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At least 523 records · Page 29Linked to original sources
PubMed2004

The use of modified single pencil beam dose kernels to improve IMRT dose calculation accuracy.

Intensity modulated radiation therapy (IMRT) is used to deliver highly conformal radiation doses to tumors while sparing nearby sensitive tissues. Discrepancies between calculated and measured dose distributions have been reported for regions of high dose gradients corresponding to complex radiation fluence patterns. For the single pencil beam convolution dose calculation algorithm, the ability to resolve areas of high dose structure is partly related to the shape of the pencil beam dose kernel (similar to how a photon detector's point spread function relates to imaging resolution). Improvements in dose calculation accuracy have been reported when the treatment planning system (TPS) is recommissioned using high-resolution measurement data as input. This study proposes to improve the dose calculation accuracy for IMRT planning by modifying clinical dose kernel shapes already present in the TPS, thus avoiding the need to reacquire higher resolution commissioning data. The in-house optimization program minimizes a cost-function based on a two-dimensional composite dose subtraction/distance-to-agreement (gamma) analysis. The final modified kernel shapes are reintroduced into the treatment planning system and improvements to the dose calcula tion accuracy for complex IMRT dose distributions evaluated. The central kernel value (radius =0 cm) has the largest effect on the dose calculation resolution and is the focus of this study.

Algorithms↗
PubMed1992

Ribosomal proteins from Thermus thermophilus for structural investigations.

In parallel with crystallographic studies of ribosomes from Thermus thermophilus, a long-term program on the crystallization and structural investigations of ribosomal proteins from the same microorganism has been started at the Institute of Protein Research (Pushchino, Russia). At present, more than half of the individual ribosomal proteins from T thermophilus have been purified without denaturating agents on a preparative scale and some of them have been obtained in the crystalline form. X-ray structural analysis of two ribosomal proteins, L1 and S6, is being carried out jointly with the Institute of Molecular Biology (Moscow, Russia) and laboratory of professor A Liljas (Lund University, Sweden). L1 is the large protein of the large ribosomal subunit. It can bind not only to a specific site on the 23S rRNA, but also to the mRNA that codes for L1 and L11, thereby acting as a translational repressor for the synthesis of these proteins. The crystals of L1 are orthorhombic and diffract to about 2 A resolution. Native data and data for several heavy atom derivatives have been collected. S6 is a small acidic protein from the small ribosomal subunit. The crystals of S6 are orthorhombic and diffract to 2 A resolution. Native data and derivatives' data have been collected.

Amino Acid Sequence↗
PubMed1996

Anatomy of the temporal bone: detailed three-dimensional display based on image data from high-resolution helical CT: a preliminary report.

Our purpose was to demonstrate the application of helical computed tomography (CT) for computer graphics of the normal temporal bone with special regard to inner ear structures. Three-dimensional reconstruction of temporal bones was performed from helical CT data on 41 patients with various otologic diseases. Image postprocessing was carried out on an independent work station. In contrast to former surface-rendered three-dimensional visualizations of the temporal bone, a volumetric-rendering algorithm was used. This technique allows automated segmentation, thresholding, and simultaneous visualization of different planes (cube-cutting) in near-real time. We were able to demonstrate the three-dimensional display of the labyrinth during clinical routine. Anatomic details (internal auditory canal, cochlea, vestibulum, semicircular canals, distal part of the vestibular aqueduct, complete ossicular chain, fallopian canal, internal carotid canal) were comprehensively demonstrated by interactive segmentation or thresholding. Difficulties were found in three-dimensional delineation of the complete vestibular and cochlear aqueduct, as well as the modiolus. Initial experience with an advanced helical CT-based three-dimensional display showed excellent images of temporal bone anatomy. Validation studies with correlative histologic sections and surgical dissections remain to be done.

Ear, External↗
PubMed2003

Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data.

