bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability
Authors: Usher Ken C. , De La Cruz Aida Flor A. , Dahlquist Fredrick W. , James Remington S. , Swanson Ronald V. , Simon Melvin I. 
Published: July 2010

AbstractThe crystal structure of CheY protein from Thermotoga maritime has been determined in four crystal forms with and without Mg++ bound, at up to 1.9 resolution. Structural comparisons with CheY from Escherichia coli shows substantial similarity in their folds, with some concerted changes propagating away from the active site that suggest how phosphorylated CheY, a signal transduction protein in bacterial chemotaxis, is recognized by its targets. A highly conserved segment of the protein (the “‐γ‐turn loop,” residues 55‐61), previously suggested to be a rigid recognition determinant, is for the first time seen in two alternative conformations in the different crystal structures. Although CheY from Thermotoga has much higher thermal stability than its mesophilic counterparts, comparison of structural features previously proposed to enhance thermostability such as hydrogen bonds, ion pairs, compactness, and hydrophobic surface burial would not suggest it to be so.
Formation and movement of Fe(III) in horse spleen, H‐ and L‐recombinant ferritins. A fluorescence study
Authors: Cavallo Stefano , Mei Giampiero , Stefanini Simonetta , Rosato Nicola , Finazzi‐Agró Alessandro , Chiancone Emilia 
Published: July 2010

AbstractIron oxidation and incorporation into apoferritins of different subunit composition, namely the recombinant H and L homopolymers and the natural horse spleen heteropolymer (10‐15% H), have been followed by steady‐state and time‐resolved fluorescence. After aerobic addition of 100 Fe(II) atoms/polymer, markedly different kinetic profiles are observed. In the rL‐homopolymer a slow monotonic fluorescence quenching is observed which reflects binding, slow oxidation at the threefold apoferritin channels, and diffusion into the protein cavity. In the rH‐homopolymer a fast fluorescence quenching is followed by a partial, slow recovery. The two processes have been attributed to Fe(II) binding and oxidation at the ferroxidase centers and to Fe(III) released into the cavity, respectively. The fluorescence kinetics of horse spleen apoferritin is dominated by the H chain contribution and resembles that of the H homopolymer. It brings out clearly that the rate of the overall process is limited by the rate at which Fe(III) leaves the ferroxidase centers of the H chains where binding of incoming Fe(II) and its oxidation take place. The data obtained upon stepwise addition of iron and the results of optical absorption measurements confirm this picture. The correspondence between steady‐state and time‐resolved data is remarkably good; this is manifest when the latter are used to calculate the change in fluorescence intensity as apparent in the steady‐state measurements.
Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
Authors: Gerstein Mark , Levitt Michael 
Published: July 2010

AbstractWe apply a simple method for aligning protein sequences on the basis of a 3D structure, on a large scale, to the proteins in the scop classification of fold families. This allows us to assess, understand, and improve our automatic method against an objective, manually derived standard, a type of comprehensive evaluation that has not yet been possible for other structural alignment algorithms. Our basic approach directly matches the backbones of two structures, using repeated cycles of dynamic programming and least‐squares fitting to determine an alignment minimizing coordinate difference. Because of simplicity, our method can be readily modified to take into account additional features of protein structure such as the orientation of side chains or the location‐dependent cost of opening a gap. Our basic method, augmented by such modifications, can find reasonable alignments for all but 1.5% of the known structural similarities in scop, i.e., all but 32 of the 2,107 superfamily pairs. We discuss the specific protein structural features that make these 32 pairs so difficult to align and show how our procedure effectively partitions the relationships in scop into different categories, depending on what aspects of protein structure are involved (e.g., depending on whether or not consideration of side‐chain orientation is necessary for proper alignment). We also show how our pairwise alignment procedure can be extended to generate a multiple alignment for a group of related structures. We have compared these alignments in detail with corresponding manual ones culled from the literature. We find good agreement (to within 95% for the core regions), and detailed comparison highlights how particular protein structural features (such as certain strands) are problematical to align, giving somewhat ambiguous results. With these improvements and systematic tests, our procedure should be useful for the development of scop and the future classification of protein folds. Supplementary material is available at http://bioinfo.mbb.yale.edu/align.
Purification and crystallization of the CDK‐associated protein phosphatase KAP expressed in escherichia coli
Authors: Hanlon Neil , Barford David 
Published: July 2010

