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Annealing Protocol (annealing + protocol)
Selected AbstractsThe structure of receptor-associated protein (RAP)PROTEIN SCIENCE, Issue 8 2007Donghan Lee Abstract The receptor-associated protein (RAP) is a molecular chaperone that binds tightly to certain newly synthesized LDL receptor family members in the endoplasmic reticulum (ER) and facilitates their delivery to the Golgi. We have adopted a divide-and-conquer strategy to solve the structures of the individual domains of RAP using NMR spectroscopy. We present here the newly determined structure of domain 2. Based on this structure and the structures of domains 1 and 3, which were solved previously, we utilized experimental small-angle neutron scattering (SANS) data and a novel simulated annealing protocol to characterize the overall structure of RAP. The results reveal that RAP adopts a unique structural architecture consisting of three independent three-helix bundles that are connected by long and flexible linkers. The flexible linkers and the quasi-repetitive structural architecture may allow RAP to adopt various possible conformations when interacting with the LDL receptors, which are also made of repetitive substructure units. [source] Synthesis and NMR solution structure of an ,-helical hairpin stapled with two disulfide bridgesPROTEIN SCIENCE, Issue 5 2000Philippe Barthe Abstract Helical coiled-coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of ,-helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites, thus allowing the engineering of novel functional miniproteins. We have synthesized a 38-amino acid peptide, ,2p8, encompassing the ,-helical hairpin present in the structure of p8MTCP1, as an ,-helical scaffold particularly promising for its stability and permissiveness of sequence mutations. The three-dimensional structure of this peptide has been solved using homonuclear two-dimensional NMR techniques at 600 MHz. After sequence specific assignment, a total of 285 distance and 29 dihedral restraints were collected. The solution structure of ,2p8 is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics, using simulated annealing protocol with the AMBER force field. The RMSD values for the backbone and all heavy atoms are 0.65 ± 0.25 and 1.51 ± 0.21 Å, respectively. Excised from its protein context, the ,-hairpin keeps its native structure: an ,-helical coiled-coil, similar to that found in superhelical structures, with two helices spanning residues 4-16 and 25,36, and linked by a short loop. This motif is stabilized by two interhelical disulfide bridges and several hydrophobic interactions at the helix interface, leaving most of its solvent-exposed surface available for mutation. This ,-helical hairpin, easily amenable to synthetic chemistry and biological expression system, may represent a stable and versatile scaffold to display new functional sites and peptide libraries. [source] Interaction of angiotensin II with the C-terminal 300,320 fragment of the rat angiotensin II receptor AT1a monitored by NMRBIOPOLYMERS, Issue 2 2003Nicola D'Amelio Abstract Interaction between angiotensin II (Ang II) and the fragment peptide 300,320 (fCT300,320) of the rat angiotensin II receptor AT1a was demonstrated by relaxation measurements, NOE effects, chemical shift variations, and CD measurements. The correlation times modulating dipolar interactions for the bound and free forms of Ang II were estimated by the ratio of the nonselective and single-selective longitudinal relaxation rates. The intermolecular NOEs observed in NOESY spectra between HN protons of 9LysfCT and 6Hisang, 10PhefCT and 8Pheang, HN proton of 3TyrfCT and H, of 4Tyrang, 5PhefCTH, and H, of 4Tyrang indicated that Ang II aromatic residues are directly involved in the interaction, as also verified by relaxation data. Some fCT300,320 backbone features were inferred by the CSI method and CD experiments revealing that the presence of Ang II enhances the existential probability of helical conformations in the fCT fragment. Restrained molecular dynamics using the simulated annealing protocol was performed with intermolecular NOEs as constraints, imposing an ,-helix backbone structure to fCT300,320 fragment. In the built model, one strongly preferred interaction was found that allows intermolecular stacking between aromatic rings and forces the peptide to wrap around the 6Leu side chain of the receptor fragment. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 134,144, 2003 [source] Metastability in multicomponent oxide transistorsPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 3 2010Warren B. Jackson Abstract Results of an investigation of bias stress metastability of multicomponent, zinc,indium and zinc,tin oxides, transistors are investigated. The bias stress as a function of various dielectrics, passivation layers, and illumination conditions indicate that for negative gate bias stressing defects often are created in the semiconductor, probably near or at the surface, particularly if the devices are unpassivated. Oxygen vacancy formation is a likely candidate. For many dielectrics, the positive gate bias metastability appears to be dominated by charge trapping within the insulator. For zinc,tin oxide devices, the kinetics of the metastability follows a stretched exponential behavior with a power law dependence on gate voltage. Correcting for the observed Meyer,Neldel behavior, the activation energy of , is about 1.2,eV for defect generation and the disorder energy from , is about 0.06,eV. By using passivation, the best gate dielectrics and annealing protocols, we have reduced the bias stress metastability to about 0.1,V for a 25,000,s stress at 22,°C. [source] | ||||||||||