It has been shown that water molecules participate in the proton pathway of bacteriorhodopsin. Large efforts have been made to determine with various biophysical methods the number of water molecules involved. Neutron diffraction H2O/D2O exchange experiments have been often used to reveal the position of water even with low-resolution diffraction data. With this technique, care must be taken with the limitations of the difference Fourier method which are commonly applied to analyze the data. In this paper we compare the results of the difference Fourier method applied to measured diffraction data (not presented here) and models with those from alternative methods introduced here: (1) a computer model calculation procedure to determine a label's scattering length density based on a comparison of intensity differences derived from models and intensity differences from our measurements; (2) a method based on the Parseval formula. Both alternative methods have been evaluated and tested using results of neutron diffraction experiments on purple membranes (Hauss et al. 1994). Our findings indicate that the difference Fourier method applied to low-resolution diffraction data can successfully determine the position of localized water molecules but underestimates their integrated scattering length density in the presence of labels in other positions. Furthermore, we present the results of neutron diffraction experiments on purple membranes performed to determine the number of water molecules in the projected area of the Schiff base at 86%, 75% and 57% relative humidity (r.h.). We found 19 +/- 2 exchangeable protons at 75% r.h., which means at least 8-9 water molecules are indispensable for normal pump function.

Algorithms↗
PubMed2006

Evolution of Piperales--matK gene and trnK intron sequence data reveal lineage specific resolution contrast.

Piperales represent the largest basal angiosperm order with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 2000 species), Peperomia (ca. 1500-1700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of six amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogeneity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia.

Base Sequence↗
PubMed2005

Spatial orientation of the antagonist granisetron in the ligand-binding site of the 5-HT3 receptor.

The serotonin type 3 receptor (5-HT(3)R) is a member of the cys-loop ligand-gated ion channel (LGIC) superfamily. Like almost all membrane proteins, high-resolution structural data are unavailable for this class of receptors. We have taken advantage of the high degree of homology between LGICs and the acetylcholine binding protein (AChBP) from the freshwater snail Lymnea stagnalis, for which high-resolution structural data are available, to create a structural model for the extracellular (i.e., ligand-binding) domain of the 5-HT(3)R and to perform a series of ligand docking experiments to delineate the architecture of the ligand-binding site. Structural models were created using homology modeling with the AChBP as a template. Docking of the antagonist granisetron was carried out using a Lamarckian genetic algorithm to produce models of ligand-receptor complexes. Two energetically similar conformations of granisetron in the binding site were obtained from the docking simulations. In one model, the indazole ring of granisetron is near Trp90 and the tropane ring is near Arg92; in the other, the orientation is reversed. We used double-mutant cycle analysis to determine which of the two orientations is consistent with experimental data and found that the data are consistent with the model in which the indazole ring of granisetron interacts with Arg92 and the tropane ring interacts with Trp90. The combination of molecular modeling with double-mutant cycle analysis offers a powerful approach for the delineation of the architecture of the ligand-binding site.

Animals↗
PubMed2001

The 1.85 A resolution crystal structures of tissue factor in complex with humanized Fab D3h44 and of free humanized Fab D3h44: revisiting the solvation of antigen combining sites.

The outstanding importance of the antigen-antibody recognition process for the survival and defence strategy of higher organisms is in sharp contrast to the limited high resolution structural data available on antibody-antigen pairs with antigenic proteins. The limitation is the most severe for structural data not restricted to the antigen-antibody complex but extending to the uncomplexed antigen and antibody. We report the crystal structure of the complex between tissue factor (TF) and the humanized Fab fragment D3h44 at a resolution of 1.85 A together with the structure of uncomplexed D3h44 at the same resolution. In conjunction with the previously reported 1.7 A crystal structure of uncomplexed TF, a unique opportunity is generated to explore details of the recognition process. The TF.D3h44 interface is characterised by a high number of polar interactions, including as may as 46 solvent molecules. Conformational changes upon complex formation are very small and almost exclusively limited to the reorientation of side-chains. The binding epitope is in complete agreement with earlier mutagenesis experiments. A revaluation of two other antibody-antigen pairs reported at similar resolutions, shows that all these complexes are very similar with respect to the solvation of the interface, the number of solvent positions conserved in the uncomplexed and complexed proteins and the number of water molecules expelled from the surface and replaced by hydrophilic atoms from the binding partner upon complex formation. A strategy is proposed on how to exploit this high resolution structural data to guide the affinity maturation of humanised antibodies.

Amino Acid Sequence↗
PubMed2006

Spatial resolution dependence of DTI tractography in human occipito-callosal region.

