bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure‐based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections
Authors: Montes Matthieu , Miteva Maria A. , Villoutreix Bruno O.
Published: May 2007

Virtual ligand screening methods based on the structure of the receptor are extensively used to facilitate the discovery of lead compounds. In the present study, we investigated the LigandFit package on four different proteins (coagulation factor VIIa, estrogen receptor, thymidine kinase, and neuraminidase), a relatively large compound collection of 65,560 unique “drug‐like” molecules and four focused libraries (1950 molecules each). We performed virtual screening experiments with the large database and evaluated six scoring functions available in the package (DockScore, LigScore1, LigScore2, PLP1, PLP2, and PMF). The results showed that LigandFit is an efficient program, especially when used with LigScore1. Similar computations were carried out using focused libraries. In this situation the LigScore1 scoring function outperformed the other ones on three out of the four proteins tested. Even for the difficult neuraminidase case, the LigandFit/LigScore1 combination was still reasonably successful. Assessment of docking accuracy was also performed and again, we found that LigandFit (with DockScore and the CFF parameters) was performing well. On the basis of these results and observed increased enrichments after LigandFit/Ligscore1 screening on focused libraries, we suggest that using this program as a final step of a hierarchical protocol can be very beneficial to assist lead finding. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The crystal structure of the secreted aspartic proteinase 3 from Candida albicans and its complex with pepstatin A
Authors: Borelli Claudia , Ruge Elisabeth , Schaller Martin , Monod Michel , Korting Hans Christian , Huber Robert , Maskos Klaus
Published: May 2007

The family of secreted aspartic proteinases (Sap) encoded by 10 SAP genes is an important virulence factor during Candida albicans (C. albicans) infections. Antagonists to Saps could be envisioned to help prevent or treat candidosis in immunocompromised patients. The knowledge of several Sap structures is crucial for inhibitor design; only the structure of Sap2 is known. We report the 1.9 and 2.2 Å resolution X‐ray crystal structures of Sap3 in a stable complex with pepstatin A and in the absence of an inhibitor, shedding further light on the enzyme inhibitor binding. Inhibitor binding causes active site closure by the movement of a flap segment. Comparison of the structures of Sap3 and Sap2 identifies elements responsible for the specificity of each isoenzyme. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Using molecular dynamics to map interaction networks in an aminoacyl‐tRNA synthetase
Authors: Budiman Michael E. , Knaggs Michael H. , Fetrow Jacquelyn S. , Alexander Rebecca W.
Published: May 2007

Long‐range functional communication is a hallmark of many enzymes that display allostery, or action‐at‐a‐distance. Many aminoacyl‐tRNA synthetases can be considered allosteric, in that their trinucleotide anticodons bind the enzyme at a site removed from their catalytic domains. Such is the case with E. coli methionyl‐tRNA synthase (MetRS), which recognizes its cognate anticodon using a conserved tryptophan residue 50 Å away from the site of tRNA aminoacylation. The lack of details regarding how MetRS and tRNAMet interact has limited efforts to deconvolute the long‐range communication that occurs in this system. We have used molecular dynamics simulations to evaluate the mobility of wild‐type MetRS and a Trp‐461 variant shown previously by experiment to be deficient in tRNA aminoacylation. The simulations reveal that MetRS has significant mobility, particularly at structural motifs known to be involved in catalysis. Correlated motions are observed between residues in distant structural motifs, including the active site, zinc binding motif, and anticodon binding domain. Both mobility and correlated motions decrease significantly but not uniformly upon substitution at Trp‐461. Mobility of some residues is essentially abolished upon removal of Trp‐461, despite being tens of Ångstroms away from the site of mutation and solvent exposed. This conserved residue does not simply participate in anticodon binding, as demonstrated experimentally, but appears to mediate the protein's distribution of structural ensembles. Finally, simulations of MetRS indicate that the ligand‐free protein samples conformations similar to those observed in crystal structures with substrates and substrate analogs bound. Thus, there are low energetic barriers for MetRS to achieve the substrate‐bound conformations previously determined by structural methods. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Generation of blood group specificity: New insights from structural studies on the complexes of A‐ and B‐reactive saccharides with basic winged bean agglutinin
Authors: Kulkarni Kiran A. , Katiyar Samiksha , Surolia Avadhesha , Vijayan Mamannamana , Suguna Kaza
Published: May 2007

