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Model Refinement (model + refinement)
Selected AbstractsCrystallization of carbohydrate oxidase from Microdochium nivaleACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2009Jarmila Du Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66,Å resolution, with unit-cell parameters a = b = 55.7, c = 610.4,Å and apparent space group P6222. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5,Å, , = 95.7°. Data sets were collected to a resolution of 2.4,Å. The structure was solved by the molecular-replacement method. Model refinement is currently in progress. [source] Crystallization and preliminary structure analysis of the blue laccase from the ligninolytic fungus Panus tigrinusACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2005Marta Ferraroni The blue laccase from the white-rot basidiomycete fungus Panus tigrinus, an enzyme involved in lignin biodegradation, has been crystallized. P. tigrinus laccase crystals grew within one week at 296,K using the sitting-drop vapour-diffusion method in 22%(w/v) PEG 4000, 0.2,M CaCl2, 100,mM Tris,HCl pH 7.5. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 54.2, b = 111.6, c = 97.1, , = 97.7°, and contain 46% solvent. A complete native data set was collected to 1.4,Å resolution at the copper edge. Molecular replacement using the Coprinus cinereus laccase structure (PDB code 1hfu) as a starting model was performed and initial electron-density maps revealed the presence of a full complement of copper ions. Model refinement is in progress. The P. tigrinus laccase structural model exhibits the highest resolution available to date and will assist in further elucidation of the catalytic mechanism and electron-transfer processes for this class of enzymes. [source] Using hybrid alignment for iterative sequence database searchesCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 9 2004Yuheng Li Abstract Progressive sequence model refinement by means of iterative searches is an effective technique for high sensitivity database searches and is currently employed in popular tools such as PSI-BLAST and SAM. Recently, a novel alignment algorithm has been proposed that offers features expected to improve the sensitivity of such iterative approaches, specifically a well-characterized theory of its statistics even in the presence of position-specific gap costs. Here, we demonstrate that the new hybrid alignment algorithm is ready to be used as the alignment core of PSI-BLAST. In addition, we evaluate the accuracy of two proposed approaches to edge effect correction in short sequence alignment statistics that turns out to be one of the crucial issues in developing a hybrid-alignment based version of PSI-BLAST. Copyright © 2004 John Wiley & Sons, Ltd. [source] A Computational Approach on the Osseointegration of Bone Implants Based on a Bio-Active Interface TheoryGAMM - MITTEILUNGEN, Issue 2 2009André Lutz Abstract In this presentation an integrated approach on the simulation of osseointegration in the boneimplant interface is outlined. Besides the consistent combination of computational bone remodelling simulation and established medical imaging techniques, a new model refinement in terms of a bioactive interface theory is introduced, which enables the simulation of bone ingrowth in rough coated uncemented implants. Under consideration of seven physiological loads of daily motion the bone-implant relative micromotion in a soft tissue region around the endoprosthesis is investigated. As the micromotions are an important factor for osseointegration, because excessive micromotion leads to apposition of fibrous tissue, they are considered for the simulation of osseointegration. Results for different parameter constellations, regarding thickness and stiffness of bone-implant interface layer, are compared and the ingrowth for different configurations is predicted. With these results conclusions can be made about the stability of prosthesis in the host bone, which is an important factor for the clinical success of the treatment (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Seasonal growth patterns of wild juvenile fish: partitioning variation among explanatory variables, based on individual growth trajectories of Atlantic salmon (Salmo salar) parrJOURNAL OF ANIMAL ECOLOGY, Issue 1 2005P. J. BACON Summary 1We present an empirical, analytical model that estimates both temperature and seasonal response functions for the growth of wild juvenile fish without the need for costly tank experiments in less realistic conditions. 2Analysis of monthly recapture data on the lengths and weights of individual wild juvenile fish demonstrates that simple temperature-driven models of growth can be less informative than more realistic, empirical, models. 3A case study of wild Atlantic salmon parr (Salmo salar) showed that: most growth took place in a 10-week period in spring, at temperatures below those that previous published models report as necessary for rapid growth and at faster rates than the maximum that previous models predicted. 4Temperature and fish size allometry explained 45% of growth variation, but the effects of temperature were significantly and markedly different at different seasons. 5Seasonal effects explained an additional 18% of the variation and were strongly associated with the abundance of potential ,drift' food. 6The seasonal patterns for growth in length and weight were different, implying differential allocation of resources to structural and reserve tissues. 7The growth patterns of sexually maturing male parr and emigrants also differed in comparison to other parr. 8Condition factor, length at first capture and seasonal interactions with both early maturity and smolting explained another 7% of the variation. 