bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and characterization of a caesalpinoid (Chamaecrista fasciculata) hemoglobin: The structural transition from a nonsymbiotic hemoglobin to a leghemoglobin
Authors: Gopalasubramaniam Sabarinathan K. , Kovacs Frank , Violante‐Mota Fernando , Twigg Paul , Arredondo‐Peter Raúl , Sarath Gautam 
Published: January 2008

AbstractNonsymbiotic hemoglobins (nsHbs) and leghemoglobins (Lbs) are plant proteins that can reversibly bind O2 and other ligands. The nsHbs are hexacoordinate and appear to modulate cellular concentrations of NO and maintain energy levels under hypoxic conditions. The Lbs are pentacoordinate and facilitate the diffusion of O2 to symbiotic bacteroids within legume root nodules. Multiple lines of evidence suggest that all plant Hbs evolved from a common ancestor and that Lbs originated from nsHbs. However, little is known about the structural intermediates that occurred during the evolution of pentacoordinate Lbs from hexacoordinate nsHbs. We have cloned and characterized a Hb (ppHb) from the root nodules of the ancient caesalpinoid legume Chamaecrista fasciculata. Protein sequence, modeling data, and spectral analysis indicated that the properties of ppHb are intermediate between that of nsHb and Lb, suggesting that ppHb resembles a putative ancestral Lb. Predicted structural changes that appear to have occurred during the nsHb to Lb transition were a compaction of the CD‐loop and decreased mobility of the distal His inhibiting its ability to coordinate directly with the heme‐Fe, leading to a pentacoordinate protein. Other predicted changes include shortening of the N‐ and C‐termini, compaction of the protein into a globular structure, disappearance of positive charges outside the heme pocket and appearance of negative charges in an area located between the N‐ and C‐termini. A major consequence for some of these changes appears to be the decrease in O2‐affinity of ancestral nsHb, which resulted in the origin of the symbiotic function of Lbs. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A combination of rescoring and refinement significantly improves protein docking performance
Authors: Pierce Brian , Weng Zhiping 
Published: January 2008

AbstractTo determine the structures of protein–protein interactions, protein docking is a valuable tool that complements experimental methods to characterize protein complexes. Although protein docking can often produce a near‐native solution within a set of global docking predictions, there are sometimes predictions that require refinement to elucidate correct contacts and conformation. Previously, we developed the ZRANK algorithm to rerank initial docking predictions from ZDOCK, a docking program developed by our lab. In this study, we have applied the ZRANK algorithm toward refinement of protein docking models in conjunction with the protein docking program RosettaDock. This was performed by reranking global docking predictions from ZDOCK, performing local side chain and rigid‐body refinement using RosettaDock, and selecting the refined model based on ZRANK score. For comparison, we examined using RosettaDock score instead of ZRANK score, and a larger perturbation size for the RosettaDock search, and determined that the larger RosettaDock perturbation size with ZRANK scoring was optimal. This method was validated on a protein–protein docking benchmark. For refining docking benchmark predictions from the newest ZDOCK version, this led to improved structures of top‐ranked hits in 20 of 27 cases, and an increase from 23 to 27 cases with hits in the top 20 predictions. Finally, we optimized the ZRANK energy function using refined models, which provides a significant improvement over the original ZRANK energy function. Using this optimized function and the refinement protocol, the numbers of cases with hits ranked at number one increased from 12 to 19 and from 7 to 15 for two different ZDOCK versions. This shows the effective combination of independently developed docking protocols (ZDOCK/ZRANK, and RosettaDock), indicating that using diverse search and scoring functions can improve protein docking results. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion‐dependent enzyme: Insight into the catalytic mechanism
Authors: Shi Liang , Liu Jun‐Feng , An Xiao‐Min , Liang Dong‐Cai 
Published: January 2008