Basic winged bean agglutinin binds A‐blood group substance with higher affinity and B‐blood group substance with lesser affinity. It does not bind the O substance. The crystal structures of the lectin, complexed with A‐reactive and B‐reactive di and tri saccharides, have been determined. In addition, the complexes of the lectin with fucosylated A‐trisaccharides and B‐trisaccharides and with a variant of the A‐trisaccharide have been modeled. These structures and models provide valuable insights into the structural basis of blood group specificities. All the four carbohydrate binding loops of the lectin contribute to the primary combining site while the loop of variable length contributes to the secondary binding site. In a significant advance to the current understanding, the interactions at the secondary binding site also contribute substantially, albeit in a subtle manner, to determine the blood group specificity. Compared with the interactions of the B‐trisaccharide with the lectin, the third sugar residue of the A‐reactive trisacharide forms an additional hydrogen bond with a lysine residue in the variable loop. In the former, the formation of such a hydrogen bond is prevented by a shift in the orientation of third sugar resulting from an internal hydrogen bond in it. The formation of this bond is also facilitated by an interaction dependent change in the rotamer conformation of the lysyl residue of the variable loop. Thus, the difference in the interactions at the secondary site is generated by coordinated movements in the ligand as well as the protein. A comparison of the crystal structure and the model of the complex involving the variant of the A‐trisaccharide results in the delineation of the relative contributions of the interactions at the primary and the secondary sites in determining blood group specificity. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Modeling and analysis of molecularinteraction between Smurf1‐WW2 domain and various isoforms of LIM mineralization protein
Authors: Sangadala Sreedhara , Boden Scott D. , Metpally Raghu Prasad Rao , Reddy Boojala Vijay B.
Published: May 2007

LIM Mineralization Protein‐1 (LMP‐1) has been cloned and shown to be osteoinductive. Our efforts to understand the mode of action of LMP‐1 led to the determination that LMP‐1 interacts with Smad Ubiquitin Regulatory Factor‐1 (Smurf1). Smurf1 targets osteogenic Smads, Smad1/5, for ubiquitin‐mediated proteasomal degradation. Smurf1 interaction with LMP‐1 or Smads is based on the presence of unique WW‐domain interacting motif in these target molecules. By performing site‐directed mutagenesis and binding studies in vitro on purified recombinant proteins, we identified a specific motif within the osteogenic region of several LMP isoforms that is necessary for Smurf1 interaction. Similarly, we have identified that the WW2 domain of Smurf1 is necessary for target protein interaction. Here, we present a homology‐based modeling of the Smurf1 WW2 domain and its interacting motif of LMP‐1. We performed computational docking of the interacting domains in Smurf1 and LMPs to identify the key amino acid residues involved in their binding regions. In support of the computational predictions, we also present biochemical evidence supporting the hypothesis that the physical interaction of Smurf1 and osteoinductive forms of LMP may prevent Smurf1 from targeting osteogenic Smads by ubiquitin‐mediated proteasomal degradation. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein–protein interfaces
Authors: Noy Efrat , Tabakman Tal , Goldblum Amiram
Published: May 2007

