scholarly journals Studies on crystal structures, active-centre geometry and depurinating mechanism of two ribosome-inactivating proteins

1995 ◽  
Vol 309 (1) ◽  
pp. 285-298 ◽  
Author(s):  
Q Huang ◽  
S Liu ◽  
Y Tang ◽  
S Jin ◽  
Y Wang
Keyword(s):  
Three Dimensional ◽  
Active Centre ◽  
Ribosome Inactivating Proteins ◽  
Aromatic Stacking ◽  
Replacement Method ◽  
Isomorphous Replacement ◽  
Molecular Replacement Method ◽  
The Difference ◽  
Related Proteins ◽  
The Relationship

Two ribosome-inactivating proteins, trichosanthin and alpha-momorcharin, have been studied in the forms of complexes with ATP or formycin, by an X-ray-crystallographic method at 1.6-2.0 A (0.16-0.20 nm) resolution. The native alpha-momorcharin had been studied at 2.2 A resolution. Structures of trichosanthin were determined by a multiple isomorphous replacement method. Structures of alpha-momorcharin were determined by a molecular replacement method using refined trichosanthin as the searching model. Small ligands in all these complexes have been recognized and built on the difference in electron density. All these structures have been refined to achieve good results, both in terms of crystallography and of ideal geometry. These two proteins show considerable similarity in their three-dimensional folding and to that of related proteins. On the basis of these structures, detailed geometries of the active centres of these two proteins are described and are compared with those of related proteins. In all complexes the interactions between ligand atoms and protein atoms, including hydrophobic forces, aromatic stacking interactions and hydrogen bonds, are found to be specific towards the adenine base. The relationship between the sequence conservation of ribosome-inactivating proteins and their active-centre geometry was analysed. A depurinating mechanism of ribosome-inactivating proteins is proposed on the basis of these results. The N-7 atom of the substrate base group is proposed to be protonated by an acidic residue in the active centre.

scholarly journals Three-dimensional analysis of acetabular cup orientation and an evaluation of the relationship with pelvic sagittal parameters

2019 ◽  
Vol 27 (2) ◽  
pp. 230949901986122
Author(s):  
Ali Sahin ◽  
Mehmet Emin Simsek ◽  
Safa Gursoy ◽  
Mustafa Akkaya ◽  
Cetin Isik ◽  
...  
Keyword(s):  
Pelvic Tilt ◽  
Three Dimensional ◽  
Preoperative Assessment ◽  
Statistical Correlation ◽  
Acetabular Cup ◽  
Pelvic Parameters ◽  
Sagittal Parameters ◽  
The Mean ◽  
The Difference ◽  
The Relationship

Background: This study aimed to evaluate the effect of total hip arthroplasty (THA) on sagittal pelvic parameters and to evaluate the effect of sagittal pelvic parameters on acetabular cup orientation. Methods: The study included 86 patients who underwent THA for a diagnosis of unilateral coxarthrosis between 2011 and 2015. Measurements were taken of the preoperative and postoperative acetabular cup inclination (ACI), anteversion, and sagittal pelvic parameters. The effect of THA on sagittal pelvic parameters and the effects of the sagittal pelvic parameters on acetabular cup orientation were investigated. Results: The sagittal pelvic tilt values calculated were mean 9.7° ± 6.3° (2°; 23°) preoperatively and 11.0° ± 6.1° (2°; 25°) postoperatively. The increase in postoperative pelvic incidence (PI) values was determined to be statistically significant ( p < 0.05). The preoperative PI values had no significant effect on ACI, but in cases with high preoperative PI values, a tendency to high anteversion values was determined. The mean inclination values were found to be 40.2° ± 11.0° in the low PI group, 41.7° ± 7.4° in the normal PI group, and 44.1° ± 8.3° in the high PI group. As no increase in inclination values was observed with an increase in PI values, no statistical correlation was determined ( p = 0.343). Average of anteversion values in the low PI group was 9.2° ± 13.7°, in the normal PI group 19.3° ± 10.5°, and in the high PI group 21.1° ± 12.5°. The difference between the groups was statistically significant ( p = 0.001). Conclusion: Evaluating the results of this study, it can be concluded that varying PI values do affect the acetabular cup anterversion in THA. So, preoperative assessment of PI values is important in preventing postoperative acetabular cup malposition.

