A Functional Loop Spanning Distant Domains of Glutaminyl-tRNA Synthetase Also Stabilizes a Molten Globule State

Molten globule and other disordered states of proteins are now known to play important roles in many cellular processes. From equilibrium unfolding studies of two paralogous proteins and their variants, glutaminyl-tRNA synthetase (GlnRS) and two of its variants [glutamyl-tRNA synthetase (GluRS) and its isolated domains, and a GluRS− GlnRS chimera], we demonstrate that only GlnRS forms a molten globule-like intermediate at low urea concentrations. We demonstrated that a loop in the GlnRS C-terminal anticodon binding domain that promotes communication with the N-terminal domain and indirectly modulates amino acid binding is also responsible for stabilization of the molten globule state. This loop was inserted into GluRS in the eukaryotic branch after the archaea−eukarya split, right around the time when GlnRS evolved. Because of the structural and functional importance of the loop, it is proposed that the insertion of the loop into a putative ancestral GluRS in eukaryotes produced a catalytically active molten globule state. Because of their enhanced dynamic nature, catalytically active molten globules are likely to possess broad substrate specificity. It is further proposed that the putative broader substrate specificity allowed the catalytically active molten globule to accept glutamine in addition to glutamic acid, leading to the evolution of GlnRS. Many functional proteins fold into a well-defined threedimensional structure. However, it is now clear that not all proteins fold into a uniquely defined native state conformation. Many are intrinsically unfolded, while others can be partially folded or present in a molten globule-like structure in which the fold is compact but the internal mobility is significantly enhanced.1 The molten globule class of compact states is ubiquitous in nature, and in many cases, they are produced under mildly denaturing conditions.2 However, for many proteins, a molten globule state has not yet been detected under several denaturing conditions, indicating that they are energetically far removed from the native state. The physicochemical properties that stabilize a molten globule state with respect to the native state have not been fully elucidated, except in a few cases. The most important insight has come from pairs of paralogs in which one protein forms the molten globule state under mild denaturing conditions and the other does not.3 A classic example is that of the lysozyme− lactalbumin pair. It has been concluded that non-native interactions of a small part of bovine α-lactalbumin play a crucial role in the stabilization of the molten globule state.4 It is not known whether non-native contacts of a small region in a protein play important roles in the stabilization of the molten globule state of other proteins as well. If thi