We investigate the extent to which ensembles of flexible fragments (FF), generated by our loop conformational search method, include conformations that are near experimental and reflect conformational changes that these FFs undergo when binary protein–protein complexes are formed. Twenty‐eight FFs, which are located in protein–protein interfaces and have different conformations in the bound structure (BS) and unbound structure (UbS) were extracted. The conformational space of these fragments in the BS and UbS was explored with our method which is based on the iterative stochastic elimination (ISE) algorithm. Conformational search of BSs generated bound ensembles and conformational search of UbSs produced unbound ensembles. ISE samples conformations near experimental (less than 1.05 Å root mean square deviation, RMSD) for 51 out of the 56 examined fragments in the bound and unbound ensembles. In 14 out of the 28 unbound fragments, it also samples conformations within 1.05 Å from the BS in the unbound ensemble. Sampling the bound conformation in the unbound ensemble demonstrates the potential biological relevance of the predicted ensemble. The 10 lowest energy conformations are the best choice for docking experiments, compared with any other 10 conformations of the ensembles. We conclude that generating conformational ensembles for FFs with ISE is relevant to FF conformations in the UbS and BS. Forming ensembles of the isolated proteins with our method prior to docking represents more comprehensively their inherent flexibility and is expected to improve docking experiments compared with results obtained by docking only UbSs. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structural and biochemical characterization of inhibitor‐1α
Authors: Huang Hsien‐Bin , Chen Yi‐Chen , Lee Ting‐Ting , Huang Yi‐Choang , Liu Hsin‐Tzu , Liu Chen‐Kuang , Tsay Huey‐Jen , Lin Ta‐Hsien
Published: May 2007

Inhibitor‐1α is one of the isoforms of human protein phosphatase inhibitor‐1. It is a product of alternative splicing of inhibitor‐1 gene and lacks 51 internal amino acids from residue 84 to 134 of inhibitor‐1. Here we have characterized the structural and biochemical properties of inhibitor‐1α. Structural analysis of recombinant inhibitor‐1α by NMR spectroscopy revealed that inhibitor‐1α adopts a predominantly random coil conformation. Excluding the region from residue 84 to 134 of inhibitor‐1, the structural features of inhibitor‐1 and inhibitor‐1α are almost the same as each other. The IC50 value of inhibitor‐1α in inhibition of Protein phosphatase‐1 (PP1) is comparable to that of inhibitor‐1, indicating that inhibitor‐1α is a potent inhibitor of PP1 when Thr‐35 is phosphorylated by PKA. For phosphorylation by PKA and dephosphorylation by protein phosphatase‐1, ‐2A, and ‐2B, the measured kinetic parameters of inhibitor‐1α are very close to those of inhibitor‐1. Taken together, these results suggest that inhibitor‐1α preserves the structure of inhibitor‐1, the PP1 inhibitory activity and the functional specificities toward phosphorylation by PKA and dephosphorylation by protein phosphatase‐1, ‐2A, and ‐2B. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps
Authors: Seeliger Daniel , de Groot Bert L.
Published: May 2007

A rigorous quantitative assessment of atomic contacts and packing in native protein structures is presented. The analysis is based on optimized atomic radii derived from a set of high‐resolution protein structures and reveals that the distribution of atomic contacts and overlaps is a structural constraint in proteins, irrespective of structural or functional classification and size. Furthermore, a newly developed method for calculating packing properties is introduced and applied to sets of protein structures at different levels of resolution. The results show that limited resolution yields decreasing packing quality, which underscores the relevance of packing considerations for structure prediction, design, dynamics, and docking. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Studies of the molten globule state of ferredoxin: Structural characterization and implications on protein folding and iron–sulfur center assembly
Authors: Leal Sónia S. , Gomes Cláudio M.
Published: May 2007

