Biomedical subjects

R B Von Dreele

Publications and source records attributed to R B Von Dreele.

10 recordsLinked to original sources

PubMed2004

Binding of N-acetylglucosamine oligosaccharides to hen egg-white lysozyme: a powder diffraction study.

The binding of N-acetylglucosamine oligosaccharides (NAGn, n = 2-6) to hen egg-white lysozyme (HEWL; EC 3.2.1.17) was investigated by X-ray powder diffraction at room temperature. Each NAGn examined was found to bind to lysozyme in rapid-precipitation preparations in 1.0 M NaCl pH 6.0 buffer. The location of each NAGn was easily found from difference Fourier maps generated from structure factors extracted during preliminary Rietveld refinements. Full NAGn-protein structures were subjected to combined Rietveld and stereochemical restraint refinements (Rwp = 2.28-2.59%; Rp = 1.81-2.04%; RF2 = 3.91-5.80%) and revealed binding modes for NAGn that depended on the length of the NAG oligosaccharide. The NAG2 ligand was found in the BC sites in the cleft of HEWL, NAG3 was found to bind in both the ABC and BCD sites in the ratio 35:65 and NAG4 and NAG5 bound to the ABCD and ABCDE sites, respectively, while NAG6 only bound to sites ABCDE, leaving the F site empty with the remaining saccharide ring located in a solvent region adjacent to the A site. All protein powder diffraction patterns in this study consisted of extremely sharp Bragg peaks consistent with approximately 1 microm crystallites that were devoid of line-broadening defects. Details of the stereochemical restraints used in these refinements and their impact on structural validation are also discussed.

Acetylglucosamine↗

PubMed2001

Binding of N-acetylglucosamine to chicken egg lysozyme: a powder diffraction study.

The binding of N-acetylglucosamine (NAG) to chicken egg lysozyme (E.C. 3.2.1.17) was investigated by high-resolution X-ray powder diffraction at room temperature. NAG was found to bind to lysozyme in a rapid precipitation preparation with 0.05 M NaCl buffer pH 6.0, but not 0.05 M NaCl buffer pH 5.0. Binding was indicated by significant and readily apparent changes in the diffraction pattern from that of the apo protein precipitated from the same solvent. The location of NAG bound to lysozyme was easily found from a difference Fourier map generated from structure factors extracted during a preliminary combined Rietveld and stereochemical restraint refinement. Full protein and protein-NAG structures were refined with these techniques (R(wp) = 2.22-2.49%, R(p) = 1.79-1.95%, R(F)(2) = 4.95-6.35%) and revealed a binding mode for NAG which differed from that found in an earlier single-crystal study and probably represents a precursor trapped by rapid precipitation.

Acetylglucosamine↗

PubMed2000

Structural phase transitions of HfV2 at low temperatures.

We report a high-resolution synchrotron X-ray powder diffraction study on HfV(2), hafnium divanadium, at low temperatures. In this work we show, for the first time, a complete sequence of structural phase transitions of HfV(2) from cubic (Fd3m) to tetragonal (I4(1)/amd) to orthorhombic (Imma) in succession as temperature decreases. Peak splitting and extra diffraction peaks owing to lattice distortion can be clearly distinguished for the low-symmetry phases. The atomic positions and lattice parameters were obtained by Rietveld refinement. The bond lengths and angles of the HfV(2) crystal structure at the low-symmetry phases were correctly determined from the structure refinement. The face-centered cubic (Fd3m) unit cell (Z = 24) transforms to a body-centered tetragonal (I4(1)/amd) phase with a 45 degrees rotation relative to the cubic cell and with a reduced number of atoms (Z = 12) in the unit cell at a temperature of T = 112 K. The orthorhombic phase occurs at T = 102 K and it keeps the body-centered symmetry (Imma) and Z = 12 in the unit cell. The refinement results indicate that there may be a small amount of untransformed cubic phase left over in the lower symmetry phases. The abnormal thermal contraction of both tetragonal phase and orthorhombic phase marks the significance of structural change in HfV(2).

Journal Article↗

PubMed2000

The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding.

X-ray diffraction analysis of protein structure is often limited by the availability of suitable crystals. However, the absence of single crystals need not present an insurmountable obstacle in protein crystallography any more than it does in materials science, where powder diffraction techniques have developed to the point where complex oxide, zeolite and small organic molecular structures can often be solved from powder data alone. Here, that fact is demonstrated with the structure solution and refinement of a new variant of the T(3)R(3) Zn-human insulin complex produced by mechanical grinding of a polycrystalline sample. High-resolution synchrotron X-ray powder diffraction data were used to solve this crystal structure by molecular replacement adapted for Rietveld refinement. A complete Rietveld refinement of the 1630-atom protein was achieved by combining 7981 stereochemical restraints with a 4800-step (d(min) = 3.24 A) powder diffraction pattern and yielded the residuals R(wp) = 3.73%, R(p) = 2.84%, R(F)(2) = 8.25%. It was determined that the grinding-induced phase change is accompanied by 9.5 and 17.2 degrees rotations of the two T(3)R(3) complexes that comprise the crystal structure. The material reverts over 2-3 d to recover the original T(3)R(3) crystal structure. A Rietveld refinement of this 815-atom protein by combining 3886 stereochemical restraints with a 6000-step (d(min) = 3.06 A) powder diffraction pattern yielded the residuals R(wp) = 3.46%, R(p) = 2.64%, R(F)(2) = 7.10%. The demonstrated ability to solve and refine a protein crystal structure from powder diffraction data suggests that this approach can be employed, for example, to examine structural changes in a series of protein derivatives in which the structure of one member is known from a single-crystal study.

Humans↗

PubMed1978

Structures and moelcular motions in alkaline earth hexammines.

The alkaline earth hexammines have novel structures and molecular motions. The ammonia molecules in these compounds adopt an entirely different geometry from that of normal ammonia. There are two motional transitions as the temperature is increased. The first transition is due to ammonia rotation, and the second results from ammonia diffusion.

Magnetic Resonance Spectroscopy↗

PubMed1976