Radiolysis of water with a synchrotron x-ray beam permits the hydroxyl radical-accessible surface of an RNA to be mapped with nucleotide resolution in 10 milliseconds. Application of this method to folding of the Tetrahymena ribozyme revealed that the most stable domain of the tertiary structure, P4-P6, formed cooperatively within 3 seconds. Exterior helices became protected from hydroxyl radicals in 10 seconds, whereas the catalytic center required minutes to be completely folded. The results show that rapid collapse to a partially disordered state is followed by a slow search for the active structure.

The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic highaffinity low-molecular weight nonpeptidic substrate (K m ‫؍‬ 16 M), and the structure was refined to an R-factor of 18.2% at 1.9 Å resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1% at 1.85 Å. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B͞C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.Protein-tyrosine phosphatases (PTPases), working in concert with protein-tyrosine kinases, regulate a vast array of cellular events, including passage through the cell cycle, proliferation and differentiation, metabolism, cytoskeletal organization, neuronal development, and the immune response (1, 2). PTPases constitute a large family of enzymes that parallel protein-tyrosine kinases in their structural diversity and complexity. A recent estimate suggests that as many as 500 PTPase genes may be encoded within the human genome (2). In vivo, PTPases catalyze the removal of the phosphoryl group from phosphotyrosine (pTyr) residue(s) in protein substrates. However, the K m value for free pTyr is three to four orders of magnitude higher than the best protein͞peptide substrates (3, 4). Several groups have demonstrated that PTPases display a range of k cat ͞K m values for pTyr-containing peptides. This sequence specificity has been exploited in the design of potent and selective PTPase inhibitors by incorporating a nonhydrolyzable pTyr analog into optimal peptide templates (5). However, owing to proteolytic susceptibility and weak partitioning across the plasma membrane, peptide-based compounds are not highly desirable for the development of medicinally effective drugs.As an initial step toward the development of selective, low-molecular weight nonpeptidic PTPase inhibitors, we investigated the active site substrate specificity of PTP1, the rat structural homologue of human protein-tyrosine phosphatase 1B (PTP1B). PTP1B (3) is the prototypical intracellular PTPase and is found in a wide varie...