The biological insertion of iron–sulfur clusters (Fe–S) involves the interaction of (metallo) chaperons with a partly folded target polypeptide. In this respect, the study of nonnative protein conformations in iron–sulfur proteins is relevant for the understanding of the folding process and cofactor assembly. We have investigated the formation of a molten globule state in the [3Fe4S][4Fe4S] ferredoxin from the thermophilic archaeon Acidianus ambivalens (AaFd), which also contains a structural zinc site. Biophysical studies have shown that, at acidic pH, AaFd retains structural folding and metal centers. However, upon increasing the temperature, a series of successive modifications occur within the protein structure: Fe–S disassembly, loss of tertiary contacts and dissociation of the Zn2+ site, which is simultaneous to alterations on the secondary structure. Upon cooling, an apo‐ferredoxin state is obtained, with characteristics of a molten globule: compactness identical to the native form; similar secondary structure evidenced by far‐UV CD; no near‐UV CD detected tertiary contacts; and an exposure of the hydrophobic surface evidenced by 1‐anilino naphthalene‐8‐sulfonic acid (ANS) binding. In contrast to the native form, this apo ferredoxin state undergoes reversible thermal and chemical unfolding. Its conformational stability was investigated by guanidinium chloride denaturation and this state is ∼1.5 kcal mol−1 destabilised in respect to the holo ferredoxin. The single tryptophan located nearby the Fe–S pocket probed the conformational dynamics of the molten globule state: fluorescence quenching, red edge emission shift analysis and resonance energy transfer to bound ANS evidenced a restricted mobility and confinement within a hydrophobic environment. The possible physiological relevance of molten globule states in Fe–S proteins and the hypothesis that their structural flexibility may be important to the understanding of metal center insertion are discussed. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Conformational contagion in a protein: Structural properties of a chameleon sequence
Authors: Takano Kazufumi , Katagiri Yoshiaki , Mukaiyama Atsushi , Chon Hyongi , Matsumura Hiroyoshi , Koga Yuichi , Kanaya Shigenori
Published: May 2007

Certain sequences, known as chameleon sequences, take both α‐ and β‐conformations in natural proteins. We demonstrate that a wild chameleon sequence fused to the C‐terminal α‐helix or β‐sheet in foreign stable proteins from hyperthermophiles forms the same conformation as the host secondary structure. However, no secondary structural formation is observed when the sequence is attached to the outside of the secondary structure. These results indicate that this sequence inherently possesses an ability to make either α‐ or β‐conformation, depending on the sequentially neighboring secondary structure if little other nonlocal interaction occurs. Thus, chameleon sequences take on a satellite state through contagion by the power of a secondary structure. We propose this “conformational contagion” as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Fold recognition by concurrent use of solvent accessibility and residue depth
Authors: Liu Song , Zhang Chi , Liang Shide , Zhou Yaoqi
Published: May 2007

Recognizing the structural similarity without significant sequence identity (called fold recognition) is the key for bridging the gap between the number of known protein sequences and the number of structures solved. Previously, we developed a fold‐recognition method called SP3 which combines sequence‐derived sequence profiles, secondary‐structure profiles and residue‐depth dependent, structure‐derived sequence profiles. The use of residue‐depth‐dependent profiles makes SP3 one of the best automatic predictors in CASP 6. Because residue depth (RD) and solvent accessible surface area (solvent accessibility) are complementary in describing the exposure of a residue to solvent, we test whether or not incorporation of solvent‐accessibility profiles into SP3 could further increase the accuracy of fold recognition. The resulting method, called SP4, was tested in SALIGN benchmark for alignment accuracy and Lindahl, LiveBench 8 and CASP7 blind prediction for fold recognition sensitivity and model‐structure accuracy. For remote homologs, SP4 is found to consistently improve over SP3 in the accuracy of sequence alignment and predicted structural models as well as in the sensitivity of fold recognition. Our result suggests that RD and solvent accessibility can be used concurrently for improving the accuracy and sensitivity of fold recognition. The SP4 server and its local usage package are available on http://sparks.informatics.iupui.edu/SP4. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A model‐based proposal for the role of UreF as a GTPase‐activating protein in the urease active site biosynthesis
Authors: Salomone‐Stagni Marco , Zambelli Barbara , Musiani Francesco , Ciurli Stefano
Published: May 2007

