bluuebunny/crossref_metadata_2025_split huggingface dataset:
E. R. Love's integral equation for the circular plate condenser
Authors: Reich Edgar 
Published: February 2009

AbstractIn a classical paper, E. R. Love considered a certain function defined by a singular integral which is harmonic outside a circular disk. Love's objective was to derive a simple integral equation whose solution leads to a useful formula for the capacitance of the condenser consisting of two parallel circular plates. We close a gap in Love's derivation by finding a new nonsingular representation of Love's singular integral which permits one to draw the required conclusions about its boundary values and thereby establishes the correctness of Love's expression for the capacitance.
On existence, uniqueness and Lr-exponential stability for stationary solutions to the MHD equations in three-dimensional domains
Authors: Zhao Chunshan , Li Kaitai 
Published: February 2009

AbstractThe existence of stationary solutions to the MHD equations in three-dimensional bounded domains will be proved. At the same time if the assumption of smallness is made on external forces, uniqueness of the stationary solutions can be guaranteed and it can be shown that any Lr (r > 3) global bounded non-stationary solution to the MHD equations approaches the stationary solution under both L2 and Lr norms exponentially as time goes to infinity.
A note on the extension of a family of biorthogonal Coifman wavelet systems
Authors: Jiang Zhuhan , Guo Xiling 
Published: February 2009

AbstractWavelet systems with a maximum number of balanced vanishing moments are known to be extremely useful in a variety of applications such as image and video compression. Tian and Wells recently created a family of such wavelet systems, called the biorthogonal Coifman wavelets, which have proved valuable in both mathematics and applications. The purpose of this work is to establish along with direct proofs a very neat extension of Tian and Wells' family of biorthogonal Coifman wavelets by recovering other “missing” members of the biorthogonal Coifman wavelet systems.
Persistence and global stability in a delayed predator-prey system with Holling-type functional response
Authors: Xu Rui , Chen Lansun , Chaplain M. A. J. 
Published: February 2009

AbstractA delayed predator-prey system with Holling type III functional response is investigated. It is proved that the system is uniformly persistent under some appropriate conditions. By means of suitable Lyapunov functionals, sufficient conditions are derived for the local and global asymptotic stability of a positive equilibrium of the system. Numerical simulations are presented to illustrate the feasibility of our main results.
Effects of velocity-slip and viscosity variation on journal bearings
Authors: Rao R. Raghavendra , Prasad K. R. 
Published: February 2009

AbstractA generalised form of the Reynolds equation for two symmetrical surfaces is derived by considering slip at the bearing surfaces. This equation is then used to study the effects of velocity-slip for the lubrication of journal bearings using half-Sommerfeld boundary conditions. Expressions for pressure and load capacity and the coefficient of friction are obtained and numerically analysed for various parameters. It is found that the load capacity decreases with slip. This is unfavourable for lubrication. The coefficient of friction decreases with a high viscous layer and increases with slip.
A fast algorithm for constructing orthogonal multiwavelets
Authors: Shouzhi Yang 
Published: February 2009

AbstractMultiwavelets possess some nice features that uniwavelets do not. A consequence of this is that multiwavelets provide interesting applications in signal processing as well as in other fields. As is well known, there are perfect construction formulas for the orthogonal uniwavelet. However, a good formula with a similar structure for multiwavelets does not exist. In particular, there are no effective methods for the construction of multiwavelets with a dilation factor a (a ≥ 2, a ∈ Z). In this paper, a procedure for constructing compactly supported orthonormal multiscaling functions is first given. Based on the constructed multiscaling functions, we then propose a method of constructing multiwavelets, which is similar to that for constructing uniwavelets. In addition, a fast numerical algorithm for computing multiwavelets is given. Compared with traditional approaches, the algorithm is not only faster, but also computationally more efficient. In particular, the function values of several points are obtained simultaneously by using our algorithm once. Finally, we give three examples illustrating how to use our method to construct multiwavelets.
Rolling of a rigid ball on a horizontal deformable surface
Authors: Brearley Maurice N. , De Mestre Neville J. 
Published: February 2009