AbstractThe kinase associated phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates the cell cycle control protein, cyclin dependent kinase‐2 on Thr 160 in a cyclin dependent manner (Poon & Hunter, 1995). We report here the over‐expression of KAP in Escherichia coli as an N‐terminal His‐tagged protein using a modified pET‐28a T7‐expression vector. The recombinant protein was purified to homogeneity and crystallized. The crystals diffract to 2.3 Ǎ resolution when exposed to synchrotron radiation and belong to space group P6122, or its enantiomorph P6522, with unit cell dimensions a= b 74.5 Ǎ, c = 139.5 Ǎ.
Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: A 2.2 Å resolution structure in a hexagonal crystal form
Authors: Yan Youwei , Li Ying , Munshi Sanjeev , Sardana Vinod , Cole James L. , Sardana Mohinder , Kuo Lawarence C. , Chen Zhongguo , Steinkuehler Christian , Tomei Licia , Francesco Raffaele De 
Published: July 2010

AbstractThe crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6322 to a resolution of 2.2 Å. This protease is bound with a 14‐mer peptide representing the central region of the NS4A protein. There are two molecules of the NS31_180‐NS4A21′‐34′ complex per asymmetric unit. Each displays a familiar chymotrypsin‐like fold that includes two β‐barrel domains and four short α‐helices. The catalytic triad (Ser‐139, His‐57, and Asp‐81) is located in the crevice between the β‐barrel domains. The NS4A peptide forms an almost completely enclosed peptide surface association with the protease. In contrast to the reported H strain complex of NS3 protease‐NS4A peptide in a trigonal crystal form (Kim JL et al., 1996, Cell 87:343‐355), the N‐terminus of the NS3 protease is well‐ordered in both molecules in the asymmetric unit of our hexagonal crystal form. The folding of the N‐terminal region of the NS3 protease is due to the formation of a three‐helix bundle as a result of crystal packing. When compared with the unbound structure (Love RA et al., 1996, Cell 87:331‐342), the binding of the NS4A peptide leads to the ordering of the N‐terminal 28 residues of the NS3 protease into a β‐strand and an α‐helix and also causes local rearrangements important for a catalytically favorable conformation at the active site. Our analysis provides experimental support for the proposal that binding of an NS4A‐mimicking peptide, which increases catalytic rates, is necessary but not sufficient for formation of a well‐ordered, compact and, hence, highly active protease molecule.
Heterogeneity of packing: Structural approach
Authors: Kurochkina Natalya , Privalov George 
Published: July 2010

AbstractAnalysis of the heterogeneity of packing in proteins showed that different groups of the protein preferentially contribute to low‐ or high‐density regions. Statistical distribution reveals the two preferable values for packing density in the form of two peaks. One peak occurs in the range of densities 0.55‐0.65, the other occurs in the range 0.75‐0.8. The high‐density peak is originated primarily by high packing inside the hydrogen bonded backbone and to some extent by side chains. Polar/charged and apolar side chains both contribute to the low‐density peak. The average packing density values of individual atomic groups significantly vary for backbone atoms as well as for side chain atoms. The carbonyl oxygen atoms of protein backbone and the end groups of side chains show lower packing density than the rest of the protein. The side‐chain atomic groups of a secondary structure element when packed against the neighboring secondary structure element form stronger contacts with the side chains of this element than with its backbone. Analysis of the low‐density regions around each buried peptide group was done for the set of proteins with different types of packing, including α‐α, α‐β, and β‐β packing. It was shown that cavities are regularly situated in the groove of secondary structure element packed against neighboring elements for all types of packing. Low density in the regions surrounding the peptide groups and the end groups of side chains can be explained by their positioning next to a cavity formed upon the association of secondary structure elements. The model proposed can be applied to the analysis of protein internal motions, mechanisms of cellular signal transduction, diffusion through protein matrix, and other events.
A cognate tRNA specific conformational change in glutaminyl‐tRNA synthetase and its implication for specificity
Authors: Mandal Amit Kumar , Bhattacharyya Anusree , Bhattacharyya Subhra , Bhattacharyya Tista , Roy Siddhartha 
Published: July 2010