9However, individual fish did not grow consistently better, or worse, than the ,average' fish. 10This study emphasizes the necessity to test the adequacy of laboratory-based physiological models with suitably detailed field data and to focus model refinement by identifying processes which otherwise confound interpretation. [source] EXPO2009: structure solution by powder data in direct and reciprocal spaceJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2009Angela Altomare The program EXPO2009 is the evolution of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004). J. Appl. Cryst. 37, 1025,1028]. EXPO2009 performs all the steps of ab initio structure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced in EXPO2009 for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compounds, when traditional approaches like direct methods may fail. The EXPO2009 graphical interface has been optimized and made very user friendly. [source] Can a physics-based, all-atom potential find a protein's native structure among misfolded structures?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2007Abstract Recent work has shown that physics-based, all-atom energy functions (AMBER, CHARMM, OPLS-AA) and local minimization, when used in scoring, are able to discriminate among native and decoy structures. Yet, there have been only few instances reported of the successful use of physics based potentials in the actual refinement of protein models from a starting conformation to one that ends in structures, which are closer to the native state. An energy function that has a global minimum energy in the protein's native state and a good correlation between energy and native-likeness should be able to drive model structures closer to their native structure during a conformational search. Here, the possible reasons for the discrepancy between the scoring and refinement results for the case of AMBER potential are examined. When the conformational search via molecular dynamics is driven by the AMBER potential for a large set of 150 nonhomologous proteins and their associated decoys, often the native minimum does not appear to be the lowest free energy state. Ways of correcting the potential function in order to make it more suitable for protein model refinement are proposed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Laboratory evaluation of two bioenergetics models applied to yellow perch: identification of a major source of systematic errorJOURNAL OF FISH BIOLOGY, Issue 2 2003P. G. Bajer Laboratory growth and food consumption data for two size classes of age 2 year yellow perch Perca flavescens, each fed on two distinct feeding schedules at 21° C, were used to evaluate the abilities of the Wisconsin (WI) and Karas,Thoresson (KT) bioenergetics models to predict fish growth and cumulative consumption. Neither model exhibited consistently better performance for predicting fish body masses across all four fish size and feeding regime combinations. Results indicated deficiencies in estimates of resting routine metabolism by both models. Both the WI and KT models exhibited errors for predicting growth rates, which were strongly correlated with food consumption rate. Consumption-dependent prediction errors may be common in bioenergetics models and are probably the result of deficiencies in parameter values or assumptions within the models for calculating energy costs of specific dynamic action, feeding activity metabolism or egestion and excretion. Inter-model differences in growth and consumption predictions were primarily the result of differences in egestion and excretion costs calculated by the two models. The results highlighted the potential importance of parameters describing egestion and excretion costs to the accuracy of bioenergetics model predictions, even though bioenergetics models are generally regarded as being insensitive to these parameters. The findings strongly emphasize the utility and necessity of performing laboratory evaluations of all bioenergetics models for assurance of model accuracy and for facilitation of model refinement. [source] Overview and new developments in softer X-ray (2Å < , < 5Å) protein crystallographyJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004John R. Helliwell New methodologies with synchrotron radiation and X-ray free electron lasers (XFELs) in structural biology are being developed. Recent trends in harnessing softer X-rays in protein crystallography for phase determination are described. These include reference to a data-collection test at 2.6 Å wavelength with a lysozyme crystal on SRS station 7.2 (Helliwell, 1983) and also use of softer X-rays (2,Å wavelength) to optimise f," at the xenon L1 absorption edge in the Single Isomorphous Replacement Optimised Anomalous Scattering ('SIROAS') structure determination of apocrustacyanin A1 with four, partially occupied, xenon atoms (Cianci et al., 2001; Chayen et al., 2000). The hand of the protein was determined using the f," enhanced sulphur anomalous signal from six disulphides in the protein dimer of 40,kDa. In a follow-up study the single wavelength xenon L1 -edge f," optimised data set alone was used for phase determination and phase improvement by solvent flattening etc. (CCP4 DM) (Olczak et al., 2003). Auto-tracing of the protein was feasible but required additional diffraction data at higher resolution. This latter could be avoided in future by using improved tilted detector settings during use of softer X-rays, i.e. towards back-scattering recording (Helliwell, 2002). The Olczak et al. study has already led to optimisation of the new SRS beamline MPW,MAD,10 (see www.nwsgc.ac.uk) firstly involving the thinning of the beryllium windows as much as possible and