PubMed · 12120501
The source did not provide an abstract. Follow the original record for more information.
Explore connections, maps & timelines
Siân Renfrey, James Featherstone. 2002. Structural proteomics.. https://doi.org/10.1038/nrd766
Cite the original work for its findings. Save a collection to share your selection of sources.
KEEP EXPLORING
Ribonuclease MC1 (RNase MC1), isolated from bitter gourd seeds, is a uridine specific RNase belonging to the RNase T2 family. Mutations of Asn71 in RNase MC1 to the amino acids Thr (N71T) and Ser (N71S) in guanosine preferential RNases altered the substrate specificity from uridine specific to guanosine specific, as shown by the transphosphorylation of diribonucleoside monophosphates [Numata, T., et al. (2001) Biochemistry 40, 524-530]. To elucidate the structural basis for the alteration of substrate specificity, crystal structures of the RNase MC1 mutants N71T and N71S, free or complexed with 5'-GMP, were determined at resolutions higher than 2 A. In the N71T-5'-GMP and N71S-5'-GMP complexes, the guanine moiety was, as in the case of the uracil moiety bound to wild-type RNase MC1, firmly stabilized in the B2 site by an extensive network of hydrogen bonds and hydrophobic interactions. Structure comparisons showed that mutations of Asn71 to Thr or Ser cause an enlargement of the B2 site, which then make it feasible to insert a guanine base into the B2 site of mutants N71T and N71S. This binding further allows for hydrogen bonding interaction of the side chain hydroxyl groups of Thr71 or Ser71 with the N7 atom of the guanine base. The mode of guanine binding of mutants N71T and N71S was found to be essentially identical to that of a guanosine preferential RNase NW from Nicotiana glutinosa. In particular, hydrogen bonds between the N7 atom of the guanine base and the hydroxyl groups of the amino acids at position 71 (RNase MC1 numbering) were completely conserved in three guanosine preferential enzymes, thereby indicating that the hydrogen bond may play an essential role in guanine binding in guanosine preferential RNases in the RNase T2 family. Consequently, it can be concluded that amino acids at position 71 (RNase MC1 numbering) serve as one of the determinants for substrate specificity (or preference) in the RNase T2 fimily by changing the size and shape of the B2 site.
Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I; Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, II; Boc-Aib-Ala-Phe-Aib-Phe-Ala-Val-Aib-OMe, III. X-ray diffraction studies reveal that all three peptides adopt helical conformations in the solid state with the Phe side chains projecting outward. Interhelix association in the crystals is promoted by Phe-Phe interactions. A total of 15 unique aromatic pairs have been characterized in the three independent crystal structures. In peptides I and II, the aromatic side chains lie on the same face of the helix at i/i + 4 positions resulting in both intrahelix and interhelix aromatic interactions. In peptide III, the Phe side chains are placed on the opposite faces of the helix, resulting in exclusive intermolecular aromatic interactions. The distances between the centroids of aromatic pair ranges from 5.11 to 6.86 A, while the distance of closest approach of ring carbon atoms ranges from 3.27 to 4.59 A. Examples of T-shaped and parallel-displaced arrangements of aromatic pairs are observed, in addition to several examples of inclined arrangements. The results support the view that the interaction potential for a pair of aromatic rings is relatively broad and rugged with several minima of similar energies, separated by small activation barriers.
To study the interaction of the fac-[M(CO)(3)](+) moiety (M = (99m)Tc, (188)Re) with DNA bases, we reacted [M(OH(2))(3)(CO)(3)](+) with 9-methylguanine (9-MeG), guanosine (G), and 2-deoxyguanosine (2dG). Two bases bind to the metal center via the N7 atoms. X-ray structure analysis of [(99)Tc(CH(3)OH)(9-MeG)(2)(CO)(3)](+) (4) (monoclinic, I2/a, a = 28.7533(14) A, b = 8.0631(4) A, c = 32.3600(15) A, beta = 91.543(6) degrees, V = 7499.6(6) A(3), Z = 8) and [Re(OH(2))(9-MeG)(2)(CO)(3)](+) (7) (monoclinic, P2(1)/n, a = 12.2873(11) A, b = 16.0707(13) A, c = 14.1809(16) A, beta = 103.361(12) degrees, V = 2724.4(5) A(3), Z = 4) reveals that the two bases are in a head-to-tail (HT) orientation. Kinetic studies show that the rates of substitution of the purine bases are comparable to that of one of the active forms of cisplatin. The bis-substituted complexes are generally less stable than the platinum adducts, and metalation of the bases is reversible.