AbstractConformational changes that occur upon substrate binding are known to play crucial roles in the recognition and specific aminoacylation of cognate tRNA by glutaminyl‐tRNA synthetase. In a previous study we had shown that glutaminyl‐tRNA synthetase labeled selectively in a nonessential sulfhydryl residue by an environment sensitive probe, acrylodan, monitors many of the conformational changes that occur upon substrate binding. In this article we have shown that the conformational change that occurs upon tRNAGln binding to glnRS/ATP complex is absent in a noncognate tRNA tRNAGlu‐glnRS/ATP complex. CD spectroscopy indicates that this cognate tRNAGln‐induced conformational change may involve only a small change in secondary structure. The Van't Hoff plot of cognate and noncognate tRNA binding in the presence of ATP is similar, suggesting similar modes of interaction. It was concluded that the cognate tRNA induces a local conformational change in the synthetase that may be one of the critical elements that causes enhanced aminoacylation of the cognate tRNA over the noncognate ones.
Crystallization and preliminary X‐ray analysis of a 1:1 complex between a designed monomeric interferon‐gamma and its soluble receptor
Authors: Randal M. , Kossiakoff A. A. 
Published: July 2010

AbstractA variant of human interferon‐gamma (IFN‐γ) has been created in which the two chains of the homodimeric cytokine were linked N‐ to C‐terminus by an eight residue polypeptide linker. The sequence of this linker was derived from a loop in bira bifunctional protein, and was determined from a structural database search. This “single‐chain” variant was used to create an IFN‐γ molecule that binds only a single copy of the α‐chain receptor, rather than the 2 α‐chain receptor: 1 IFN‐γ binding stoichiometry observed for the native hormone. Crystals have been grown of a 1:1 complex between this single‐chain molecule and the extracellular domain of its α‐chain receptor. These crystals diffract beyond 2.0 Å, significantly better than the 2.9 Å observed for the native 2:1 complex. Density calculations suggest these crystals contain two complexes in the asymmetric unit; a self‐rotation function confirms this conclusion.
Incidental adenocarcinoma of the prostate: The role of repeat transurethral resection in staging
Authors: Paul Sonda L. , Barton Grossman H. , MacGregor Robert J , Gikas Paul W. 
Published: July 2010

AbstractAccurate staging of patients with incidental prostatic adenocarcinoma (A1 vs A2) is crucial to the selection of appropriate treatment. To evaluate the potential sampling error in specimens obtained by transurethral resection, repeat resection was performed on 31 patients pathologically staged as A1 (five or less chips with tumor). Second specimens showed no tumor in 22 (71 %), stage A1 in six (20%), and stage A2 in three (9%). The weight of tissue removed at reresection was greater in patients found to have more extensive involvement (P < 0.005). No patient with initial Gleason score 2, 3, or 4 had stage A2 at reresection. Repeat resection is not routinely necessary, but may be helpful when the tumor is high grade but of minimal extent, in an anxious younger patient who may wish therapy if disease persists, or where some suspicion of an incomplete resection exists.
Susceptibility of the prostate cancer cell to different physical, hormonal, and chemical agents: Present status and theoretical prospects for improved prostate cancer therapy
Authors: Hechter Oscar 
Published: July 2010

AbstractThe benefits and limitations of present modes of treatment of prostatic cancer with physical, hormonal, and chemical agents are briefly reviewed. The theoretical possibility that the heterogenous clones that comprise prostatic cancer might be killed or controlled by selective targeting of cytotoxic agents (actual or potential) to malignant cells is discussed in terms of two types of delivery vehicles to provide for cell selectivity: (1) monoclonal antibodies against specific cell surface markers on cancer cells and (2) steroid ligands for receptors present in clones of malignant cells. The problems and prospects of these selective delivery systems as potential therapeutic modalities for prostatic cancer are considered.
Hyperthermia in the treatment of prostate cancer
Authors: Servadio C. , Leib Z. 
Published: July 2010

