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Domain Motion (domain + motion)

Distribution by Scientific Domains

Chemistry	80%

Selected Abstracts

Observation of Protein Domain Motions by Neutron Spectroscopy

CHEMPHYSCHEM, Issue 6 2010
Michael Monkenbusch Dr.
Abstract High-resolution inelastic neutron scattering, which is available with neutron spin-echo spectroscopy (NSE) is introduced as a tool for the analysis of biomolecule ,exibility. Coherent scattering in a range where it is sensitive to length scales of nanometers and covering a time range from picoseconds to several 100 ns makes the motion of larger subdomains within proteins visible. We show that and how the internal domain motion within a protein in solution can be measured. Comparison with displacement patterns from normal mode analysis provides further insight into the nature of the geometry of the motions that lead to the oberved dynamic signature. The NSE experiment on alcohol dehydrogenase (ADH) is used as example to illustrate the general principles of the method. [source]

Control of Crystal Orientation and Piezoelectric Response of Lead Zirconate Titanate Thin Films Near the Morphotropic Phase Boundary

JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 4 2002
Ken-ichi Kakimoto
PbZr0.53Ti0.47O3 (PZT) thin films with various preferred crystallographic orientations were synthesized on various substrates using pulsed laser deposition techniques. Larger piezoelectric displacement, which involved the bending vibration of the PZT film/substrate, was observed in randomly oriented PZT thin film than that in (100)- and (111)-preferred texture films. This result was discussed by correlation with the number of effective spontaneous polarization axes in the morphotropic phase boundary of the PZT system. Moreover, polarization fatigue was found to lower the electric-field-induced displacement significantly, indicating a large contribution of ferroelectric domain motion to the piezoelectric response of PZT thin films under bipolar drive. [source]

Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp.

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009
C-1: towards understanding the mechanism of the closure of the interdomain cleft
NAD+ -dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD+ to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95,Å resolution, respectively. MorFDH is similar to the previously studied FDH from the bacterium Pseudomonas sp. 101 in overall structure, cofactor-binding mode and active-site architecture, but differs in that the eight-residue-longer C-terminal fragment is visible in the electron-density maps of MorFDH. MorFDH also differs in the organization of the dimer interface. The holo MorFDH structure supports the earlier hypothesis that the catalytic residue His332 can form a hydrogen bond to both the substrate and the transition state. Apo MorFDH has a closed conformation of the interdomain cleft, which is unique for an apo form of an NAD+ -dependent dehydrogenase. A comparison of the structures of bacterial FDH in open and closed conformations allows the differentiation of the conformational changes associated with cofactor binding and domain motion and provides insights into the mechanism of the closure of the interdomain cleft in FDH. The C-terminal residues 374,399 and the substrate (formate ion) or inhibitor (azide ion) binding are shown to play an essential role in the transition from the open to the closed conformation. [source]

Observation of Protein Domain Motions by Neutron Spectroscopy

Applications of time-resolved resonance energy transfer measurements in studies of the molecular crowding effect,

JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004
Varda Ittah
Abstract The native structures of many globular proteins are only weakly stabilized and form in solution ensembles of multiple conformers. The energy differences between the conformers are assumed to be small. This is the case of flexible multidomain proteins where domain motions were observed. High concentrations of inert macrosolute, which create a crowded or confined environment, can cause shifts of the distribution of the conformers of such proteins towards the more compact structures. This effect may also promote compact structures in partially folded proteins. Time-resolved dynamic non-radiative excitation energy transfer (tr-RET) is suitable for detection of either subtle or major changes in distributions of intramolecular distances in protein molecules in solutions. Two experiments were performed which demonstrated the applicability of tr-RET for detection of the effect of macrosolutes on the conformational ensembles of flexible states of protein molecules. The distribution of distances between residues 203 and 169 in the CORE domain of E. coli adenylate kinase (AK) in the denatured state was determined in the presence of high concentrations of dextran 40. A significant shift of the mean of the distribution was observed without reduction of its width. This was interpreted as a shift to compact structure without change of the degree of disorder of the chain. In a second experiment the distribution of the distance between residues 55 and 169 in AK, which spans the cleft between the CORE and the AMPbind domains, was monitored. No clear effect of high concentrations of dextran 40 was found. These experiments show the strength of the application of tr-RET in investigation of changes in the sub-states of flexible conformations of globular protein. Networks of pairs of labeled sites can be prepared and tr-RET experiments can be performed in order to search for the segments of the protein molecules, which respond to the presence of inert macromolecules in their environment. Copyright © 2004 John Wiley & Sons, Ltd. [source]