AbstractGlycerophosphodiester phosphodiesterase (GDPD; EC 3.1.4.46) catalyzes the hydrolysis of a glycerophosphodiester to an alcohol and glycerol 3‐phosphate in glycerol metabolism. It has an important role in the synthesis of a variety of products that participate in many biochemical pathways. We report the crystal structure of the Thermoanaerobacter tengcongensis GDPD (ttGDPD) at 1.91 Å resolution, with a calcium ion and glycerol as a substrate mimic coordinated at this calcium ion (PDB entry 2pz0). The ttGDPD dimer with an intermolecular disulfide bridge and two hydrogen bonds is considered as the potential functional unit. We used site‐directed mutagenesis to characterize ttGDPD as a metal ion‐dependent enzyme, identified a cluster of residues involved in substrate binding and the catalytic reaction, and we propose a possible general acid‐base catalytic mechanism for ttGDPD. Superposing the active site with the homologous structure GDPD from Agrobacterium tumefaciens (PDB entry 1zcc), which binds a sulfate ion in the active site, the sulfate ion can represent the phosphate moiety of the substrate, simulating the binding mode of the true substrate of GDPD. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Detailed conformational dynamics of juxtamembrane region and activation loop in c‐Kit kinase activation process
Authors: Zou Jun , Wang Yi‐Dong , Ma Fan‐Xin , Xiang Ming‐Li , Shi Bing , Wei Yu‐Quan , Yang Sheng‐Yong 
Published: January 2008

AbstractThe stem cell factor receptor (c‐Kit) plays critical roles in initiating cell growth and proliferation. Its kinase functional abnormity has been thought to associate with several human cancers. The regulation of c‐Kit kinase activity is achieved by phosphorylation on the residues Tyr568 and Tyr570 within juxtamembrane region (JMR) and subsequent structural transition of JMR and activation loop (A‐loop). However, the detailed conformational dynamics of JMR and A‐loop are far from clear, especially whether their conformational changes are coupled or not during the kinase activation transition. In this investigation, the complete conformational transition pathway was determined using a series of nanosecond conventional molecular dynamics (MD) and targeted molecular dynamics (TMD) simulations in explicit water systems. The results of the MD simulations show that the phosphorylation of residues Tyr568 and Tyr570 within JMR induces the detachment of JMR from the kinase C‐lobe and increases the fluctuation in the structure of JMR, thus appearing to initiate the kinase activation process. During the course of the TMD simulation, which characterizes the conformational transition of c‐Kit from autoinhibitory to activated state, the JMR undergoes a rapid departure from the allosteric binding site and drifts into solvent, followed by the conformational flip of A‐loop from inactive (fold) state to active (extended) state. A change in the orientation of helix αC in response to the motion of JMR and A‐loop has also been observed. The computational results presented here indicate that the dissociation of JMR from the kinase domain is prerequisite to c‐Kit activation, which is consistent with previous experiments. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Comprehensive description of protein structures using protein folding shape code
Authors: Yang Jiaan 
Published: January 2008

AbstractUnderstanding and describing three‐dimensional (3D) protein structures have dominated biological and biochemistry research for many years. A comprehensive description of protein folding structure is essential for the advancement of protein research. In this study, a novel description method is developed to generate a set of folding patterns with specific shape features, as well as vector characteristics in space. To accomplish the goal, this method embeds features from geometry, morphology and topology together into an algorithmic approach to achieve a full description for proteins. A set of 27 vectors is derived mathematically from an enclosed space, and each vector represents a 3D folding shape of five successive Cα atoms in the protein backbone. The 27 vectors are represented by 27 symbols, which are called as the protein folding shape code (PFSC). The PFSC method offers a digital description of folding shapes along a protein backbone, which facilitates protein structure analysis. The PFSC method provides a tool to study the similarity and dissimilarity for protein or protein conformers. The PFSC results show overall agreement with structural assignments from the protein data bank, as well as results from other methods. All results show that the PFSC method is a reliable tool with explicit meaning for protein folding shape description. Protiens 2008. © 2008 Wiley‐Liss, Inc.
Molecular dynamics study of Pseudomonas aeruginosa lectin‐II complexed with monosaccharides
Authors: Mishra Navnit Kumar , Kulhánek Petr , Šnajdrová Lenka , Petřek Martin , Imberty Anne , Koča Jaroslav 
Published: January 2008