AbstractThe rolling of a ball on a horizontal deformable surface was investigated under the assumptions that the ball was a rigid sphere and the surface was elastic. Finite strain theory was used to develop theoretical results which were found to match observations well in cases where the ball and surface involved were such as to ensure no slipping at the region of contact, including a lawn bowl rolling on a grass rink and a billiard ball rolling on carpet. The theory did not match well the behaviour of a golf ball on a grass green because the ball was too light to enforce the no-slipping condition.
Independent non-identical five-parameter gamma-Weibull variates and their sums
Authors: Leipnik Roy B. , Pearce Charles E. M. 
Published: February 2009

AbstractGamma-Weibull variates with five parameters are defined by multiplication of gamma and Weibull densities and renormalising. Sums of independent such variates are distributed as combinations of products of gammas and confluent hypergeometric functions and are explicitly determined. Sums of independent non-identical Weibulls arise as a special case. These variates can be used to model moderately extreme scenarios between gamma and Weibull that occur in many natural applications. All results are exact.
Nonnegative solutions for a heterogeneous degenerate competition model
Authors: Suárez Antonio 
Published: February 2009

AbstractThis paper deals with the existence, uniqueness and qualitative properties of nonnegative and nontrivial solutions of a spatially heterogeneous Lotka-Volterra competition model with nonlinear diffusion. We give conditions in terms of the coefficients involved in the setting of the problem which assure the existence of nonnegative solutions as well as the uniqueness of a positive solution. In order to obtain these results we employ monotonicity methods, singular spectral theory and a fixed point index.
A bioeconomic model of nonselective harvesting of two competing fish species
Authors: Purohit D. , Chaudhuri K. S. 
Published: February 2009

AbstractThis paper deals with the combined bioeconomic harvesting of two competing fish species, each of which obeys the Gompertz law of growth. The catch-rate functions are chosen so as to reflect saturation effects with respect to stock abundance as well as harvesting effort. The stability of the dynamical system is discussed and the existence of a bionomic equilibrium is examined. The optimal harvest policy is studied with the help of Pontryagin's maimum principle. The results are illustrated with the help of a numerical example.
Solution conditions can promote formation of either amyloid protofilaments or mature fibrils from the HypF N‐terminal domain
Authors: Chiti Fabrizio , Bucciantini Monica , Capanni Cristina , Taddei Niccolò , Dobson Christopher M. , Stefani Massimo 
Published: February 2009

AbstractThe HypF N‐terminal domain has been found to convert readily from its native globular conformation into protein aggregates with the characteristics of amyloid fibrils associated with a variety of human diseases. This conversion was achieved by incubation at acidic pH or in the presence of moderate concentrations of trifluoroethanol. Electron microscopy showed that the fibrils grown in the presence of trifluoroethanol were predominantly 3–5 nm and 7–9 nm in width, whereas fibrils of 7–9 nm and 12–20 nm in width prevailed in samples incubated at acidic pH. These results indicate that the assembly of protofilaments or narrow fibrils into mature amyloid fibrils is guided by interactions between hydrophobic residues that may remain exposed on the surface of individual protofilaments. Therefore, formation and isolation of individual protofilaments appears facilitated under conditions that favor the destabilization of hydrophobic interactions, such as in the presence of trifluoroethanol.
Effects of charged amino‐acid mutation on the solution structure of cytochrome b5 and binding between cytochrome b5 and cytochrome c
Authors: Qian Chengmin , Yao Yong , Ye Keqiong , Wang Jinfeng , Tang Wenxia , Wang Yunhua , Wang Wenhu , Lu Junxia , Xie Yi , Huang Zhongxian 
Published: February 2009