planning for a MAR Research tilted detector `desk top beamline' geometry. Thus the use of softer, i.e. 2 to 3,Å wavelength range, X-rays will allow optimisation of xenon and iodine L -edge f," and enhancing of sulphur f," signals for higher throughput protein crystallography. Softer X-rays utilisation in protein crystallography includes work done on SRS bending-magnet station 7.2 in the early 1980s by the author as station scientist (Helliwell, 1984). In the future development of XFELs these softer X-ray wavelengths could also be harnessed and relax the demands to some extent on the complexity and cost of an XFEL. Thus, by use of say 4,Å XFEL radiation and use of a back-scattering geometry area detector the single molecule molecular transform could be sampled to a spatial resolution of 2,Å, sufficient, in principle, for protein model refinement (Miao et al., 1999). Meanwhile, Miao et al. (2003) report the first experimental recording of the diffraction pattern from intact Escherichia coli bacteria using coherent X-rays, with a wavelength of 2,Å, at a resolution of 30,nm and a real-space image constructed. The new single-particle X-ray diffraction-imaging era has commenced. [source] Investigations of the bond-selective response in a piezoelectric Li2SO4·H2O crystal to an applied external electric fieldACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2009O. Schmidt Piezoelectric lithium sulfate monohydrate, Li2SO4·H2O, was analyzed with respect to the relationship between the static structural properties of the crystal and its response to an external electric field. The static electron density was determined via standard low-temperature X-ray data collection at 90,(5) K using an Enraf,Nonius CAD-4 diffractometer, Mo K, radiation and multipole model refinement. Then a synchrotron-radiation experiment using the D3 beamline at HASYLAB was conducted in order to investigate the structural deformations in Li2SO4·H2O caused by an applied external electric field. In particular, the shifts of Bragg-peak positions induced by the electric field were measured and the piezoelectric constants d211, d222, d233 and d213 of Li2SO4·H2O were obtained from the shifts. With the same experimental setup the variations of more than 100 Bragg intensities were measured under an applied electric field. The data were used to refine the corresponding displacements of individual atoms within the unit cell. The distortions of the cation,anion bond lengths in the LiO4, LiO3(H2O) and SO4 tetrahedra were evaluated and then analyzed in terms of the electron-density-related properties of the Li,O and S,O bonds. The two lithium structural units were found to be strongly deformed by the applied electric field, while the SO4 tetrahedron changed less. This is in agreement with the low bond strength of the Li,O bonds. [source] On the use of logarithmic scales for analysis of diffraction dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Alexandre Urzhumtsev Predictions of the possible model parameterization and of the values of model characteristics such as R factors are important for macromolecular refinement and validation protocols. One of the key parameters defining these and other values is the resolution of the experimentally measured diffraction data. The higher the resolution, the larger the number of diffraction data Nref, the larger its ratio to the number Nat of non-H atoms, the more parameters per atom can be used for modelling and the more precise and detailed a model can be obtained. The ratio Nref/Nat was calculated for models deposited in the Protein Data Bank as a function of the resolution at which the structures were reported. The most frequent values for this distribution depend essentially linearly on resolution when the latter is expressed on a uniform logarithmic scale. This defines simple analytic formulae for the typical Matthews coefficient and for the typically allowed number of parameters per atom for crystals diffracting to a given resolution. This simple dependence makes it possible in many cases to estimate the expected resolution of the experimental data for a crystal with a given Matthews coefficient. When expressed using the same logarithmic scale, the most frequent values for R and Rfree factors and for their difference are also essentially linear across a large resolution range. The minimal R -factor values are practically constant at resolutions better than 3,Å, below which they begin to grow sharply. This simple dependence on the resolution allows the prediction of expected R -factor values for unknown structures and may be used to guide model refinement and validation. [source] A multivariate likelihood SIRAS function for phasing and model refinementACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2009Pavol Skubák A likelihood function based on the multivariate probability distribution of all observed structure-factor amplitudes from a single isomorphous replacement with anomalous scattering experiment has been derived and implemented for use in substructure refinement and phasing as well as macromolecular model refinement. Efficient calculation of a multidimensional integration required for function evaluation has been achieved by approximations based on the function's properties. The use of the function in both phasing and protein model building with iterative refinement was essential for successful automated model building in the test cases presented. [source] On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determinationACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2009Santosh Panjikar A combination of molecular replacement and single-wavelength anomalous diffraction phasing has been incorporated into the automated structure-determination platform