UreF is a protein that plays a role in the in vivo urease activation as a chaperone involved in the insertion of two Ni2+ ions in the apo‐urease active site. The molecular details of this process are unknown. In the absence of any molecular information on the UreF protein class, and as a step toward the comprehension of the relationships between UreF function and structure, we applied a structural modeling approach to infer useful biochemical knowledge on Bacillus pasteurii UreF (BpUreF). Similarity searches and multiple alignment of UreF protein sequences indicated that this class of proteins has a low homology with proteins of known structure. Fold recognition methods were therefore used to identify useful protein structural templates to model the structure of BpUreF. In particular, the templates belong to the class of GTPase‐activating proteins. Modeling of BpUreF based on these templates was performed using the program MODELLER. The structure validation yielded good statistics, indicating that the model is plausible. This result suggests a role for UreF in urease active site biosynthesis as a regulator of the activity of UreG, a small G protein involved in the in vivo apo‐urease activation process and established to catalyze GTP hydrolysis. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Intrinsic disorder in yeast transcriptional regulatory network
Authors: Singh Gajinder Pal , Dash Debasis
Published: May 2007

Intrinsic disorder has been shown to be important in mediating protein–protein and protein–DNA interactions. Proteins involved in regulatory functions are particularly enriched in intrinsic disorder. In this study we explored the role of intrinsic disorder in transcriptional regulatory network of yeast. Using disorder prediction programs we show that transcription factors (TFs) regulating large number of targets (transcriptional hubs) have significantly increased intrinsic disorder, though targets regulated by multiple TFs did not show increased intrinsic disorder. Intrinsic disorder may allow these transcriptional hubs to bind to diverse promoter regions of their targets in different contexts, and may also allow complex regulatory control of transcriptional hubs that are involved in coordinating different cellular processes. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Evaluation of antioxidative properties of Allium species growing wild in Italy
Authors: Nencini Cristina , Cavallo Federica , Capasso Anna , Franchi Gian Gabriele , Giorgio Giorgi , Micheli Lucia
Published: May 2007

The genus Allium (Alliaceae) is an important dietary source of antioxidant phytochemical products. The antioxidant activity of some Allium species is well known but no information is available on the in vitro antioxidant activities of Italian Allium species growing wild. The aim of this study was to examine the in vitro antioxidant activity of aqueous extracts of different parts belonging to three Allium species growing wild, endemic to Italian flora: Allium neapolitanum Cyr., Allium subhirsutum L. and Allium roseum L., compared with the in vitro antioxidant activity of aqueous extracts of bulbs and leaves of the greatly studied garlic (Allium sativum L.). The antioxidant potential of extracts was evaluated using two different spectrophotometric assays: the DPPH test and FRAP assay. Furthermore the polyphenolic content was determined in all Allium species.

The flowers of species growing wild showed the higher antioxidant power. Interesting results were shown even by the leaves, while the antioxidant capacity of the bulbs was lower. A correlation between the phenolic contents and the antioxidant activity was discovered.

The differences in antioxidant capacity reflect the variability in the Allium species and the parts of the plant used and that the bulb of Allium sativum did not show higher antioxidant power. Copyright © 2007 John Wiley & Sons, Ltd.
Acanthopanax senticosus inhibits nitric oxide production in murine macrophages In Vitro and In Vivo
Authors: Lin Qiu‐Ye , Jin Li‐Ji , Ma Yong‐Sheng , Shi Ming , Xu Yong‐Ping
Published: May 2007