AbstractThe solution structure of oxidized bovine microsomal cytochrome b5 mutant (E48, E56/A, D60/A) has been determined through 1524 meaningful nuclear Overhauser effect constraints together with 190 pseudocontact shift constraints. The final family of 35 conformers has rmsd values with respect to the mean structure of 0.045±0.009 nm and 0.088±0.011 nm for backbone and heavy atoms, respectively. A characteristic of this mutant is that of having no significant changes in the whole folding and secondary structure compared with the X‐ray and solution structures of wild‐type cytochrome b5. The binding of different surface mutants of cytochrome b5 with cytochrome c shows that electrostatic interactions play an important role in maintaining the stability and specificity of the protein complex formed. The differences in association constants demonstrate the electrostatic contributions of cytochrome b5 surface negatively charged residues, which were suggested to be involved in complex formation in the Northrup and Salemme models, have cumulative effect on the stability of cyt c‐cyt b5 complex, and the contribution of Glu48 is a little higher than that of Glu44. Moreover, our result suggests that the docking geometry proposed by Northrup, which is involved in the participation of Glu48, Glu56, Asp60, and heme propionate of cytochrome b5, do occur in the association between cytochrome b5 and cytochrome c.
Motif‐based fold assignment
Authors: Salwiński Łukasz , Eisenberg David 
Published: February 2009

AbstractConventional fold recognition techniques rely mainly on the analysis of the entire sequence of a protein. We present an MBA method to improve performance of any conventional sequence‐based fold assignment. The method uses sequence motifs, such as those defined in the Prosite database, and the SwissProt annotation of the fold library. When combined with a simple SDP method, the coverage of MBA is comparable to the results obtained with PSI‐BLAST. However, the set of the MBA predictions is significantly different from that of PSI‐BLAST, leading to a 40% increase of the coverage for the combined MBA/PSI‐BLAST method. The MBA approach can be easily adopted to include the results of sequence‐independent function prediction methods and alternative motif and annotation databases. The method is available through the web server localized at http://www.doe‐mbi.ucla.edu/mba.
Structure and dynamics of translation initiation factor aIF‐1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy
Authors: Li Wei , Hoffman David W. 
Published: February 2009

AbstractTranslation initiation factor 1A (aIF‐1A) from the archaeon Methanococcus jannaschii was expressed in Escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional NMR methods. The protein was found to be a member of the OB‐fold family of RNA‐associated proteins, containing a barrel of five beta‐strands, a feature that is shared with the homologous eukaryotic translation initiation factor 1A (eIF‐1A), as well as the prokaryotic translation initiation factor IF1. External to the β barrel, aIF‐1A contains an α‐helix at its C‐terminal and a flexible loop at its N‐terminal, features that are qualitatively similar to those found in eIF‐1A, but not present in prokaryotic IF1. The structural model of aIF‐1A, when used in combination with primary sequence information for aIF‐1A in divergent species, permitted the most‐conserved residues on the protein surface to be identified, including the most likely candidates for direct interaction with the 16S ribosomal RNA and other components of the translational apparatus. Several of the conserved surface residues appear to be unique to the archaea. Nitrogen‐15 relaxation and amide exchange rate data were used to characterize the internal motions within aIF‐1A, providing evidence that the protein surfaces that are most likely to participate in intermolecular interactions are relatively flexible. A model is proposed, suggesting some specific interactions that may occur between aIF‐1A and the small subunit of the archaeal ribosome.
Surface interactions in the complex between cytochrome f and the E43Q/D44N and E59K/E60Q plastocyanin double mutants as determined by 1H‐NMR chemical shift analysis
Authors: Bergkvist Anders , Ejdebäck Mikael , Ubbink Marcellus , Karlsson B. Göran 
Published: February 2009

AbstractA combination of site‐directed mutagenesis and NMR chemical shift perturbation analysis of backbone and side‐chain protons has been used to characterize the transient complex of the photosynthetic redox proteins plastocyanin and cytochrome f. To elucidate the importance of charged residues on complex formation, the complex of cytochrome f and E43Q/D44N or E59K/E60Q spinach plastocyanin double mutants was studied by full analysis of the 1H chemical shifts by use of two‐dimensional homonuclear NMR spectra. Both mutants show a significant overall decrease in chemical shift perturbations compared with wild‐type plastocyanin, in agreement with a large decrease in binding affinity. Qualitatively, the E43Q/D44N mutant showed a similar interaction surface as wild‐type plastocyanin. The interaction surface in the E59K/E60Q mutant was distinctly different from wild type. It is concluded that all four charged residues contribute to the affinity and that residues E59 and E60 have an additional role in fine tuning the orientation of the proteins in the complex.
Crystal structure of calcium‐free human sorcin: A member of the penta‐EF‐hand protein family
Authors: Xie Xiaoling , Dwyer Maureen D. , Swenson Lora , Parker Matthew H. , Botfield Martyn C. 
Published: February 2009

