Identifying Packing Contacts That Drive Conformational Polymorphism. Charles W. Carter, Jr.^*, Valentin Ilyin^*, Yuhui Yin^*, Xin Huang^*, Stephen Cammer^[daggerdbl], Weifan Zheng^[daggerdbl], and Alexander Tropsha^[daggerdbl], ^*Department of Biochemistry and Biophysics, CB 7260 and ^[daggerdbl]School of Pharmacy, CB 7360, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514

The ligand-free Tryptophanyl-tRNA synthetase (TrpRS) structure revealed a large (r.m.s. ~4 Å) and surprisingly complicated structural rearrangement, relative to complexed forms of the enzyme (Carter, IUCR-XVII MS03.03.04, Ilyin, IUCR-XVII PS04.06.11). This change was anticipated from low-angle scattering measurements, and superficially resembles a previously described conformational isomerism between TrpRS and TyrRS. However, the details are unrelated to the apparent division of the mainchain into "Rossmann-fold" and small helical domains (Doublié, 1995, Structure 3:17). The arrangement of secondary structures, per se, is therefore not a reliable guide to the rigid-body behavior of this enzyme. Analysis by distance-based clustering methods using individual nonpolar atoms (Ilyin, 1994, Prot. Eng. 7:1189) and by Delaunay tessellation and log-likelihood scoring of nearest-neighbor residue compositions (Tropsha, Pacific Symposium on Biocomputing '96:614) identify nearly the same, discrete regions of high-quality side-chain packing. The two analyses are complementary, the former depends on energy considerations; the latter on statistical frequencies of quadruplets (Delaunay simplices) with specific compositions in the database of known structures. Likelihood scoring of Delaunay simplices provides an unusually revealing visualization tool. Unexpectedly infrequent tetrahedra are associated with fluid regions of the protein, while unexpectedly frequent tetrahedra are clustered within the rigid bodies defined independently from X-ray coordinates. The predominant, high-scoring cluster provides a secure pocket in the small domain for the highly conserved Ile 16 from the "TIGN" signature sequence in the amino-terminal a-helix of the Rossmann fold. As a consequence, the two "signature" sequences that reside in the Rossmann-fold domain are tightly coupled to the small helical domain, operating as part of that domain when the active site opens in ligand-free TrpRS. This coupling also may help orient the tRNA anticodon-binding site properly for acyl-transfer to tRNA, following closure of the active-site and aminoacid activation.

(Supported by NIH GM48519-03)