AbstractWe present the results of a series of 10‐ns molecular dynamics simulations on Pseudomonas aeruginosa lectin‐II (PA‐IIL) and its complexes with four different monosaccharides. We compare the saccharide‐free, saccharide‐occupied, and saccharide‐ and ion‐free forms of the lectin. The results are coupled with analysis of the water density map and calcium coordination. The water density pattern around the binding site in the free lectin molecular dynamics was fitted with that in the X‐ray and with the hydroxyl groups of the monosaccharide within the lectin/monosaccharide complexes and the best ligand was predicted based on the best fit. Interestingly, the water density pattern around the binding site in the uncomplexed lectin exactly fitted the O2, O3, and O4 hydroxyl groups of the fucose complex with the lectin. This observation could lead to a hypothesis that the replacement of these three water molecules from the binding site by the monosaccharide decreases the entropy of the complex and increases the entropy of the water molecules, which favors the binding. It suggests that the high density peaks of the solvent around the binding site in the free protein could be the tool to predict hydroxyl group orientation of the sugar in the protein/sugar complexes. The high affinity of PA‐IIL binding site is also attributed to the presence of two calcium ions, each of them making five to six coordinations with the protein part and two coordinations with either water or the monosaccharide. When the calcium ions are removed from the simulated system, they are replaced by sodium ions from the solvent. These observations rationalize the high binding affinity of PA‐IIL towards fucose. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Identifying stabilizing key residues in proteins using interresidue interaction energy matrix
Authors: Bendová‐Biedermannová Lada , Hobza Pavel , Vondrášek Jiří 
Published: January 2008

AbstractWe are proposing an interresidue interaction energy map (IEM) – a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair‐wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp‐cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force‐field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp‐cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein – a P12W mutant of the Trp‐cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified the thermodynamically more stable variants in both cases and therefore can also be used as a tool for the relative measurement of protein stability. Finally, we will point out the important role played by dispersion energy, which contributes significantly to the total stabilization energy and whose role in aromatic pairs is clearly dominant. Surprisingly, the dispersion energy plays an even more important role in the interaction of prolines with aromatic systems. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural properties of the DNA‐bound form of a novel tandem repeat DNA‐binding domain, STPR
Authors: Saito Shin , Yokoyama Takuya , Aizawa Tomoyasu , Kawaguchi Kyosuke , Yamaki Takeshi , Matsumoto Daisuke , Kamijima Tatsuro , Kamiya Masakatsu , Kumaki Yasuhiro , Mizuguchi Mineyuki , Takiya Sigeharu , Demura Makoto , Kawano Keiichi 
Published: January 2008

AbstractFibroin‐modulator‐binding protein 1 (FMBP‐1) is a predicted transcription factor of the silkworm fibroin gene. The DNA‐binding domain of FMBP‐1 consists of four almost perfect tandem repeats of 23 amino acids each (R1–R4), and is referred to as the score and three amino acid peptide repeat (STPR) domain. This characteristic domain is conserved in eukaryotes, but the DNA‐binding mode is not known. In this study, the structural properties of the DNA‐bound form of the STPR domain were characterized. The combined experiments indicated that the STPR domain bound to the DNA duplex with a 1:1 binding ratio. The specific DNA caused considerable changes in the thermal unfolding profile and the digestion pattern of the STPR domain. These data suggested that the domain adapts a quite rigid helix‐rich structure in the DNA‐bound state, even though it moves flexibly in the absence of DNA. Furthermore, mutual induced‐fit conformational change was also observed in DNA. Finally, we determined the DNA‐binding surface of the STPR third repeat (R3) by alanine scanning mutagenesis; a particular site, composed of hydrophobic and hydrophilic residues, was identified. Notably, the substitution of Arg‐9 in R3 with alanine residue, which is located in the middle of the surface, drastically abolished the α‐helix‐inducing and DNA‐binding abilities. From these results, we predicted the DNA‐binding mode of the STPR domain. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Real‐value prediction of backbone torsion angles
Authors: Xue Bin , Dor Ofer , Faraggi Eshel , Zhou Yaoqi 
Published: January 2008