AbstractSorcin is a 22 kD calcium‐binding protein that is found in a wide variety of cell types, such as heart, muscle, brain and adrenal medulla. It belongs to the penta‐EF‐hand (PEF) protein family, which contains five EF‐hand motifs that associate with membranes in a calcium‐dependent manner. Prototypic members of this family are the calcium‐binding domains of calpain, such as calpain dVI. Full‐length human sorcin has been crystallized in the absence of calcium and the structure determined at 2.2 Å resolution. Apart from an extended N‐terminal portion, the sorcin molecule has a globular shape. The C‐terminal domain is predominantly α‐helical, containing eight α‐helices and connecting loops incorporating five EF hands. Sorcin forms dimers through the association of the unpaired EF5, confirming this as the mode of association in the dimerization of PEF proteins. Comparison with calpain dVI reveals that the general folds of the individual EF‐hand motifs are conserved, especially that of EF1, the novel EF‐hand motif characteristic of the family. Detailed structural comparisons of sorcin with other members of PEF indicate that the EF‐hand pair EF1–EF2 is likely to correspond to the two physiologically relevant calcium‐binding sites and that the calcium‐induced conformational change may be modest and localized within this pair of EF‐hands. Overall, the results derived from the structural observations support the view that, in sorcin, calcium signaling takes place through the first pair of EF‐hands.
Structure and function of the bacterial mechanosensitive channel of large conductance
Authors: Oakley Aaron J. , Martinac Boris , Wilce Matthew C.J. , Martinac Boris 
Published: February 2009

AbstractMechanosensation in bacteria involves transducing membrane stress into an electrochemical response. In Escherichia coli and other bacteria, this function is carried out by a number of proteins including MscL, the mechanosensitive channel of large conductance. MscL is the best characterized of all mechanosensitive channels. It has been the subject of numerous structural and functional investigations. The explosion in experimental data on MscL recently culminated in the solution of the three‐dimensional structure of the MscL homologue from Mycobacterium tuberculosis. In this review, much of these data are united and interpreted in terms of the newly published M. tuberculosis MscL crystal structure.
Differences in the roles of conserved glutamic acid residues in the active site of human class 3 and class 2 aldehyde dehydrogenases
Authors: Mann Craig J. , Weiner Henry 
Published: February 2009

AbstractAlthough the three‐dimensional structure of the dimeric class 3 rat aldehyde dehydrogenase has recently been published (Liu ZJ et al., 1997, Nature Struct Biol 4:317–326), few mechanistic studies have been conducted on this isoenzyme. We have characterized the enzymatic properties of recombinant class 3 human stomach aldehyde dehydrogenase, which is very similar in amino acid sequence to the class 3 rat aldehyde dehydrogenase. We have determined that the rate‐limiting step for the human class 3 isozyme is hydride transfer rather than deacylation as observed for the human liver class 2 mitochondrial enzyme. No enhancement of NADH fluorescence was observed upon binding to the class 3 enzyme, while fluorescence enhancement of NADH has been previously observed upon binding to the class 2 isoenzyme. It was also observed that binding of the NAD cofactor inhibited the esterase activity of the class 3 enzyme while activating the esterase activity of the class 2 enzyme. Site‐directed mutagenesis of two conserved glutamic acid residues (209 and 333) to glutamine residues indicated that, unlike in the class 2 enzyme, Glu333 served as the general base in the catalytic reaction and E209Q had only marginal effects on enzyme activity, thus confirming the proposed mechanism (Hempel J et al., 1999, Adv Exp Med Biol 436:53‐59). Together, these data suggest that even though the subunit structures and active site residues of the isozymes are similar, the enzymes have very distinct properties besides their oligomeric state (dimer vs. tetramer) and substrate specificity.
Pressure response of protein backbone structure. Pressure‐induced amide 15N chemical shifts in BPTI
Authors: Akasaka Kazuyuki , Li Hua , Yamada Hiroaki , Li Renhao , Thoresen Todd , Woodward Clare K. 
Published: February 2009