AbstractHyperthermia—the sustained heating of tissues to temperatures of 42oC to 43.5oC− increasingly is being studied by scientists as a new tool to destroy cancer cells, either alone or in conjunction with other well established forms of treatment, such as radiotherapy and chemotherapy. Many studies on tissue cultures, on animals and also on humans, have established the fact that this new nonconventional adjuvant form of treatment is actually effective. Progress is being made in the development of the necessary technology for delivering the desired and controlled form of heat to the diseased site, while protecting the surrounding healthy tissues from irreversible damage. Initial clinical trials in this direction are very promising and seem to offer new avenues in the methods of treatment for cancer of the prostate.
Immunotherapy of prostate cancer: A review
Authors: Guinan P. , Ray P. , Shaw M. 
Published: July 2010

AbstractTumors are antigenic and patients can mount an immune response against their tumors. Prostate cancer patients are sensitized to their malignancies and immunotherapeutic efforts have been successful. As with other tumors, it is unlikely that immunotherapy alone will be curative, but will play a role in combination therapy along with surgery, radiation, and chemotherapy. But before its rightful place can be delineated, additional clinical and laboratory studies must be completed.
Laser ablation of AgSbS2 and cluster analysis by time‐of‐flight mass spectrometry
Authors: Houška Jan , Peña‐Méndez Eladia Maria , Kolář Jakub , Frumar Miloslav , Wágner Tomáš , Havel Josef 
Published: July 2010

AbstractThin films of AgSbS2 are important for phase‐change memory applications. This solid is deposited by various techniques, such as metal organic chemical vapour deposition or laser ablation deposition, and the structure of AgSbS2(s), as either amorphous or crystalline, is already well characterized. The pulsed laser ablation deposition (PLD) of solid AgSbS2 is also used as a manufacturing process. However, the processes in plasma have not been well studied. We have studied the laser ablation of synthesized AgSbS2(s) using a nitrogen laser of 337 nm and the clusters formed in the laser plume were identified. The ablation leads to the formation of various single charged ternary AgpSbqSr clusters. Negatively charged AgSbS, AgSb2S, AgSb2S, AgSb2S and positively charged ternary AgSbS+, AgSb2S+, AgSb2S, AgSb2S clusters were identified. The formation of several singly charged Ag+, Ag, Ag, Sb, Sb, S ions and binary AgpSr clusters such as AgSb, Ag3S−, SbS (r = 1–5), Sb2S−, Sb2S, Sb3S (r = 1–4) and AgS, SbS+, SbS, Sb2S+, Sb2S, Sb3S (r = 1–4), AgSb was also observed. The stoichiometry of the clusters was determined via isotopic envelope analysis and computer modeling. The relation of the composition of the clusters to the crystal structure of AgSbS2 is discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Brownfields—A Canadian Perspective
Authors: Velderman B. J. , Zapf‐Gilje R. , Fortin F. , DuBois D. 
Published: July 2010

AbstractBarriers to redevelopment of contaminated lands have led to vacant or underutilized sites termed “brown fields.” These barriers fall into six categories: regulatory, technical/scientific, legal/liability, financial, urbanplanning, and communications. The lack of protection to innocent parties, such as developers and lenders, and the lack of guidance for applying sitespecific and risk‐based remediation approaches are two key barriers to redevelopment. This article presents guiding principles for redeveloping brownfields and recommends best practices toward overcoming existing barriers to such redevelopment. Success stories of redeveloped contaminated industrial sites are provided to illuminate the effectiveness of the best practices approach.
Recent Developments in Cleanup Technologies
Authors: Simon John A. 
Published: July 2010

AbstractAlthough the reaction mechanics are somewhat mysterious, the use of iron forin situgroundwater treatment has recently gained considerable attention and respect in the remediation industry. The basic scientific principles of both applications of iron have been known for over a century; however, both were nearly unheard of as remediation technologies five years ago. Both technologies have a strong potential for widespread use. They are commercially available, have been proven in field studies, are less expensive than traditional pump and treat technologies, and, in many types of groundwater systems, may be able to meet difficult‐to‐achieve groundwater treatment standards. As these technologies continue to undergo development, there could be considerably more aggressive applications used to treat ground‐water containing high concentrations of chlorinated organics and DNAPLs.
Time domain constrained H∞‐synthesis
Authors: Apkarian Pierre , Ravanbod‐Hosseini Laleh , Noll Dominikus 
Published: July 2010