Diffusion tensor imaging (DTI) and fiber tracking have been used to measure the fiber structural connectivity in humans in a non-invasive manner. However, low sensitivity is a principal limitation of these methods, causing a large number of possibly missing fiber tracts (FTs). Here we studied how the spatial resolution affects the sensitivity of the fiber tracing by rescaling data to different resolutions. Our data suggest that the spatial resolution can change the degree of the asymmetric cross-callosal connections in the lower visual field (loVF) compared to the upper visual field (upVF). Among connections from loVF, a larger voxel size resulted in a smaller number of FTs that was not commensurate to the number of seed points, while the number of connections from upVF was not significantly affected by variation in seeding point numbers. We conclude from our study that the spatial resolution of the acquired data will have to be taken into consideration in interpreting DTI fiber tracking data. Our results further suggest that the acquisition resolution of around 2 mm iso-voxel in the conventional DTI scheme can reconstruct the asymmetric upper and lower white matter structure in occipito-callosal region.

Adult↗
PubMed1995

Proteins at atomic resolution.

Experimental advances in data collection, including bright sources, cryogenic cooling and two-dimensional detectors, have made it tractable to record data to beyond 1.2 A for several proteins, yielding high-accuracy models and fine details of structure. For small metalloproteins, atomic-resolution data have enabled ab initio solution of the phase problem.

Computers↗
PubMed2006

Fat suppression with spectrally selective inversion vs. high spectral and spatial resolution MRI of breast lesions: qualitative and quantitative comparisons.

PURPOSE: To compare conventional fat-suppressed MR images of the breast to images derived from high spectral and spatial resolution MR data. Image quality and the level of fat suppression are compared qualitatively and quantitatively. MATERIALS AND METHODS: Women with suspicious breast lesions found on X-ray mammography were imaged on 1.5 Tesla GE SIGNA scanners. High spectral and spatial resolution (HiSS) data were acquired using echo-planar spectroscopic imaging. Images with intensity proportional to the water signal peak height in each voxel were synthesized. Conventional fat-suppressed images were acquired using a frequency selective inversion method. The experimental (HiSS) and conventional images were compared by experienced radiologists to evaluate the quality of fat suppression. In addition, fat suppression and image quality were evaluated quantitatively. RESULTS: Fat suppression, tumor edge delineation, lesion conspicuity, and image texture were improved in the peak height images derived from HiSS data. CONCLUSION: The results demonstrate that the water peak height images obtained from HiSS data potentially could improve the quality of fat suppression, detection and diagnosis of breast cancer. HiSS allowed detection of lesions and evaluation of lesion morphology prior to contrast media injection. J. Magn. Reson. Imaging 2006. (c) 2006 Wiley-Liss, Inc.

Adipose Tissue↗
PubMed2000

Three-dimensional structure of Chlamydomonas reinhardtii and Synechococcus elongatus photosystem II complexes allows for comparison of their oxygen-evolving complex organization.

Electron microscopy and single-particle analyses have been carried out on negatively stained photosystem II (PSII) complexes isolated from the green alga Chlamydomonas reinhardtii and the thermophilic cyanobacterium Synechococcus elongatus. The analyses have yielded three-dimensional structures at 30-A resolution. Biochemical analysis of the C. reinhardtii particle suggested it to be very similar to the light-harvesting complex II (LHCII).PSII supercomplex of spinach, a conclusion borne out by its three-dimensional structure. Not only was the C. reinhardtii LHCII.PSII supercomplex dimeric and of comparable size and shape to that of spinach, but the structural features for the extrinsic OEC subunits bound to the lumenal surface were also similar thus allowing identification of the PsbO, PsbP, and PsbQ OEC proteins. The particle isolated from S. elongatus was also dimeric and retained its OEC proteins, PsbO, PsbU, and PsbV (cytochrome c(550)), which were again visualized as protrusions on the lumenal surface of the complex. The overall size and shape of the cyanobacterial particle was similar to that of a PSII dimeric core complex isolated from spinach for which higher resolution structural data are known from electron crystallography. By building the higher resolution structural model into the projection maps it has been possible to relate the positioning of the OEC proteins of C. reinhardtii and S. elongatus with the underlying transmembrane helices of other major intrinsic subunits of the core complex, D1, D2, CP47, and CP43 proteins. It is concluded that the PsbO protein is located over the CP47 and D2 side of the reaction center core complex, whereas the PsbP/PsbQ and PsbV/PsbU are positioned over the lumenal surface of the N-terminal region of the D1 protein. However, the mass attributed to PsbV/PsbU seems to bridge across to the PsbO, whereas the PsbP/PsbQ proteins protrude out more from the lumenal surface. Nevertheless, within the resolution and quality of the data, the relative positions of the center of masses for OEC proteins of C. reinhardtii and S. elongatus are similar and consistent with those determined previously for the OEC proteins of spinach.