Auto-Rickshaw. The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building. The improvement over the standard SAD or MR approaches is illustrated by ten test cases taken from the JCSG diffraction data-set database. Poor MR or SAD phases with phase errors larger than 70° can be improved using the described procedure and a large fraction of the model can be determined in a purely automatic manner from X-ray data extending to better than 2.6,Å resolution. [source] Crystallization and preliminary X-ray diffraction studies of vitamin D3 hydroxylase, a novel cytochrome P450 isolated from Pseudonocardia autotrophicaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Yoshiaki Yasutake Vitamin D3 hydroxylase (Vdh) is a novel cytochrome P450 monooxygenase isolated from the actinomycete Pseudonocardia autotrophica and consisting of 403 amino-acid residues. Vdh catalyzes the activation of vitamin D3via sequential hydroxylation reactions: these reactions involve the conversion of vitamin D3 (cholecalciferol or VD3) to 25-hydroxyvitamin D3 [25(OH)VD3] and the subsequent conversion of 25(OH)VD3 to 1,,25-dihydroxyvitamin D3 [calciferol or 1,,25(OH)2VD3]. Overexpression of recombinant Vdh was carried out using a Rhodococcus erythropolis expression system and the protein was subsequently purified and crystallized. Two different crystal forms were obtained by the hanging-drop vapour-diffusion method at 293,K using polyethylene glycol as a precipitant. The form I crystal belonged to the trigonal space group P31, with unit-cell parameters a = b = 61.7, c = 98.8,Å. There is one Vdh molecule in the asymmetric unit, with a solvent content of 47.6%. The form II crystal was grown in the presence of 25(OH)VD3 and belonged to the orthorhombic system P212121, with unit-cell parameters a = 63.4, b = 65.6 c = 102.2,Å. There is one Vdh molecule in the asymmetric unit, with a solvent content of 46.7%. Native data sets were collected to resolutions of 1.75 and 3.05,Å for form I and form II crystals, respectively, using synchrotron radiation. The structure solution was obtained by the molecular-replacement method and model refinement is in progress for the form I crystal. [source] Improvement and validation of a snow saltation model using wind tunnel measurementsEARTH SURFACE PROCESSES AND LANDFORMS, Issue 14 2008Andrew Clifton Abstract A Lagrangian snow saltation model has been extended for application to a wide variety of snow surfaces. Important factors of the saltation process, namely number of entrained particles, ejection angle and speed, have been parameterized from data in the literature. The model can now be run using simple descriptors of weather and snow conditions, such as wind, ambient pressure and temperature, snow particle sizes and surface density. Sensitivity of the total mass flux to the new parameterizations is small. However, the model refinements also allow concentration and mass flux profiles to be calculated, for comparison with measurements. Sensitivity of the profiles to the new parameterizations is considerable. Model results have then been compared with a complete set of drifting snow data from our cold wind tunnel. Simulation mass flux results agree with wind tunnel data to within the bounds of measurement uncertainty. Simulated particle sizes at 50 mm above the surface are generally larger than seen in the tunnel, probably as the model only describes particles in saltation, while additional smaller particles may be present in the wind tunnel at this height because of suspension. However, the smaller particles carry little mass, and so the impact on the mass flux is low. The use of simple input data, and parameterization of the saltation process, allows the model to be used predictively. This could include applications from avalanche warning to glacier mass balance. Copyright © 2008 John Wiley & Sons, Ltd. [source] Experimental charge-density study of paracetamol , multipole refinement in the presence of a disordered methyl groupACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009Joanna M. B A high-resolution single-crystal X-ray study of paracetamol has been performed at 85,K. Different approaches to modeling the experimental electron density (ED) were tested for the dynamically disordered portions of the molecule in order to check to what extent it is possible to obtain a proper ED distribution in the ordered part. Models were examined in which the methyl-group ED was built from pseudoatoms taken from the University at Buffalo Pseudoatom Databank or the Invariom database, with multipole parameters for the remaining atoms being obtained from free refinement. The ,, restricted multipolar model (KRMM) and free ,, refinements were compared; restriction of the ,, parameters was essential in order to obtain values of the electrostatic interaction energy consistent with the results of theoretical single-point periodic calculations. After simultaneous use of KRMM refinement and the databases to model the methyl group, the bond critical point properties and interaction electrostatic energy values were found to be closer to those obtained from theory. Additionally, some discrepancies in the ED distribution and dipole moment among transferred aspherical atom model refinements utilizing both theoretical databases and parameters from theoretical periodic calculations are shown. Including the influence of the crystal field in the periodic calculations increases the ED in the hydroxyl and amide groups, thus leading to higher values of the electrostatic interaction energy, changes in the electrostatic potential values mapped on the isodensity surface and changes in the shape of the anisotropic displacement parameters with respect to results found for both database models. [source] | |||||||||||||