AbstractStructured H∞‐synthesis subject to time domain performance specifications is introduced. Our method allows to control trajectories of the linearized system and the underlying nonlinear dynamics simultaneously. A non‐smooth bundle optimization method for this class of programs is proposed and discussed. Our approach is tested against two benchmark studies: control of a rotational actuator to attenuate vibration noise, and control of a continuous crystallizer. Our algorithm gives a local convergence certificate and is suited for systems with large state dimension. Copyright © 2010 John Wiley & Sons, Ltd.
Inequalities in probability theory and turán‐type problems for graphs with colored vertices
Authors: Sidorenko A. F. 
Published: July 2010

AbstractThe “best” inequalities of type P{(ζ, η)⊂ E} ≧f(P{η⊂ D1}P{η⊂Dm}) for independent and identically distributed random elements ζ and η can be reduced to Turán‐type problems for graphs with colored vertices. In the present work we describe a finite algorithm for obtaining the asymptotical solution for an arbitrary problem of such type. In the case of two colors we obtain the final form of asymptotic solution without using the algorithm.
The blocking probability of spider‐web networks
Authors: Pippenger Nicholas 
Published: July 2010

AbstractWe determine the limiting behavior of the blocking probability for spider‐web networks, a class of crossbar switching networks proposed by Ikeno. We use a probabilistic model proposed by the author, in which the busy links always form disjoint routes through the network. We show that if the occupancy probability is below the threshold 2 ‐ √2 = 0.5857…, then the blocking probability tends to zero, whereas above this threshold it tends to one. This provides a theoretical explanation for results observed empirically in simulations by Bassalygo, Neiman, and Vvedenskaya.
Probabilistic analysis of some distributed algorithms
Authors: Louchard G. , Schott R. 
Published: July 2010

AbstractIn this paper we analyze: (i) a storage allocation algorithm (D.E. Knuth, The Art of Computer Programming‐Vol. I, Addison‐Wesley, Reading, MA, 1969, Ex. 2.2.2.13) which permits one to maintain two stacks inside a shared (continuous) memory area of a fixed size, and (ii) the well‐known banker algorithm which plays a fundamental role in parallel processing (J. Francon, Combinatoire et Parallelisme; Journees Informatique et Mathematique; Lumigny, October 15‐17, 1987; A. N. Habermann, in Current Trends in Programming Methodology, Vol. 3, K. M. Chandy and R. T. Yeh, Eds., Prentice‐Hall, Englewood Cliffs, NJ, 1987; J. Peterson and A. Silberschatz, Operating Systems Concepts, Addison‐Wesley, Reading, MA, 1983). The natural formulation of the problems to be solved here is in terms of random walks. For (i) the random walk Ym(‐) takes place in a triangle in a two‐dimensional lattice space with two reflecting barriers along the axes (a deletion has no effect on an empty stack) and one absorbing barrier along the diagonal (the algorithm stops when the combined sizes of the stacks exhaust the available storage). For (ii) the random walk takes place in a rectangle with broken corner and has four reflecting barriers and one absorbing barrier (see Fig. 10). With the help of diffusion techniques, we obtain, asymptotically as m: →∞.the distributions of the hitting place (Zm) and hitting time (Tm) on the absorbing boundary.the joint distribution of Zm and Tm.the distribution P[Ym(n) ≦ ym, n < Tm].
Limit laws for local counters in random binary search trees
Authors: Devroye Luc 
Published: July 2010

AbstractLimit laws for several quantities in random binary search trees that are related to the local shape of a tree around each node can be obtained very simply by applying central limit theorems for w‐dependent random variables. Examples include: the number of leaves (Ln), the number of nodes with k descendants (k fixed), the number of nodes with no left child, the number of nodes with k left descendants. Some of these results can also be obtained via the theory of urn models, but the present method seems easier to apply.
Stability of vertices in random boolean cellular automata
Authors: Luczak Tomasz , Cohen Joel E. 
Published: July 2010

AbstractBased on computer simulations, Kauffman (Physica D, 10, 145‐156, 1984) made several generalizations about a random Boolean cellular automaton which he invented as a model of cellular metabolism. Here we give the first rigorous proofs of two of Kauffman's generalizations: a large fraction of vertices stabilize quickly, consequently the length of cycles in the automaton's behavior is small compared to that of a random mapping with the same number of states; and reversal of the states of a large fraction of the vertices does not affect the cycle to which the automaton moves.