Molecular dynamics of apo-adenylate kinase: a principal component analysis.
Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when its open form closes over its substrates, AMP and Mg2+-ATP. The third domain, the Core, is relatively stable during closing. The resulting trajectory is analyzed with a principal component analysis method that decomposes the atom motions into modes ordered by their decreasing contributions to the total protein fluctuation. Simulations at 303 K (normal T) and 500 K (high T) reveal that at both temperatures the first three modes account for 70% of the total fluctuation. The residues that contribute the most to these three modes are concentrated in the Lid and AMP-binding domains. Analysis of the normal T modes indicates that the Lid and AMP-binding domains sample a broad distribution of conformations indicating that AKE is designed to provide its substrates with a large set of conformations. The high T results show that the Lid initially closes toward the Core. Subsequently, the Lid rotates to a new stable conformation that is different from what is observed in the substrate-bound AKE. These results are discussed in the context of experimental data that indicate that adenylate kinases do sample more than one conformational state in solution and that each of these conformational states undergoes substantial fluctuations. A pair of residues is suggested for labeling that would be useful for monitoring distance fluctuations by energy transfer experiments.