Arginine Kinase. Joint Crystallographic and NMR RDC Analyses link Substrate-Associate
 

Arginine Kinase. Joint Crystallographic and NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility.

Related Articles Arginine Kinase. Joint Crystallographic and NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility.

J Mol Biol. 2010 Nov 11;

Authors: Niu X, Brüschweiler-Li L, Davulcu O, Skalicky JJ, Brüschweiler R, Chapman MS

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a "high energy" phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and -bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, "substrate-induced" motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection.

PMID: 21075117 [PubMed - as supplied by publisher]



Source: PubMed