Conformational structure and binding mode of glyceraldehyde-3-phosphate dehydrogenase to tRNA studied by Raman and CD spectroscopy

Abstract

Recently it has been suggested that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays a role in nuclear tRNA export. As the structural basis of binding of GAPDH to tRNA is as yet unknown, we have employed Raman and CD spectroscopy as probes of the solution structures of GAPDH from rabbit and tRNA Phe from brewers yeast. Additionally, we have obtained the Raman and CD spectra of GAPDH when bound to tRNA Phe. In the complex we find the following results: (a) The most part of the tRNA Phe structure is conserved, but with a slight perturbation toward a B-like form. (b) No significant changes in the secondary structure of the protein upon binding are observed. (c) The surface enhanced Raman spectra are consistent with a GAPDH-tRNA Phe complex molecular model that involves the insertion of tRNA Phe into the GAPDH tetramer groove containing the R and P axes. (d) The specific interactions that occur between GAPDH and the tRNA Phe involve, mainly, stacking between nucleobases and aromatic amino-acid residues, and ionic interactions of basic amino-acid residues with phosphate groups of the ribose-phosphate backbone. The above stacking interactions are also supported by the significant relatedness that we have found between an amino-acid sequence (residues 303–308) of GAPDH and RNP2 binding motifs of some RNA binding proteins.