Initial Structural Model Research Articles

Phase transformation of Ca4[Al6O12]SO4 and its disordered crystal structure at 1073 K

The phase transformation of Ca4[Al6O12]SO4 and the crystal structure of its high-temperature phase were investigated by differential thermal analysis, temperature-dependent Raman spectroscopy and high-temperature X-ray powder diffraction (CuKα1). We determined the starting temperature of the orthorhombic-to-cubic transformation during heating (=711K) and that of the reverse transformation during cooling (=742K). The thermal hysteresis was negative (=−31K), suggesting the thermoelasticity of the transformation. The space group of the high temperature phase is I4¯3m with the unit-cell dimensions of a=0.92426(2)nm and V=0.78955(2)nm3 (Z=2) at 1073K. The initial structural model was derived by the direct methods and further refined by the Rietveld method. The final structural model showed the orientational disordering of SO4 tetrahedra. The maximum-entropy method-based pattern fitting method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. At around the transformation temperature during heating, the vibrational spectra, corresponding to the Raman-active SO4 internal stretching mode, showed the continuous and gradual change in the slope of full width at half maximum versus temperature curve. This strongly suggests that the orthorhombic-to-cubic phase transformation would be principally accompanied by the statistical disordering in orientation of the SO4 tetrahedra, without distinct dynamical reorientation.

Electron density distribution and disordered crystal structure of 8H-SiAlON, Si3−xAl1+xOxN5−x (x~2.2)

The 8H-SiAlON crystal with general formula Si3−xAl1+xOxN5−x was characterized using laboratory X-ray powder diffraction (CuKα1), transmission electron microscopy and energy dispersive X-ray spectroscopy. The [Si: Al] molar ratios were determined to be [0.21(1): 0.79(1)], corresponding to x=2.2(1). The Si0.8(1)Al3.2(1)O2.2(1)N2.8(1) compound is hexagonal with space group P63/mmc (Z=2). The unit-cell dimensions are a=0.298877(8)nm, c=2.30872(5)nm and V=0.178602(8)nm3. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of two of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The reliability indices calculated from the MPF were Rwp=4.74%, S (=Rwp/Re)=1.30, Rp=3.40%, RB=1.04% and RF=0.74%. The disordered crystal structure was successfully described by overlapping four types of domains with ordered atom arrangements. The distribution of atomic positions in each of the domains can be achieved in the space group P63mc. Two of the four types of domains are related by a pseudo-symmetry inversion, and the two remaining domains also have each other the inversion pseudo-symmetry.

Probing the U-Shaped Conformation of Caveolin-1 in a Bilayer

Caveolin induces membrane curvature and drives the formation of caveolae that participate in many crucial cell functions such as endocytosis. The central portion of caveolin-1 contains two helices (H1 and H2) connected by a three-residue break with both N- and C-termini exposed to the cytoplasm. Although a U-shaped configuration is assumed based on its inaccessibility by extracellular matrix probes, caveolin structure in a bilayer remains elusive. This work aims to characterize the structure and dynamics of caveolin-1 (D82–S136; Cav182–136) in a DMPC bilayer using NMR, fluorescence emission measurements, and molecular dynamics simulations. The secondary structure of Cav182–136 from NMR chemical shift indexing analysis serves as a guideline for generating initial structural models. Fifty independent molecular dynamics simulations (100 ns each) are performed to identify its favorable conformation and orientation in the bilayer. A representative configuration was chosen from these multiple simulations and simulated for 1 μs to further explore its stability and dynamics. The results of these simulations mirror those from the tryptophan fluorescence measurements (i.e., Cav182–136 insertion depth in the bilayer), corroborate that Cav182–136 inserts in the membrane with U-shaped conformations, and show that the angle between H1 and H2 ranges from 35 to 69°, and the tilt angle of Cav182–136 is 27 ± 6°. The simulations also reveal that specific faces of H1 and H2 prefer to interact with each other and with lipid molecules, and these interactions stabilize the U-shaped conformation.

Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations.

A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.