AbstractThe backbone structure of a protein is largely determined by the ϕ and ψ torsion angles. Thus, knowing these angles, even if approximately, will be very useful for protein‐structure prediction. However, in a previous work, a sequence‐based, real‐value prediction of ψ angle could only achieve a mean absolute error of 54° (83°, 35°, 33° for coil, strand, and helix residues, respectively) between predicted and actual angles. Moreover, a real‐value prediction of ϕ angle is not yet available. This article employs a neural‐network based approach to improve ψ prediction by taking advantage of angle periodicity and apply the new method to the prediction to ϕ angles. The 10‐fold‐cross‐validated mean absolute error for the new method is 38° (58°, 33°, 22° for coil, strand, and helix, respectively) for ψ and 25° (35°, 22°, 16° for coil, strand, and helix, respectively) for ϕ. The accuracy of real‐value prediction is comparable to or more accurate than the predictions based on multistate classification of the ϕ−ψ map. More accurate prediction of real‐value angles will likely be useful for improving the accuracy of fold recognition and ab initio protein‐structure prediction. The Real‐SPINE 2.0 server is available on the website http://sparks.informatics.iupui.edu. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Terrain‐based vehicle orientation estimation combining vision and inertial measurements
Authors: Gupta Vishisht , Brennan Sean 
Published: January 2008

AbstractA novel method for estimating vehicle roll, pitch, and yaw using machine vision and inertial sensors is presented that is based on matching images captured from an on‐vehicle camera to a rendered representation of the surrounding terrain obtained from a three‐dimensional (3D) terrain map. U.S. Geographical Survey Digital Elevation Maps were used to create a 3D topology map of the geography surrounding the vehicle, and it is assumed in this work that large segments of the surrounding terrain are visible, particularly the horizon lines. The horizon lines seen in the captured video from the vehicle are compared to the horizon lines obtained from a rendered geography, allowing absolute comparisons between rendered and actual scene in roll, pitch, and yaw. A kinematic Kalman filter modeling an inertial navigation system then uses the scene matching to generate filtered estimates of orientation. Numerical simulations verify the performance of the Kalman filter. Experiments using an instrumented vehicle operating at the test track of the Pennsylvania Transportation Institute were performed to check the validity of the method. When compared to estimates from a global positioning system/inertial measurement unit (IMU) system, the roll, pitch, and yaw estimates from vision/IMU Kalman filter show an agreement with a (2σ) bound of 0.5, 0.26, and 0.8 deg, respectively. © 2008 Wiley Periodicals, Inc.
Three Dimensional Computerized Microtomography in the Analysis of Sculpture
Authors: Badde Aurelia , Illerhaus Bernhard 
Published: January 2008

AbstractThe Alte Nationalgalerie, Staatliche Museen zu Berlin (SMB) and the Federal Institute for Materials Research and Testing (BAM) tested the accomplishment of the three dimensional computerized microtomography (3D‐µCT)—a new flat panel detector computerized tomography (CT) system at the BAM with extended energy range, with high voltage X‐ray tubes (330 and 225 kV), with micrometer focal spot size and micrometer resolution and enlarged object size (up to 70 cm diameter)—for examining plaster statues.The high spatial and density resolution of the tomograph enable detailed insights into the individual work processes of the investigated cast plaster statues. While initiated in support of the conservation process, computed tomography (CT) analysis has assisted in revealing relative chronologies within the series of the cast works of art, thus serving as a valuable tool in the art‐historical appraisal of the oeuvres.The image‐processing systems visualize the voids and cracks within and the cuts through the original cast works. Internal structures, armoring, sculptural reworking as well as restorative interventions are virtually reconstructed.The authors are currently employing the 3D‐µCT systems at the BAM into the detection of defects in Carrara marble sculpture. Microcracks, fractures, and material flaws are visualized at spatial resolution down to 10µm. Computerized reconstruction of ultrasound tomography is verified by analyzing correlations in the results obtained from the complementary application of these two non‐destructive testing (NDT) methods of diagnosis. SCANNING 30: 000–000, 2008. © 2008 Wiley Periodicals, Inc.
Disciplinary authority and accountability in scientific practice and learning
Authors: Ford Michael 
Published: January 2008

