Methods and Guidelines for Analyzing the Conformational Dynamics of Proteins in the Antigen Presentation Pathway

Endoplasmic reticulum aminopeptidase 1 (ERAP1) digests antigenic precursors up to the optimum length for binding to the major histocompatibility complex (MHC) class I. This zinc-dependent aminopeptidase has been found in a catalytically active closed conformation and in open conformations that expose its substrate-binding cavity to the bulk solvent. Therefore, its activity has been linked to catalytic cycles between conformational states that accommodate substrate binding, peptide hydrolysis and product release. During the last decade, X-ray crystallography in conjunction with biophysical and enzymatic studies has deciphered the remarkable peptide-length dependence of ERAP1, the allosteric regulation mechanism, and the role of disease-associated polymorphisms. In this regard, molecular dynamics (MD) simulations have contributed to atomic-level investigations of ERAP1 conformational dynamics. This chapter provides a detailed protocol to generate the systems required to carry out and analyze atomistic MD simulations of ERAP1 with a bound inhibitor in explicit solvent, starting from different conformational states. This protocol is also applicable to the analysis of the conformational dynamics of other aminopeptidases in the antigen presentation pathway.