Caveolin in Bilayers: Can the Intramembrane U-Shaped Conformation Really Exist

Caveolin induces membrane curvature and drives the formation of caveolae that participate in many crucial cell functions such as endocytosis. The central portion of caveolin-1 contains two helices (H1 and H2) connected by a three-residue break with both N- and C-termini exposed to the cytoplasm. Although a U-shaped configuration is assumed based on its inaccessibility by extracellular matrix probes, caveolin structure in a bilayer remains elusive. This work aims to characterize the structure and dynamics of caveolin-1 (D82 to S136; Cav182-136) in a DMPC bilayer using NMR, fluorescence emission measurements, and molecular dynamics (MD) simulations. The secondary structure of Cav182-136 from NMR chemical shift indexing analysis serves as guideline for generating initial structural models. 50 independent MD simulations (80 ns each) are performed to identify its favorable conformation and orientation in the bilayer. Using the short simulations as a guideline, a representative configuration was chosen and simulated for 1 μs to further explore its stability and dynamics. The results of these simulations mirror those from the tryptophan fluorescence measurements (i.e., Cav182-136 insertion depth in the bilayer), and corroborate that Cav182-136 inserts in the membrane with a U-shaped conformation. The angle between H1 and H2 ranges from 35° to 69°, and the tilt angle of Cav182-136 is 27° ± 6°. The simulations also show that specific faces of H1 and H2 prefer to interact with each other and with lipid molecules, and these interactions stabilize the U-shaped conformation.

Experimentally Defined Structural Model of the Human Proton-Coupled Folate Transporter

Folate cofactors, Vitamin B9, play crucial roles in more than a hundred one-carbon metabolism reactions in mammalian cells. Humans cannot synthesize folates de novo and absorption through the diet is the only source of this vitamin. The proton-coupled folate transporter (PCFT) mediates this uptake in the upper small intestine by a pH-dependent process. PCFT also transports folates into the central nervous system. Point mutations in the PCFT gene cause Hereditary Folate Malabsorption (HFM), with associated hematological and neurological defects due to impaired folate transport. Certain solid tumor cell lines express high levels of PCFT mRNA. Importantly, the overall expression of PCFT is limited to only certain tissues in humans. Therefore, PCFT is a molecular target for specific delivery of anti-folate chemotherapeutic agents to tumor cells. Unfortunately, the success rate of anti-folate agents to reach clinical use is very low due to their side-effects. A structural model of PCFT can aid the development of specific anti-folate agents for their PCFT-targeted delivery and thus minimize their side-effects. To optimize and verify an initial structural model of PCFT, we applied a wide array of experimental approaches: solvent accessibility profiling through substituted cysteine accessibility scanning, studying the helix packing, and assaying the functionality of PCFT mutants. We complemented the experimental data with theoretical approaches for structure prediction such as homology modeling/threading, ligand docking and an extensive review of other secondary transporters and folate transport proteins. With these combined approaches, we have developed a structural model of PCFT that accurately reflects our experimental observations. This model forms a basis to understand the impacts of HFM mutations, and to develop folate analogues for folate deficiency intervention. Additionally, it will aid the design of PCFT structure-based anti-folate agents for the treatment of cancer.

Electron density distribution and disordered crystal structure of 15R-SiAlON, SiAl4O2N4

The crystal structure of SiAl4O2N4 was characterized by laboratory X-ray powder diffraction (CuKα1). The title compound is trigonal with space group R3̄m. The hexagonal unit-cell dimensions (Z=3) are a=0.301332(3)nm, c=4.18616(4)nm and V=0.3291825(5)nm3. The initial structural model was successfully derived by the charge-flipping method and further refined by the Rietveld method. The final structural model showed the positional disordering of one of the three (Si,Al) sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The reliability indices calculated from the MPF were Rwp=5.05%, S (=Rwp/Re)=1.21, Rp=3.77%, RB=1.29% and RF=1.01%. The disordered crystal structure was successfully described by overlapping three types of domains with ordered atom arrangements. The distribution of atomic positions in one of the three types of domains can be achieved in the space group R3̄m. The atom arrangements in the other two types of domains are noncentrosymmetrical with the space group R3m. These two structural configurations are related by the pseudo-symmetry inversion.

Structure Modeling Using Genetically Engineered Crosslinking

Class B G-protein-coupled receptors are exciting drug targets, yet the structure of a complete receptor bound to a peptide agonist has remained elusive. Coin et al. present a model of the receptor CRF1R bound to its native ligand based on partial structures and 44 spatial constraints revealed by new crosslinking approaches.

