Torrey Pines Institute for Molecular Studies

About: Torrey Pines Institute for Molecular Studies is a nonprofit organization based out in San Diego, California, United States. It is known for research contribution in the topics: Antigen & T cell. The organization has 2323 authors who have published 2217 publications receiving 112618 citations.

Crystal structure of Trbp111: a structure-specific tRNA-binding protein

Abstract: Trbp111 is a 111 amino acid Aquifex aeolicus structure-specific tRNA-binding protein that has homologous counterparts distributed throughout evolution. A dimer is the functional unit for binding a single tRNA. Here we report the 3D structures of the A.aeolicus protein and its Escherichia coli homolog at resolutions of 2.50 and 1.87 A, respectively. The structure shows a symmetrical dimer of two core domains and a central dimerization domain where the N- and C-terminal regions of Trbp111 form an extensive dimer interface. The core of the monomer is a classical oligonucleotide/oligosaccharide-binding (OB) fold with a five-stranded ss-barrel and a small capping helix. This structure is similar to that seen in the anticodon-binding domain of three class II tRNA synthetases and several other proteins. Mutational analysis identified sites important for interactions with tRNA. These residues line the inner surfaces of two clefts formed between the ss-barrel of each monomer and the dimer interface. The results are consistent with a proposed model for asymmetrical docking of the convex side of tRNA to the dimer.

Novel-prodrugs for phosphorus-containing compounds

Abstract: Prodrugs of formula (I), their uses, their intermediates, and their method of manufacture are described, wherein V is selected from the group consisting of -H, aralkyl, alicyclic, aryl, substituted aryl, heteroaryl, substituted heteroaryl, 1-alkenyl, 1-alkynyl, and -R9; or together V and Z are connected via 3-5 atoms to form a cyclic group, optionally containing 1 heteroatom, substituted with hydroxy, acyloxy, alkoxycarbonyloxy, or aryloxycarbonyloxy attached to a carbon atom that is three atoms from an oxygen attached to the phosphorus; or together V and Z are connected via 3-5 atoms to form a cyclic group, optionally containing 1 heteroatom, that is fused to an aryl group at the beta and gamma position to the oxygen attached to the phosphorus; or together V and W are connected via 3 carbon atoms to form an optionally substituted cyclic group containing 6 carbon atoms and substituted with one substituent selected from the group consisting of hydroxy, acyloxy, alkoxycarbonyloxy, alkylthiocarbonyloxy, and aryloxycarbonyloxy, attached to a carbon atom that is three atoms from an oxygen attached to the phosphorus; W and W' are independently selected from the group consisting of -H, alkyl, aralkyl, alicyclic, aryl, substituted aryl, heteroaryl, substituted heteroaryl, 1-alkenyl, 1-alkynyl, and -R9; Z is selected from the group consisting of -CHR2OH, -CHR?2OC(O)R3, -CHR2OC(S)R3, -CHR2OC(S)OR3, -CHR2OC(O)SR3, -CHR2OCO?2R?3, -OR2, -SR2, -CHR2N?3, -CH2aryl, -CH(aryl)OH, -CH(CH=CR22)OH, -CH(C CR?2)OH, -R2, -NR2?2, -OCOR3, -OCO?2?R?3, -SCOR3?, -SCO?2R?3, -NHCOR2, -NHCO?2?R?3, -CH?2NHaryl, -(CH2)p-OR2, and -(CH?2?)p-SR?2; R2? is an R3 or -H; R3 is selected from the group consisting of alkyl, aryl, aralkyl, and alicyclic; and R9 is selected from the group consisting of alkyl, aralkyl, and alicyclic; p is an integer from 2 to 3; with the provisos that a) V, Z, W, and W' are not all -H; and b) when z is -R2, then at least one of V and W is not -H, or -R9; and M is selected from the group that attached to PO?3?2-, P2O63-, or P?3O9?4- is biologically active in vivo, and that is attached to the phosphorus in formula (I) via a carbon, oxygen, or nitrogen atom; and pharmaceutically acceptable prodrugs and salts thereof.

Enzymatic turnover of macromolecules generates long-lasting protein–water-coupled motions beyond reaction steady state

Abstract: The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray– and terahertz- based time-resolved spectroscopic tools to study protein–water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme–substrate–water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme–collagen system. The long-lasting changes in protein–water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.