Relationship Between Weightbearing Ankle Dorsiflexion Passive Range of Motion and Ankle Kinematics During Gait

2017 ◽  
Vol 107 (1) ◽  
pp. 39-45 ◽  
Author(s):  
Min-Hyeok Kang ◽  
Jae-Seop Oh
Keyword(s):  
Range Of Motion ◽  
Three Dimensional ◽  
Knee Extension ◽  
Ankle Dorsiflexion ◽  
Physically Active ◽  
Ankle Kinematics ◽  
The Difference ◽  
Analysis System ◽  
The Relationship ◽  
Paired T Test

Background: Measurement of weightbearing ankle dorsiflexion (DF) passive range of motion (PROM) has been suggested as a way to estimate ankle kinematics during gait; however, no previous study has demonstrated the relationship between ankle DF during gait and ankle DF PROM with knee extension. We examine the relationship between maximum ankle DF during gait and nonweightbearing and weightbearing ankle DF PROM with knee extension. Methods: Forty physically active individuals (mean ± SD age, 21.63 ± 1.73 years) participated in this study. Ankle DF PROM with knee extension was measured in the nonweightbearing and weightbearing conditions; maximum ankle DF during gait was assessed using a three-dimensional motion analysis system. The relationship between each variable was calculated using the Pearson product moment correlation coefficient, and the difference in ankle DF PROM between the nonweightbearing and weightbearing conditions was analyzed using a paired t test. Results: The weightbearing measurement (r = 0.521; P &lt; .001) for ankle DF PROM showed a greater correlation with maximum ankle DF during gait than did the nonweightbearing measurement (r = 0.245; P = .029). Ankle DF PROM was significantly greater in the weightbearing than in the nonweightbearing condition (P &lt; .001) despite a significant correlation between the two measurements (r = 0.402; P &lt; .001). Conclusions: These findings indicate that nonweightbearing and weightbearing measurements of ankle DF PROM with knee extension should not be used interchangeably and that weightbearing ankle DF PROM with the knee extended is more appropriate for estimating ankle DF during gait.

Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template

1998 ◽  
Vol 54 (1) ◽  
pp. 86-89 ◽  
Author(s):  
Peer R. E. Mittl ◽  
Patrick Chène ◽  
Markus G. Grütter
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Additional Information ◽  
Nmr Structures ◽  
Replacement Method ◽  
Tetramerization Domain ◽  
Structure Solution ◽  
Molecular Replacement Method

The molecular replacement method is a powerful technique for crystal structure solution but the use of NMR structures as templates often causes problems. In this work the NMR structure of the p53 tetramerization domain has been used to solve the crystal structure by molecular replacement. Since the rotation- and translation-functions were not sufficiently clear, additional information about the symmetry of the crystal and the protein complex was used to identify correct solutions. The three-dimensional structure of residues 326–356 was subsequently refined to a final R factor of 19.1% at 1.5 Å resolution.

Three-dimensional structure of β-momorcharin at 2.55 Å resolution

1999 ◽  
Vol 55 (6) ◽  
pp. 1144-1151 ◽  
Author(s):  
Yu-Ren Yuan ◽  
Yong-Ning He ◽  
Jian-Ping Xiong ◽  
Zong-Xiang Xia
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Ribosome Inactivating Protein ◽  
Three Dimensional Structure ◽  
Replacement Method ◽  
Enzymatic Function ◽  
Molecular Replacement Method

β-Momorcharin (Mr ≃ 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of β-momorcharin has been determined using the molecular-replacement method and refined to 2.55 Å resolution. The final structural model gave an R factor of 17.2% and root-mean-square deviations of 0.016 Å and 1.76° from ideal bond lengths and bond angles, respectively. β-Momorcharin contains nine α-helices, two 310 helices and three β-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of β-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, β-GlcNAc–(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each β-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.

The Structure of haemoglobin - VII. Determination of phase angles in the non-centrosymmetric [100] zone

1958 ◽  
Vol 247 (1250) ◽  
pp. 302-336 ◽  
Keyword(s):  
Standard Error ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Anomalous Scattering ◽  
Heavy Atoms ◽  
Replacement Method ◽  
Isomorphous Replacement ◽  
Arbitrary Phase ◽  
Phase Angles

In the last paper in this series a Fourier projection down the [010] axis of horse haemoglobin was given (Bragg & Perutz 1954). This projection was centrosymmetric. As a first step towards the three-dimensional analysis, the projection down [100] has now been attacked. This projection is non-centrosymmetric, and arbitrary phase angles have had to be determined. All the fundamental problems of a three-dimensional study are met, but only a small number of reflexions need be dealt with. The isomorphous replacement method has been used successfully with three mercury derivatives of haemoglobin. This provided a test of new methods for finding the vectors relating heavy atoms. Particular attention has been given to estimation of errors, and to their effect on the results. Further information about the phases has been derived from anomalous scattering by the mercury atoms, using CrKα and CuKα radiation. By combining these results, the phases of most reflexions out to a spacing of about 6 Å have been determined with a standard error of about 25°. Ambiguous results are obtained for a few reflexions. The resulting electron density projection shows peaks up to four times the estimated standard error. The prospects for three-dimensional structure analysis at 6 Å resolution are favourable. If the polypeptide chain is coiled in the α-form, the contrast should be sufficient for it to show up throughout its length.