Electron density distribution and crystal structure of 21R-AlON, Al7O3N5

The crystal structure of Al7O3N5was characterized by laboratory X-ray powder diffraction (CuKα1). The title compound is trigonal with a space groupR3m(centrosymmetric). The hexagonal unit-cell dimensions (Z = 3) area = 0.305 06(1) nm,c = 5.7216(1) nm, andV = 0.461 11(2) nm3. The initial structural model was derived by the charge-flipping method and refined by the Rietveld method. The final structural model showed the positional disordering of two of the four Al sites. The maximum-entropy method-based pattern fitting method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The disordered crystal structure was successfully described by overlapping five types of domains with ordered atom arrangements. The distribution of atomic positions in one of the five types of domains can be achieved in the space groupR3m. The atom arrangements in the four other domains are non-centrosymmetric with the space groupR3m. Two of the four types of domains are related by a pseudo-symmetrical inversion, and the two remaining domains also have each other in the inversion pseudo-symmetry.

Electron density distribution and crystal structure of 27R-AlON, Al9O3N7

The crystal structure of Al 9 O 3 N 7 was characterized by laboratory X-ray powder diffraction (Cu K α 1 ). The title compound is trigonal with space group R 3̄ m (centrosymmetric). The hexagonal unit-cell dimensions ( Z =3) are a =0.30656(2) nm, c =7.2008(3) nm and V =0.58605(5) nm 3 . The initial structural model was derived by the powder charge-flipping method and subsequently refined by the Rietveld method. The final structural model showed the positional disordering of two of the five types of Al sites. The maximum-entropy method-based pattern fitting method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The disordered crystal structure was successfully described by overlapping five types of domains with ordered atom arrangements. The distribution of atomic positions in one of the five types of domains can be achieved in the space group R 3 ¯ m . The atom arrangements in the four other domains are noncentrosymmetric with the space group R 3 m . Two of the four types of domains are related by a pseudo-symmetry inversion, and the two remaining domains also have each other the inversion pseudo-symmetry. The very similar domain structure has been also reported for 21 R -AlON (Al 7 O 3 N 5 ) in our previous study. A bird’s eye view of electron densities up to 50% (0.074 nm −3 ) of the maximum on the plane parallel to (110) with the corresponding atomic arrangements of Al 9 O 3 N 7 . • Crystal structure of Al 9 O 3 N 7 is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • The maximum-entropy method-based pattern fitting method is used to confirm the validity of the model. • The disordered structure is described by overlapping five types of domains with ordered atom arrangements.

Syntheses and crystal structures of Li(Ta0.89Ti0.11)O2.945and (Li0.977Eu0.023)(Ta0.89Ti0.11)O2.968

Crystal structures of Li(Ta0.89Ti0.11)O2.945and (Li0.977Eu0.023)(Ta0.89Ti0.11)O2.968were investigated by laboratory X-ray powder diffraction. Both title compounds were trigonal with space groupR3candZ = 6. The hexagonal unit-cell dimensions werea = 0.514 82 9(2) nm,c = 1.377 61 2(4) nm, andV = 0.316 21 6(2) nm3for the former compound anda = 0.517 71 2(2) nm,c = 1.373 50 0(6) nm, andV = 0.318 81 2(3) nm3for the latter. The initial structural models, being isostructural with LiTaO3, were refined by the Rietveld method. The maximum-entropy method-based pattern fitting (MPF) method was subsequently used to confirm the validity of the structural models, in which conventional structure bias caused by assuming intensity partitioning was minimized. Atomic arrangements of the final structural models were in excellent agreement with the three-dimensional electron-density distributions determined by MPF.

Automatic model bank selection in multiple model identification of gas turbine dynamics

A multiple model structure of a prototype industrial gas turbine system is constructed under normal operation using a systematic method that incorporates non-linearity measure and H-gap metric tools with the multiple models technique. First, two new non-linearity indices for multiple input–multiple output systems are introduced and employed for decomposing the operating space of a gas turbine into some linear and non-linear modes. The non-linear modes may be further partitioned into some linear modes. The input and output data in each of the linear modes are used to construct an initial multiple model structure. In order to avoid the increase of the number of linear local models, the H-gap metric is extended to multiple input–multiple output systems and used to measure the similarity between linear local models and to merge the similar models. As a result, an algorithm is proposed for construction of multiple linear local models. The algorithm is employed for the identification of a single-shaft prototype industrial gas turbine.

