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Multiple Conformations (multiple + conformation)
Selected AbstractsSpecific cleavage of the DNase-I binding loop dramatically decreases the thermal stability of actinFEBS JOURNAL, Issue 18 2010Anastasia V. Pivovarova Differential scanning calorimetry was used to investigate the thermal unfolding of actin specifically cleaved within the DNaseI-binding loop between residues Met47-Gly48 or Gly42-Val43 by two bacterial proteases, subtilisin or ECP32/grimelysin (ECP), respectively. The results obtained show that both cleavages strongly decreased the thermal stability of monomeric actin with either ATP or ADP as a bound nucleotide. An even more pronounced difference in the thermal stability between the cleaved and intact actin was observed when both actins were polymerized into filaments. Similar to intact F-actin, both cleaved F-actins were significantly stabilized by phalloidin and aluminum fluoride; however, in all cases, the thermal stability of the cleaved F-actins was much lower than that of intact F-actin, and the stability of ECP-cleaved F-actin was lower than that of subtilisin-cleaved F-actin. These results confirm that the DNaseI-binding loop is involved in the stabilization of the actin structure, both in monomers and in the filament subunits, and suggest that the thermal stability of actin depends, at least partially, on the conformation of the nucleotide-binding cleft. Moreover, an additional destabilization of the unstable cleaved actin upon ATP/ADP replacement provides experimental evidence for the highly dynamic actin structure that cannot be simply open or closed, but rather should be considered as being able to adopt multiple conformations. Structured digital abstract ,,MINT-7980274: Actin (uniprotkb:P68135) and Actin (uniprotkb:P68135) bind (MI:0407) by biophysical (MI:0013) [source] Dissociation mechanisms and implication for the presence of multiple conformations for peptide ions with arginine at the C-terminus: time-resolved photodissociation studyJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 7 2010So Hee Yoon Abstract Time-resolved photodissociation (PD) patterns of singly protonated peptides with arginine at the C-terminus (C-arg peptide ions) have been used to classify the dissociation channels into two categories, i.e. high-energy channels generating v, w and x and low-energy ones generating b, y and z. x + 1 formed by C,CO cleavage seems to be the intermediate ion in high-energy channels just as a + 1 is for N-arg peptide ions. Difference in time-resolved pattern indicates that the two sets of channels, high- and low-energy ones, are not in direct competition. Noncompetitive dissociation is also indicated by the observation of anomalous effect of matrix used in matrix-assisted laser desorption ionization, a cooler matrix generating more high-energy product ions both in spontaneous dissociation and in PD. Results from detailed investigation suggest that the two sets of channels start from two (or more) different conformations. Copyright © 2010 John Wiley & Sons, Ltd. [source] Protein,protein docking with multiple residue conformations and residue substitutionsPROTEIN SCIENCE, Issue 6 2002David M. Lorber Abstract The protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side-chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformations were docked into both the complexed (bound) and unbound conformations of the cognate receptors, and their energies were evaluated using an atomistic potential function. The following questions were considered: (1) does the ensemble of precalculated ligand conformations contain a structure similar to the bound form of the ligand? (2) Can the large number of conformations that are calculated be efficiently docked into the receptors? (3) Can near-native complexes be distinguished from non-native complexes? Results from seven test systems suggest that the precalculated ensembles do include side-chain conformations similar to those adopted in the experimental complexes. By assuming additivity among the side chains, the ensemble can be docked in less than 12 h on a desktop computer. These multiconformer dockings produce near-native complexes and also non-native complexes. When docked against the bound conformations of the receptors, the near-native complexes of the unbound ligand were always distinguishable from the non-native complexes. When docked against the unbound conformations of the receptors, the near-native dockings could usually, but not always, be distinguished from the non-native complexes. In every case, docking the unbound ligands with flexible side chains led to better energies and a better distinction between near-native and non-native fits. An extension of this algorithm allowed for docking multiple residue substitutions (mutants) in addition to multiple conformations. The rankings of the docked mutant proteins correlated with experimental binding affinities. These results suggest that sampling multiple residue conformations and residue substitutions of the unbound ligand contributes to, but does not fully provide, a solution to the protein docking problem. Conformational sampling allows a classical atomistic scoring function to be used; such a function may contribute to better selectivity between near-native and non-native complexes. Allowing for receptor flexibility may further extend these results. [source] Structure analysis of endosialidase NF at 0.98,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2010Eike C. Schulz Endosialidase NF (endoNF) is a bacteriophage-derived endosialidase that specifically degrades ,-2,8-linked polysialic acid. The structure of a new crystal form of endoNF in complex with sialic acid has been refined at 0.98,Å resolution. The 210,kDa homotrimeric multi-domain enzyme displays outstanding stability and resistance to SDS. Even at atomic resolution, only a minor fraction of side chains possess alternative conformations. However, multiple conformations of an active-site residue imply that it has an important catalytic function in the cleavage mechanism of polysialic acid. [source] Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3,Å X-ray diffraction dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2008Eiji Nishibori Accurate structural refinement of a putative acylphosphatase using 1.3,Å X-ray diffraction data was carried out using charge densities determined by the maximum-entropy method (MEM). The MEM charge density clearly revealed detailed features of the solvent region of the putative acylphosphatase crystalline structure, some of which had never been observed in conventional Fourier maps. The structural model in the solvent region was constructed as distributions of anisotropic water atoms. The omit-difference MEM maps and the difference MEM maps were effective in revealing details of the protein structure, such as multiple conformations of the side chains of amino-acid residues, anisotropy of atoms and H atoms. By model building using the MEM charge densities, the reliability factors R1 and Rfree in the SHELX refinement were dramatically improved from 17.9% and 18.3% to 9.6% and 10.0%, respectively. The present results prove the usefulness of MEM in improving the accuracy of refinement of protein crystal structures. [source] Structures of aminoglycoside acetyltransferase AAC(6,)-Ii in a novel crystal form: structural and normal-mode analysesACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2005David L. Burk The aminoglycoside-modifying enzyme aminoglycoside 6,- N -acetyltransferase type Ii [AAC(6,)-Ii] has been crystallized with its cofactor coenzyme A in space group C2221, with unit-cell parameters a = 71.5, b = 127.4, c = 76.9,Å and one physiologically relevant dimer species per asymmetric unit. The space group previously observed for this complex was P212121, with two dimers per asymmetric unit. By comparing the six available protomer structures of the AAC(6,)-Ii,CoA complex, it has been possible to identify regions of plasticity within the protein. Normal-mode analysis of this complex suggests that this plasticity is not an artefact of crystal-packing forces, but that the region of the protomer that displays multiple conformations is intrinsically flexible. It is conjectured that the flexibility is relevant for the cooperative activity observed for the enzyme. [source] | ||||||||||