Excess nitric oxide (NO) production has been implicated in inflammatory diseases. The present study investigated the inhibitory effect of the stem bark extract of Acanthopanax senticosus (A. senticosus) on NO production in murine macrophages in vitro and in vivo. In vitro exposure of RAW264.7 cells to 1, 10, 50, 100, 250, 500 and 1000 µg/mL of A. senticosus extract significantly suppressed NO production induced by lipopolysaccharide (LPS) and interferon gamma (IFN‐γ) in a dose‐dependent manner. In vitro exposure of mouse resident peritoneal macrophages to 1, 10, 100 and 1000 µg/mL of A. senticosus extract significantly suppressed NO production induced by LPS and IFN‐γ in a dose‐dependent manner. In vivo administration of A. senticosus extract (50, 100 and 200 mg/kg) to KM mice dose‐dependently inhibited LPS and IFN‐γ induced production of NO in isolated mouse peritoneal macrophages ex vivo. Exposure to A. senticosus extract had no effect on cell viability and systemic toxicity. The results demonstrated that the stem bark extract of A. senticosus extract inhibits NO production in murine macrophages in vitro and in vivo. Copyright © 2007 John Wiley & Sons, Ltd.
Analysis of effects of the herbal preparation circulat on gene expression levels in cultured human fibroblasts
Authors: Antoshechkin A. , Olalde J. , Magarici M. , Muhammad A. , Salom A. , Suarez J. , Amendola F.
Published: May 2007

Circulat is a systemic standardized plant extract formulation that was developed for the prevention of severe manifestations of type 2 diabetes such as necrotic damage of the plantar foot. With the aim of revealing the molecular mechanisms underlying Circulat's biological activity, the effects of Circulat treatment on gene expression levels were examined in the cultured human fibroblast cell line MRC‐5 using Affymetrix oligonucleotide microarrays. The analysis identified 187 genes, the expression levels of which underwent significant changes upon Circulat treatment. These include four genes (IL6, HMGA1, SLC19A2 and C4A) that have been implicated previously in the development of diabetes. A large proportion of the identified genes are involved in energy metabolism, protein synthesis, glucose metabolism and signaling pathways. Synergistic action of the Circulat components has also been revealed. Prospective applications of microarray analysis in phytopharmacology are discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Hypochlorous acid scavenging capacity of garlic
Authors: Pedraza‐Chaverrí José , Arriaga‐Noblecía Gabriela , Medina‐Campos Omar Noel
Published: May 2007

The ability of the following aqueous garlic extracts to scavenge hypochlorous acid (HOCl) was studied: (a) unheated extract of raw garlic (RG), (b) heated extract of raw garlic (HRG), (c) extract of boiled garlic cloves (BG) and (d) extract of microwave‐treated garlic cloves (MG). The HOCl scavenging activity was evaluated following changes in the absorption spectrum of catalase (370–450 nm). RG, HRG and BG scavenged HOCl in a concentration‐dependent way: the IC50 (mg/mL) values for RG, HRG and BG were 0.339 ± 0.028, 0.632 ± 0.030 and 0.690 ± 0.031, respectively. The HOCl scavenging ability of garlic was significantly decreased when garlic cloves or the extract of raw garlic were heated (BG and HRG, respectively); this scavenging ability was eliminated when garlic was subjected to microwave heating (MG). The IC50 value for the reference compound, ascorbic acid, was 0.500 ± 0.049 mg/mL. In summary, raw garlic concentration‐dependently scavenged HOCl; this ability was eliminated in extracts of microwave‐treated garlic cloves but not in heated extracts of raw garlic or extracts of boiled garlic cloves. Copyright © 2007 John Wiley & Sons, Ltd.
The electronic structure of molybdenum (II) clusters with chelate ligands
Authors: Yusha Sergei N. , Projavkin Alexander A. , Dementyev Ilia A. , Kozin Andrei O. , Korolkov Dmitry V.
Published: May 2007

The electronic structures of divalent molybdenum binuclear clusters with chelate ligands [Mo2(O2CH)4], [Mo2(O2CCH3)4], [Mo2(O2CCF3)4], [Mo2(O2CCFH2)4], [Mo2(O2CCOOH)4], and [Mo2(SO4)4]4− are calculated and interpreted using theory of density functional; one‐electron redox reactions and addition reactions for these clusters are modeled. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
The influence of molecular structure on the change of the arrhenius factor of gas‐phase elimination of nitric acid from nitroalkanes
Authors: Shamsutdinov A. F. , Shamsutdinov T. F. , Chachkov D. V. , Shamov A. G. , Khrapkovskii G. M.
Published: May 2007