Site Occupancy of the B2 Phase in Ti-25Al-zMo Alloys

The structure of the B2 phase has been investigated in Ti-25Al-30Mo, Ti-25Al-35Mo and Ti-25Al-40Mo alloys using Rietveld refinement of X-ray diffraction data in homogenized condition. Different initial structure models have been used for the refinement based on the analyzed alloy chemistry. Site occupancy models for the general alloy compositions (xTi-yAl-zMo) wherein the Ti (x) is less than 50 atom % have been proposed. The site occupancy of the B2 phase has been calculated and compared with those of earlier experimental and theoretical investigations. The lattice parameter of the B2 phase decreases with increase in Mo content at constant Al.

Synthesis and Disordered Crystal Structure of Al3O3.5C0.5

The crystal structure of Al3O3.5C0.5 (Z = 3) has been characterized by X-ray powder diffraction (XRPD), transmission electron microscopy, and electron probe microanalysis. The title compound is trigonal with space group R3̅m (centrosymmetric) and hexagonal unit-cell dimensions a = 0.29588(1) nm, c = 2.84080(7) nm, and V = 0.21538(1) nm(3). The initial structural model was determined by the charge-flipping method and subsequently refined by the Rietveld method. The final structural model showed the positional disordering of one of the two types of Al sites. The maximum-entropy method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The reliability indices calculated from the MPF were Rwp = 4.03%, S (= Rwp/Re) = 1.17, Rp = 3.08%, RB = 0.82%, and RF = 0.72%. The crystal was composed of antiphase domains, suggesting the occurrence of the high-low phase transition during the cooling process. The transition would be accompanied by the loss of unit-lattice translation, and hence the disordered structural model determined by XRPD might be of the average structure of the low-temperature phase.

Trilayer-cubic core–shell structure of PbS/EuS nanocrystals revealed by the combination of the synchrotron small-angle X-ray scattering method and energy-dispersive X-ray spectroscopy

Multilayer nanostructure analysis has been carried out for core-shell PbS/EuS nanocrystals by the combination of the synchrotron small-angle X-ray scattering (SAXS) method and energy-dispersive X-ray spectroscopy (EDS). SAXS patterns of a dilute hexane solution of the PbS/EuS nanocrystals were measured at a high signal-to-noise ratio by using synchrotron radiation. Initial structure models used for SAXS data analyses were obtained from EDS images of the particle where Eu and O atoms are localized only in the shell part of a quasi-cubic particle and, on the other hand, Pb and S atoms in the core. By simulating the intensity of SAXS using multilayer-cubic models with various core-shell electron density distributions, it was found that the particle structure was explained approximately as a trilayer-cubic model having the PbS core and the EuS/Eu2O3 shell. The diagonal length of the cubic particle was ca. 9.4 nm and the estimated thicknesses of EuS and Eu2O3 layers in the shell were ca. 1.9 and 2.9 nm at maximum, respectively.

Precise generation of systems biology models from KEGG pathways

BackgroundThe KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models.ResultsHere, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more.Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages.ConclusionsBuilding correct BioPAX and SBML signaling models from the KEGG database is a unique characteristic of the proposed method. Further, there is no other approach that is able to appropriately construct metabolic models from KEGG pathways, including correct reactions with stoichiometry. The resulting initial models, which contain valid and comprehensive SBML or BioPAX code and a multitude of cross-references, lay the foundation to facilitate further modeling steps.

From Perception to Functional Outcome in Schizophrenia

CONTEXT Schizophrenia remains a highly disabling disorder, but the specific determinants and pathways that lead to functional impairment are not well understood. It is not known whether these key determinants of outcome lie on 1 or multiple pathways. OBJECTIVE To evaluate theoretically based models of pathways to functional outcome starting with early visual perception. The intervening variables were previously established determinants of outcome drawn from 2 general categories: ability (ie, social cognition and functional capacity) and beliefs/motivation (ie, defeatist beliefs, expressive and experiential negative symptoms). We evaluated an integrative model in which these intervening variables formed a single pathway to poor outcome. DESIGN This was a cross-sectional study that applied structural equation modeling to evaluate the relationships among determinants of functional outcome in schizophrenia. SETTING Assessments were conducted at a Veterans Administration Medical Center. PARTICIPANTS One hundred ninety-one clinically stable outpatients with schizophrenia or schizoaffective disorder were recruited from the community. RESULTS A measurement model showed that the latent variables of perception, social cognition, and functional outcome were well reflected by their indicators. An initial untrimmed structural model with functional capacity, defeatist beliefs, and expressive and experiential negative symptoms had good model fit. A final trimmed model was a single path running from perception to ability to motivational variables to outcome. It was more parsimonious and had better fit indices than the untrimmed model. Further, it could not be improved by adding or dropping connections that would change the single path to multiple paths. The indirect effect from perception to outcome was significant. CONCLUSIONS The final structural model was a single pathway running from perception to ability to beliefs/motivation to outcome. Hence, both ability and motivation appear to be needed for community functioning and can be modeled effectively on the same pathway.