AbstractThe effect of pressure on amide 15N chemical shifts was studied in uniformly 15N‐labeled basic pancreatic trypsin inhibitor (BPTI) in 90%H2O/10%H2O, pH 4.6, by H‐15N heteronuclear correlation spectroscopy between 1 and 2,000 bar. Most 15N signals were low field shifted linearly and reversibly with pressure (0.468 ± 0.285 ppm/2 kbar), indicating that the entire polypeptide backbone structure is sensitive to pressure. A significant variation of shifts among different amide groups (0‐1.5 ppm/2 kbar) indicates a heterogeneous response throughout within the three‐dimensional structure of the protein. A tendency toward low field shifts is correlated with a decrease in hydrogen bond distance on the order of 0.03 Å/2 kbar for the bond between the amide nitrogen atom and the oxygen atom of either carbonyl or water. The variation of 15N shifts is considered to reflect site‐specific changes in Φ, ψ angles. For β‐sheet residues, a decrease in ψ angles by 1‐2°/2 kbar is estimated. On average, shifts are larger for helical and loop regions (0.553 ± 0.343 and 0.519 ± 0.261 ppm/2 kbar, respectively) than for β‐sheet (0.295 ± 0.195 ppm/2 kbar), suggesting that the pressure‐induced structural changes (local compressibilities) are larger in helical and loop regions than in β‐sheet. Because compressibility is correlated with volume fluctuation, the result is taken to indicate that the volume fluctuation is larger in helical and loop regions than in β‐sheet. An important aspect of the volume fluctuation inferred from pressure shifts is that they include motions in slower time ranges (less than milliseconds) in which many biological processes may take place.
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites
Authors: Smalla Maika , Schmieder Peter , Kelly Mark , Laak Antonius Ter , Krause Gerd , Ball Linda , Wahl Martin , Bork Peer , Oschkinat Hartmut 
Published: February 2009

AbstractThe sterile alpha motif (SAM) is a protein interaction domain of around 70 amino acids present predominantly in the N‐ and C‐termini of more than 60 diverse proteins that participate in signal transduction and transcriptional repression. SAM domains have been shown to homo‐ and hetero‐oligomerize and to mediate specific protein‐protein interactions. A highly conserved subclass of SAM domains is present at the intracellular C‐terminus of more than 40 Eph receptor tyrosine kinases that are involved in the control of axonal pathfinding upon ephrin‐induced oligomerization and activation in the event of cell‐cell contacts. These SAM domains appear to participate in downstream signaling events via interactions with cytosolic proteins.We determined the solution structure of the EphB2 receptor SAM domain and studied its association behavior. The structure consists of five helices forming a compact structure without binding pockets or exposed conserved aromatic residues. Concentration‐dependent chemical shift changes of NMR signals reveal two distinct well‐separated areas on the domains' surface sensitive to the formation of homotypic oligomers in solution. These findings are supported by analytical ultracentrifugation studies. The conserved Tyr932, which was reported to be essential for the interaction with SH2 domains after phosphorylation, is buried in the hydrophobic core of the structure.The weak capability of the isolated EphB2 receptor SAM domain to form oligomers is supposed to be relevant in vivo when the driving force of ligand binding induces receptor oligomerization. A formation of SAM tetramers is thought to provide an appropriate contact area for the binding of a low‐molecular‐weight phosphotyrosine phosphatase and to initiate further downstream responses.
Local water bridges and protein conformational stability
Authors: Petukhov Michael , Cregut David , Soares Cláaaudio M. , Serrano Luis 
Published: February 2009

AbstractRecent studies have pointed out the important role of local water structures in protein conformational stability. Here, we present an accurate and computationally effective way to estimate the free energy contribution of the simplest water structure motif–the water bridge. Based on the combination of empirical parameters for accessible protein surface area and the explicit consideration of all possible water bridges with the protein, we introduce an improved protein solvation model. We find that accounting for water bridge formation in our model is essential to understand the conformational behavior of polypeptides in water. The model formulation, in fact, does not depend on the polypeptide nature of the solute and is therefore applicable to other flexible biomolecules (i.e., DNAs, RNAs, polysaccharides, etc.).