Dynamic Interaction among the Platform Domain and Two Membrane-Proximal Immunoglobulin-Like Domains of Class I Major Histocompatibility Complex: Normal Mode Analysis

Abstract

Class I major histocompatibility complex (MHC) molecules have three domains, a platform domain and two membrane-proximal immunoglobulin-like domains, an alpha3 domain and a beta2-immunoglobulin (beta2m). To understand the dynamic interactions among the three domains, we simulated the behavior of a partial model deficient in beta2m and another model deficient in the alpha3 domain, by normal mode analysis. As a result, the partial model deficient in beta2m was more flexible in interdomain conformation than the other model. The lowest frequency modes (<2 cm(-1)) observed for the simulations of the partial model deficient in beta2m showed clear interdomain motions as if each domain moved like a rigid body. Such low frequencies and clear interdomain motions were not observed for the simulations of the other model, therefore the interdomain flexibility of the partial model deficient in beta2m may be due to the lowest frequency modes (<2 cm(-1)). These results suggest that beta2m contributes to maintaining the interdomain conformation of class I MHC molecules more than the alpha3 domain does, and may offer convincing evidence to support the notion that the alpha3 domain and beta2m do not have an equal influence on the structural stability of class I MHC molecules.