Leaving the labour market: the impact of exit routes from employment to retirement on health and wellbeing in old age.

The study analyses whether and to what degree specific routes into retirement affect older people, i.e. the relationship between heterogeneous exit patterns and post-retirement health and wellbeing. We used longitudinal data from two points in time; data related to t0 were collected in 1993, 1994, 1995 and 1996 and data related to t1 were collected in 2002 and 2003 (N=589). We focused on older people (55+ at t1) who were employed at t0 and retired at t1. We used confirmative factor analysis to identify identical measures of health and wellbeing at both t0 and t1. Hence, we were able to control for pre-retirement health and wellbeing when evaluating the effects of different exit routes. These routes were defined as dependence on incomes from sickness benefit, disability pension, part-time pension, unemployment insurance and active labour market programmes. Our initial structural equation model showed a clear relation between exit routes and post-retirement wellbeing. People who prior to retirement were pushed into social benefit programmes related to health and unemployment were significantly worse off as retirees, especially those with health-related benefits. However, these relationships disappeared once pre-retirement wellbeing was added to the model. Our main conclusion is that post-retirement wellbeing first and foremost is a consequence of accumulation of advantages and disadvantages during the life course. Both labour market exit routes and post-retirement wellbeing can be seen as outcomes of this process. There are no independent effects of the retirement process. Judging from our findings, there is no reason to believe that involvement in social security programmes allowing early retirement on health grounds has any additional negative consequences for health and wellbeing.

Molecular Insight into Propeptide–Protein Interactions in Cathepsins L and O

Cathepsins are mammalian papain-like cysteine proteases that play an important role in numerous physiological and pathological processes. In the present study, various molecular dynamics (MD) simulations of pro- and mature human cathepsins L and O were performed. This study is the first to report MD simulations to complement the initial model structure of (pro-)cathepsin O through conformational sampling, thus offering insight into the maturation of procathepsin O, which to date has not been described experimentally. The overall fold of (pro-)cathepsin O appears very similar to that of (pro-)cathepsin L. The propeptide binding loop (PBL)-propeptide interface of both procathepsins is found to form a stable two-stranded β-sheet. Additional stabilization of the PBL-propeptide interface is provided by hydrophobic side chain contacts in procathepsin L, whereas this seems to be due to charge-dipole interactions in procathepsin O. Introduction of two mutations (L147P and G148P) into procathepsin O entails a significant loss of hydrogen bonding, disabling formation of the interfacial β-sheet. Simulations at different protonation states suggest that procathepsin L is more sensitive to a change in pH than procathepsin O. Potential differences between the maturation of procathepsin O and procathepsin L inferred from the MD simulations might be caused by (i) stronger PBL-propeptide interactions in procathepsin O due to salt-bridge formation across the interface, (ii) more limited entropic gain of the propeptide of procathepsin O upon release into the bulk solvent due to diverse conformational states sampled in the bound state, (iii) more pronounced entropic loss of the PBL in procathepsin O upon substrate binding caused by diverse conformational states sampled in the free, mature enzyme, and (iv) lower sensitivity of procathepsin O to pH change caused by the presence of fewer carboxylate groups at the PBL-propeptide interface.

Expression, purification, crystallization and preliminary X-ray analysis of ribitol-5-phosphate cytidylyltransferase fromBacillus subtilis

TarI is a ribitol-5-phosphate cytidylyltransferase that catalyzes the formation of CDP-ribitol, which is involved in the biosynthesis of wall teichoic acids, from CTP and ribitol 5-phosphate. TarI from Bacillus subtilis (BsTarI) was purified and crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 1.78 Å and belonged to the monoclinic space group C2, with unit-cell parameters a = 103.74, b = 60.97, c = 91.80 Å, β=113.48°. The initial structural model indicated that the crystals of BsTarI contained a dimer in the asymmetric unit.