Animals↗
PubMed2002

Determination of a transition state at atomic resolution from protein engineering data.

We present a method for determining the structure of the transition state ensemble (TSE) of a protein by using phi values derived from protein engineering experiments as restraints in molecular dynamics simulations employing a realistic all-atom molecular mechanics energy function. The method uses a biasing potential to select an ensemble of structures having phi values in agreement with the experimental data set. An application to acylphosphatase (AcP), a protein for which phi values have been measured for 24 out of 98 residues, illustrates the approach. The properties of the TSE determined in this way are compared with those of a coarse-grained model obtained using a Monte Carlo (MC) sampling method based on a C(alpha) representation of the structure. The two TSEs determined at different structural resolution are consistent and complementary. While the C(alpha) model allows better sampling of the conformation space occupied by the transition state, the all-atom model offers a more detailed description of the structural and energetic properties of the conformations included in the TSE. The combination of low-resolution C(alpha) results with all-atom molecular dynamics simulations provides a powerful and general method for determining the nature of TSEs from protein engineering data.

Acid Anhydride Hydrolases↗
PubMed2000

Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase.

beta-Hexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of beta-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. Heritable deficiency of this enzyme results in various forms of GalNAc-beta(1,4)-[N-acetylneuraminic acid (2,3)]-Gal-beta(1,4)-Glc-ceramide gangliosidosis, including Tay-Sachs disease. We have determined the x-ray crystal structure of a beta-hexosaminidase from Streptomyces plicatus to 2.2 A resolution (Protein Data Bank code ). beta-Hexosaminidases are believed to use a substrate-assisted catalytic mechanism that generates a cyclic oxazolinium ion intermediate. We have solved and refined a complex between the cyclic intermediate analogue N-acetylglucosamine-thiazoline and beta-hexosaminidase from S. plicatus to 2.1 A resolution (Protein Data Bank code ). Difference Fourier analysis revealed the pyranose ring of N-acetylglucosamine-thiazoline bound in the enzyme active site with a conformation close to that of a (4)C(1) chair. A tryptophan-lined hydrophobic pocket envelopes the thiazoline ring, protecting it from solvolysis at the iminium ion carbon. Within this pocket, Tyr(393) and Asp(313) appear important for positioning the 2-acetamido group of the substrate for nucleophilic attack at the anomeric center and for dispersing the positive charge distributed into the oxazolinium ring upon cyclization. This complex provides decisive structural evidence for substrate-assisted catalysis and the formation of a covalent, cyclic intermediate in family 20 beta-hexosaminidases.

Acetylglucosamine↗
PubMed1992

The compact domain conformation of human Glu-plasminogen in solution.

A complete understanding of the accelerating mechanisms of plasminogen activation and fibrinolysis necessarily requires structural information on the conformational forms of plasminogen. Given the absence of high-resolution structural data on plasminogen the use of lower resolution approaches has been adopted. Two such approaches have previously indicated a compact conformation of Glu-plasminogen (Tranqui, L., Prandini, M., and Chapel, A. (1979) Biol. Cellulaire, 34, 39-42; Bányai, L. and Patthy, L. (1985) Biochim. Biophys. Acta, 832, 224-227) whereas a third has suggested a fairly extended conformation (Mangel, W., Lin, B. and Ramakrishnan, V. (1990) Science, 248, 69-73). Native Glu-plasminogen has been investigated using small-angle X-ray scattering (SAXS) experiments. It is concluded that this molecule in solution is compact (radius of gyration, RG 3.05 +/- 0.02 nm and maximum intramolecular distance, Im 9.1 +/- 0.3 nm) and that the data are consistent with the right-handed spiral structure observed using electron microscopy by Tranqui et al. (1979). A spiral structure of native plasminogen would have important implications for the conformational response of plasminogen to fibrin and concomitant stimulation of plasminogen activation.

