this proposed simulation method may be suitable for simulating proline rich IDPs. Secondary structure comparison to experimental circular dichroism (CD) data will further elucidate whether or not this GaMD-lowerbarrier method produces accurate conformational ensembles.