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New Conformation (new + conformation)
Selected AbstractsFlexibility and communication within the structure of the Mycobacterium smegmatis methionyl-tRNA synthetaseFEBS JOURNAL, Issue 19 2010Henrik Ingvarsson Two structures of monomeric methionyl-tRNA synthetase, from Mycobacterium smegmatis, in complex with the ligands methionine/adenosine and methionine, were analyzed by X-ray crystallography at 2.3 Å and at 2.8 Å, respectively. The structures demonstrated the flexibility of the multidomain enzyme. A new conformation of the structure was identified in which the connective peptide domain bound more closely to the catalytic domain than described previously. The KMSKS(301-305) loop in our structures was in an open and inactive conformation that differed from previous structures by a rotation of the loop of about 90° around hinges located at Asn297 and Val310. The binding of adenosine to the methionyl-tRNA synthetase methionine complex caused a shift in the KMSKS domain that brought it closer to the catalytic domain. The potential use of the adenosine-binding site for inhibitor binding was evaluated and a potential binding site for a specific allosteric inhibitor was identified. [source] Local structure investigation of the active site of the imidazolonepropionase from Bacillus subtilis by XANES spectroscopy and ab initio calculationsJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2008Feifei Yang Imidazolonepropionase is an important enzyme that plays a crucial role in the degradation of the histidine in mammals and bacteria. In this contribution a detailed structural investigation is presented of the imidazolonepropionase from Bacillus subtilis at the zinc site by X-ray absorption near-edge structure (XANES) spectroscopy combining experimental data with ab initio calculation in the framework of the multiple-scattering theory. The resolved local structure leads to a modification of the data set in the Protein Data Bank (PDB) (PDB code 2BB0). Actually, data suggest that the carboxyl of the Asp324 moves far away from the zinc ion at the center, while the water molecule and the nearest-neighbor histidines move towards it. This new conformation and the occurrence of a short water-to-zinc bond length support the nucleophilic attack catalytic mechanism proposed for this enzyme. [source] What can we learn by computing 13C, chemical shifts for X-ray protein models?ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Yelena A. Arnautova The room-temperature X-ray structures of ubiquitin (PDB code 1ubq) and of the RNA-binding domain of nonstructural protein 1 of influenza A virus (PDB code 1ail) solved at 1.8 and 1.9,Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13C, chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and Rfree factors similar to those of the deposited X-ray structure, the 13C, chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13C, chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13C, chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13C, chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13C, chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with accuracy as good as the PDB structure. Therefore, generation of an ensemble is a necessary step to determine whether or not a single structure is sufficient for an accurate representation of both experimental X-ray data and observed 13C, chemical shifts in solution. [source] Coordination Chemistry of Conformation-Flexible 1,2,3,4,5,6-Cyclohexanehexacarboxylate: Trapping Various Conformations in Metal,Organic FrameworksCHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2008Jing Wang Abstract To study the conformations of 1,2,3,4,5,6-cyclohexanehexacarboxylic acid (H6L), eleven new coordination polymers have been isolated from hydrothermal reactions of different metal salts with 1e,2a,3e,4a,5e,6a -cyclohexanehexacarboxylic acid (3e+3a, H6LI) and characterized. They are [Cd12(,6 - LII)(,10 - LII)3(,-H2O)6(H2O)6],16.5,H2O (1), Na12[Cd6(,6 - LII)(,6 - LIII)3],27,H2O (2), [Cd3(,13 - LII)(,-H2O)] (3), [Cd3(,6 - LIII)(2,2,-bpy)3(H2O)3],2,H2O (4), [Cd4(,4 - LVI)2(4,4,-Hbpy)4(4,4,-bpy)2(H2O)4],9.5,H2O (5), [Cd2(,6 - LII)(4,4,-Hbpy)2(H2O)10],5,H2O (6), [Cd3(,11 - LVI)(H2O)3] (7), [M3(,9 - LII)(H2O)6] (M=Mn (8), Fe (9), and Ni (10)), and [Ni4(OH)2(,10 - LII)(4,4,-bpy)(H2O)4],6,H2O (11). Three new conformations of 1,2,3,4,5,6-cyclohexanehexacarboxylate, 6e (LII), 4e+2a (LIII) and 5e+1a (LVI), have been derived from the conformational conversions of LI and trapped in these complexes by controlling the conditions of the hydrothermal systems. Complexes 1 and 2 have three-dimensional (3D) coordination frameworks with nanoscale cages and are obtained at relatively low temperatures. A quarter of the LI ligands undergo a conformational transformation into LII while the others are transformed into LIII in the presence of NaOH in 2, while all of the LI are transformed into LII in the absence of NaOH in 1. Complex 3 has a 3D condensed coordination framework, which was obtained under similar reaction conditions as 1, but at a higher temperature. The addition of 2,2,-bipyridine (2,2,-bpy) or 4,4,-bipyridine (4,4,-bpy) to the hydrothermal system as an auxiliary ligand also induces the conformational transformation of H6LI. A new LVI conformation has been trapped in complexes 4,7 under different conditions. Complex 4 has a 3D microporous supramolecular network constructed from a 2D LIII -bridged coordination layer structure by ,-, interactions between the chelating 2,2,-bpy ligands. Complexes 5,7 have different frameworks with LII/LVI conformations, which were prepared by using different amounts of 4,4,-bpy under similar synthetic conditions. Both 5 and 7 are 3D coordination frameworks involving the LVI ligands, while 6 has a 3D microporous supramolecular network constructed from a 2D LII -bridged coordination layer structure by interlayer N4,4,-HbpyH,,,O(LII) hydrogen bonds. 3D coordination frameworks 8,11 have been obtained from the H6LI ligand and the paramagnetic metal ions MnII, FeII, and NiII, and their magnetic properties have been studied. Of particular interest to us is that two copper coordination polymers of the formulae [{CuII2(,4 - LII)(H2O)4}{CuI2(4,4,-bpy)2}] (12,,) and [CuII(Hbtc)(4,4,-bpy)(H2O)],3,H2O (H3btc=1,3,5-benzenetricarboxylic acid) (12,,) resulted from the same one-pot hydrothermal reaction of Cu(NO3)2, H6LI, 4,4,-bpy, and NaOH. The Hbtc2, ligand in 12,, was formed by the in situ decarboxylation of H6LI. The observed decarboxylation of the H6LI ligand to H3btc may serve as a helpful indicator in studying the conformational transformation mechanism between H6LI and LII,VI. Trapping various conformations in metal-organic structures may be helpful for the stabilization and separation of various conformations of the H6L ligand. [source] | ||||||||||