Investigating the gas phase structure of KIX with radical directed dissociation and molecular dynamics: Retention of the native structure

Evaluating protein structure in the gas phase is useful for understanding the intrinsic forces which influence protein folding and for determining the feasibility of probing condensed phase structure with gas phase interrogation. KIX is a three-helix bundle protein that has been reported previously to preserve the condensed phase structure in the gas phase. Herein, structure dependent radical directed dissociation (RDD) is used to examine the gas phase structure of KIX by establishing residue specific distance constraints which can be used to assess candidate structures obtained from molecular dynamics simulations. The data obtained by RDD is consistent with KIX structures that largely retain condensed phase structure as determined previously by NMR. There are several factors that favor retention of the KIX native fold in the gas phase. The structure is largely comprised of alpha helices, which are known to be stable in the gas phase. This is particularly true if the C-terminus of the helix is capped with a positive charge, which occurs for the two most stable helices in KIX. There are several arginine based salt bridges which link critical portions of KIX together. KIX also has an abundance of basic residues; this multiplicity increases the chance that sites which require little structural reorganization following desolvation can be charge carriers. Thus under appropriate conditions, solution phase structure can be largely retained and meaningfully examined in the gas phase.

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► Radical directed dissociation is used to examine protein structure in the gas phase.
► KIX is a three helix bundle protein that retains its native structure in the gas phase.
► Various electrostatic forces stabilize the native structure in the gas phase.