Computer Simulation↗
PubMed1999

C-H.O hydrogen bonds in minor groove of A-tracts in DNA double helices.

Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 A) indicates that in both data sets, a majority of the (3'-Ade) H2..O2(3'-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3'-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as An.Tn and GAn.TnC tracts, which leads to a narrow minor groove in these regions.

Base Pairing↗
PubMed2004

N-Terminal domain linkage modulates the folding properties of protein S epidermal growth factor-like modules.

Protein S interacts with activated protein C to play a crucial role in blood anticoagulation, and protein S deficiency is associated with increased risk of thrombosis. Despite the large volume of functional data available for this protein, no atomic resolution structure data have yet been reported. This is due at least in part to difficulties encountered when trying to produce fragments dissected from the intact protein; however, a few successful strategies have been described. In this research we have expressed a number of constructs containing protein S epidermal growth factor-like (EGF) domains 1 and 2 in Escherichia coli and Pichia pastoris. None of the proteins produced was stably folded as assayed by solution nuclear magnetic resonance spectroscopy. We therefore constructed a series of non-native protein S EGF concatemers to investigate the role of pairwise domain linkage in domain folding. Our results demonstrate that N-terminal domain linkage can either positively or negatively impact on the refolding of an adjacent domain. Furthermore, analysis of the NMR data for EGF3-4 reveals the expected interdomain NOEs that are characteristic of an extended arrangement of calcium-binding EGF domains and a similar average [(1)H]-(15)N heteronuclear NOE value for each of the two domains. These results provide the first data in support of protein S EGF3-4 adopting the same extended domain orientation as observed for the functionally distinct proteins fibrillin-1 and the low-density lipoprotein receptor. The results also have important implications for future studies, particularly when a dissection approach is used, of tandem EGF domains from protein S and other proteins.

Amino Acid Sequence↗
PubMed1994

Cartographic mapping of the skull from computed tomography scans.

Contemporary imaging technologies (i.e., computed tomography [CT] and magnetic resonance imaging) generate an overwhelming amount of data. Salient features from these data must be abstracted and presented to facilitate anatomical comprehension and imaging utility. Three-dimensional surface and volumetric reformations of CT data have extended the integration of high resolution CT data to the study and management of craniofacial deformities. Nonetheless, conventional displays of such imaging require multiple images to assess symmetry, sutural status, and traumatic disruption of the skull. We therefore devised a methodology to apply cylindrical cartographic mapping for display of the entire skull on 1 image. Cartographic mapping was used to evaluate the skulls of patients with congenital asymmetry due to hemifacial microsomia, craniosynostosis, and complex comminuted craniofacial fractures. Cartographic mapping does effectively display the entire skull in 1 image. Such images are useful to assess craniofacial symmetry, sutural status, and comminuted fractures. However, cartographic images cannot define anterior-posterior relationships, and they must be augmented with more traditional data displays for assessment of intermaxillary and jaw-cranial base relations.

Adult↗
PubMed1993

Uniqueness and the ab initio phase problem in macromolecular crystallography.

The crystallographic phase problem is indeterminate in the absence of additional chemical information. A successful ab initio approach to the macromolecular phase problem must employ sufficient chemical constraints to limit the solutions to a manageably small number. Here we show that commonly employed chemical constraints - positivity, atomicity and a solvent boundary - leave the phase problem greatly underdetermined for Fourier data sets of moderate (2.5-3.0 A) resolution. Entropy maximization is also beset by multiple false solutions: electron-density maps are readily generated which satisfy the same Fourier amplitude constraints but have higher entropies than the true solution. We conclude that a successful ab initio approach must make use of high-resolution Fourier data and/or stronger chemical constraints. One such constraint is the connectivity of the macromolecule. We describe a rapid algorithm for measuring the connectivity of a map, and show its utility in reducing the multiplicity of solutions to the phase problem.

Journal Article↗