The Arrhenius factor of gas‐phase elimination of nitric acid from nitrocompounds was estimated. Asymmetric internal rotation was taken into account. To this end, an appropriate mathematical apparatus was developed. The geometry, transition state, rotation barriers and vibration frequencies were found by the density functional theory method B3LYP/6‐31G(d) by means Gaussian 98 program. The influence of the molecular structure on the Arrhenius factor was considered. The reaction barriers were estimated theoretically. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Atomic structure under external confinements: Effect of plasma
Authors: Sil A. N. , Bhattacharyya S. , Mukherjee P. K.
Published: May 2007

Extensive nonrelativistic studies have been performed on the spectral properties of confined atomic systems under a charge neutral background. The effect of confinement on the spectral properties due to the neutral background has been analyzed using plasma model, which, for weak coupling case, can be obtained from the standard Debye screening model, and for strong coupling case, can be envisaged by ion sphere (IS) model. Further consideration has been given for estimating the effect due to spatially confined plasma, which is obtained by imposing finite boundary conditions on the wave functions. Several atomic, ionic, and exotic systems have been considered for our exclusive study. The structural properties like the ground and excited state energies, oscillator strengths, and transition probabilities for low lying excitations and spectral line shifts have been estimated for hydrogen‐ and helium‐like ions under different plasma coupling strengths. The system approaches towards gradual instability with increase of the plasma coupling strength. A gradual reduction of the ionization potential is observed and the number of bound states become finite. The behavior of ionization potentials, excitation energies, polarizabilities, oscillator strengths, and transition probabilities with respect to increased plasma strength have been found to be interesting. Our findings are in good agreement with limited experimental observations using laser produced plasmas. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Non–Born–Oppenheimer calculations of the ground state of H3
Authors: Cafiero Mauricio , Adamowicz Ludwik
Published: May 2007

We present quantum–mechanical calculations for the ground state of the H3 system performed without the Born‐Oppenehimer approximation. In the calculations we use explicitly correlated Gaussian basis functions that explicitly depend on all of the interparticle distances. These basis functions allow us to achieve high accuracy while explicitly describing nucleus–nucleus, nucleus–electron, and electron–electron correlation effects. Gaussian basis sets ranging in size from 85 to 950 functions have been optimized using a gradient‐based procedure. The issue of defining and extracting the H3 molecular structure based on the non‐BO wave function is also discussed. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Quantum chemical simulation of cytochrome P450 catalyzed aromatic oxidation: Metabolism, toxicity, and biodegradation of benzene derivatives
Authors: D'Yachkov P. N. , Kharchevnikova N. V. , Dmitriev A. V. , Kuznetsov A. V. , Poroikov V. V.
Published: May 2007

The dependences of biological oxidation and toxicity of the mono‐ and multi‐substituted benzene derivatives on the nature of substituents are studied using an oxenoid model and the quantum chemical calculations. According to this model, the P450 enzyme breaks the dioxygen molecules and generates the active atomic oxygen species (oxens); these species readily react with substrates. Using MO LCAO MNDO approach, we calculated the differences ΔE of the total energies of aromatic compounds and corresponding arene oxides containing tetrahedrally coordinated carbon atoms. We obtained that the ΔE values determine the positions of the enzyme mediated oxidation, rate of substrate biotransformation, and toxicity of the benzene derivatives. In addition to the “dynamic” reactivity index ΔE related to the enzyme‐mediated substrate biotransformation, we calculated many standard “static” reactivity indices, corresponding to the substrate molecules in the starting equilibrium geometry (the energies of the occupied and unoccupied MOs, the effective atomic charges, the free valence indices, and the superdelocalizabilities). The arene oxide stability ΔE parameter is shown to be the most adequate characteristic of both the biological oxidation process and toxicity of benzenes. The ΔE parameters were also used successfully to describe the features of di‐ and tri‐chlorinated biphenyls bacterial metabolism. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Xα‐DVM study of properties of active sites of hemoglobin upon substitution of Fe by other 3d‐metal atoms
Authors: Yuryeva Elmira I.
Published: May 2007