AbstractThis article explores the relation between how scientific knowledge is created and the reasoning involved in learning content with understanding. Although an asserted parallel between these underpins reform, little is actually known about this relation. This article offers a model of this relation that draws coherent connections between the science studies literature, which suggests ways of conceiving how scientific knowledge is created; and sociocultural learning theory, which suggests ways of conceiving scientific reasoning. This model highlights a dialectic betweenconstructionandcritiqueof claims in both scientific reasoning and practice. A “grasp” of scientific practice as such is instrumental to learning because informational content of scientific knowledge lies not only on the level of facts, but also on the levels of methods and values, and coordinating information across these levels is crucial for understanding. In contrast to prevailing constructivist ideas that highlight studentauthorityto construct knowledge as scientists do, this model emphasizes the importance of knowing how to hold claimsaccountable. Thus, the ideal vision of students makingtheir own senseof content is superceded by a more defensible ideal vision of students learning how to makescientific senseof content. © 2008 Wiley Periodicals, Inc.Sci Ed92:404–423, 2008
Nondestructive quantitative XPS imaging of depth distribution of atoms on the nanoscale
Authors: Hajati Shaaker , Coultas Sarah , Blomfield Chris , Tougaard Sven 
Published: January 2008

AbstractIt is well known that XPS imaging based on the peak intensity gives limited quantitative information. Recently, we found Tougaard's algorithm [J. Vac. Sci. Technol. 2003; A21: 1081] very robust for automatic data processing and we made a qualitative test of its ability to give an image of the amount of substance (AOS) in the outermost few nanometers as well as images of surface and bulk localized atoms [Surf. Sci. 2006; 600: 3015]. In this work, we perform a quantitative test of the algorithm's ability to produce images of Ag taken from a series of samples with increasing thicknesses of plasma patterned octadiene (2, 4, 6 and 8 nm) on Ag substrates. The obtained images of the amount of silver atoms in the outermost few nanometers of the samples were in good agreement with the nominal thicknesses. For a given sample, different sectioning of depth distributions of atoms were made, which clearly prove the ability of the method for quantitative and nondestructive determination of in‐depth distribution of atoms. We have shown that the algorithm is suitable to make 3D image of the nanoscale. Copyright © 2008 John Wiley & Sons, Ltd.
Plasmon peak inhomogeneous broadening in reflection electron energy loss spectroscopy from carbon materials
Authors: Calliari L. , Fanchenko S. , Filippi M. 
Published: January 2008

AbstractIn addition to the damping effect on plasmon peak broadening in reflection electron energy loss spectroscopy (REELS), the effect of inhomogeneous broadening is considered. The analysis of experimental data from highly oriented pyrolytic graphite (HOPG) shows that the contribution of inhomogeneous broadening is of the same order as the contribution associated with damping. In other words, the width of plasmon peaks cannot be ascribed only to damping, which is just one among several other contributions in this respect. At variance with other broadening contributions, however, damping is responsible not only for the width of plasmon peaks but also for their energy. For this reason, by showing that accounting for inhomogeneous broadening leads to decrease of the damping parameter, we also show that the plasmon peak‐shift associated with damping is less than one could expect otherwise. Copyright © 2008 John Wiley & Sons, Ltd.