The Sahara

2017 ◽  
Author(s):  
Barbara E. Barich
Keyword(s):  
Human Body ◽  
Manufacturing Process ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Dimensional Representation ◽  
Three Dimensional Representation ◽  
The Difference ◽  
Symbolic Content ◽  
The Relationship

This chapter discusses the collection of objects, in clay and stone, from various pastoral Saharan sites whose original core area lay between Libya (Tadrart Acacus) and Algeria (Tassili- n-Ajjer). The chapter starts from the general theme of the relationship between the figurines and the subjects they represent, and the difference between two-dimensional and three-dimensional representation. It goes on to discuss the manufacturing process of the clay specimens (dating from between 7000 and 4000 years ago) and the significance of the changes introduced by the Neolithic. Most of the items studied fall into the category of zoomorphic figurines, with only two anthropomorphic examples, and find in the depiction of cattle their most striking subject. These representations possess an evident symbolic content which must be framed within the pastoral ideology of the Saharan Neolithic. In the anthropomorphic figurines the representation of the human body also plays the role of recapturing the sense of wholeness.

Three-dimensional solution structure of plastocyanin from the green alga Scenedesmus obliquus

Science ◽  
1988 ◽  
Vol 240 (4850) ◽  
pp. 314-317 ◽  
Author(s):  
JM Moore ◽  
DA Case ◽  
WJ Chazin ◽  
GP Gippert ◽  
TF Havel ◽  
...  
Keyword(s):  
Green Alga ◽  
Solution Structure ◽  
Distance Geometry ◽  
Scenedesmus Obliquus ◽  
Three Dimensional ◽  
Higher Plant ◽  
Dimensional Solution ◽  
Replacement Method ◽  
Inorganic Complexes ◽  
Molecular Replacement Method

The solution conformation of plastocyanin from the green alga Scenedesmus obliquus has been determined from distance and dihedral angle constraints derived by nuclear magnetic resonance (NMR) spectroscopy. Structures were generated with distance geometry and restrained molecular dynamics calculations. A novel molecular replacement method was also used with the same NMR constraints to generate solution structures of S. obliquus plastocyanin from the x-ray structure of the homologous poplar protein. Scenedesmus obliquus plastocyanin in solution adopts a beta-barrel structure. The backbone conformation is well defined and is similar overall to that of poplar plastocyanin in the crystalline state. The distinctive acidic region of the higher plant plastocyanins, which functions as a binding site for electron transfer proteins and inorganic complexes, differs in both shape and charge in S. obliquus plastocyanin.

Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms

1999 ◽  
Vol 55 (2) ◽  
pp. 408-413 ◽  
Author(s):  
Shintaro Misaki ◽  
Yukio Morimoto ◽  
Mari Ogata ◽  
Tatsuhiko Yagi ◽  
Yoshiki Higuchi ◽  
...  
Keyword(s):  
Anaerobic Bacteria ◽  
Desulfovibrio Vulgaris ◽  
Water Molecules ◽  
Active Centre ◽  
Crystallographic Form ◽  
Crystal Forms ◽  
Replacement Method ◽  
Intermolecular Contacts ◽  
Molecular Replacement Method

The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 Å; form II, P21, a = 27.3, b = 44.9, c = 51.2 Å and β = 90.6°) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 Å to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 Å resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 32 symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 32 axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.

scholarly journals Improvements to Reference Systems and Their Relationships

1995 ◽  
Vol 166 ◽  
pp. 309-314
Author(s):  
P. K. Seidelmann
Keyword(s):  
Reference Frame ◽  
Reference Frames ◽  
Three Dimensional ◽  
Reference Systems ◽  
Basic Frame ◽  
Dynamical Time ◽  
Optical Wavelengths ◽  
The Difference ◽  
The Relationship ◽  
Optical Radar

Reference Systems include the reference frames and their relationships, time arguments, ephemerides, and the standard constants and algorithms.The extragalactic, or radio, reference frame will be the basic frame. Achieving milli to microarcsecond accuracies at optical wavelengths will reduce the disparity between optical, radar, and radio reference frame determinations. Thus, the relationships and identifications of common sources should be much more accurate. Another significant change should be the ability to determine distances, and thus space motions on a three-dimensional basis, rather than the current two-dimensional basis of proper motions.Improvements in ephemerides provide the opportunity to investigate the difference between atomic and dynamical time, the relationship between the dynamical and extragalactic reference frame and the values of precession and nutation.Also, the relationships between the bright and faint optical catalogs, the infrared, and extragalactic reference frames should be better determined. Reference frames at other wavelengths will become determinable.

scholarly journals Crystal structure of the starch-binding domain of glucoamylase fromAspergillus niger

2017 ◽  
Vol 73 (10) ◽  
pp. 550-554 ◽  
Author(s):  
Yousuke Suyama ◽  
Norifumi Muraki ◽  
Masami Kusunoki ◽  
Hideo Miyake
Keyword(s):  
Disulfide Bond ◽  
Expression System ◽  
Binding Domain ◽  
Map Comparison ◽  
X Ray ◽  
Replacement Method ◽  
Glucose Syrup ◽  
Significant Difference ◽  
Molecular Replacement Method ◽  
The Difference

Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase fromAspergillus nigeris a small globular protein containing a disulfide bond. The structure ofA. nigerSBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from anEscherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the Cαatom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, theBfactors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.

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