The aim of this study is to investigate changes in functional properties of active sites of deoxyhemoglobin upon substitution of Fe by the other 3d‐metal atoms. Relationships between parameters of electronic structure, chemical binding, and temperatures of structure stability loss of active sites of α‐ and β‐subunits of deoxyhemoglobin are estimated using the Xα‐DV method. It is shown that the calculation technique of the temperature Tm of structure stability loss of active sites of deoxyhemoglobin based on the thermodynamic uncertainty relation gives a reasonable interpretation of the maximal possible temperature for a human body living. Temperatures of structure stability loss are higher for Cr, Mn atoms (89, 42 °C) and lower for Co, Ni, Cu, Zn (40, 37, 33, 29 °C) in comparison with Fe (41 °C). Thus the calculations performed show that the temperature of structure stability loss is controlled both by the type of the 3d atom carrying oxygen and small structural differences in active sites of α‐ and β‐subunits of deoxyhemoglobin. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Randomized broadcast in networks
Authors: Feige Uriel , Peleg David , Raghavan Prabhakar , Upfal Eli
Published: May 2007

In this paper we study the rate at which a rumor spreads through an undirected graph. This study has two important applications in distributed computation: in simple, robust and efficient broadcast protocols, and in the maintenance of replicated databases.
The strong chromatic number of a graph
Authors: Alon Noga
Published: May 2007

It is shown that there is an absolute constant c with the following property: For any two graphs G1 = (V, E1) and G2 = (V, E2) on the same set of vertices, where G1 has maximum degree at most d and G2 is a vertex disjoint union of cliques of size cd each, the chromatic number of the graph G = (V, E1 U E2) is precisely cd. The proof is based on probabilistic arguments.
Gap‐Free Set Partitions
Authors: Goh William M. Y. , Schmutz Eric
Published: May 2007

A set partition is called “gap‐free” if its block sizes form an interval. In other words, there is at least one block of each size between the smallest and largest block sizes. Let B(n) and G(n), respectively, denote the number of partitions and the number of gap‐free partitions of the set [n]. We prove that

magnified image
Excluding Induced Subgraphs III: A General Asymptotic
Authors: Prömel H. J. , Steger A.
Published: May 2007

In this article we study asymptotic properties of the class of graphs not containing a fixed graph H as an induced subgraph. In particular we show that the number Forbn★(H) of such graphs on n vertices is essentially determined by the number of subgraphs of a single graph. This implies that

magnified image

Where t(H) is a graph‐theoretic parameter generalizing the chromatic number and the clique covering number. This result complements a theorem of Erdös, Frankl, and Rödl [2] who showed that the number Forbn(H) of graphs on n vertices which do not contain H as a weak subgraph is given by

magnified image
Probabilities of Sentences about Very Sparse Random Graphs
Authors: Lynch James F.
Published: May 2007

We consider random graphs with edge probability βn−α, where n is the number of vertices of the graph, β > 0 is fixed, and α = 1 or α = (l + 1) /l for some fixed positive integer l. We prove that for every first‐order sentence, the probability that the sentence is true for the random graph has an asymptotic limit.
The Evolution of Random Subgraphs of the Cube
Authors: Bollobás B. , Kohayakawa Y. , Łuczak T.
Published: May 2007

be a random Qn”‐process, that is let Q0 be the empty spanning subgraph of the cube Qn and, for 1 ⩽ t ⩽ M = nN/2 = n2n−1, let the graph Qt be obtained from Qt−1 by the random addition of an edge of Qn not present in Qt−1. When t is about N/2, a typical Qt undergoes a certain “phase transition'': the component structure changes in a sudden and surprising way. Let t = (1 + ϵ) N/2 where ϵ is independent of n. Then all the components of a typical Qt have o(N) vertices if ϵ < 0, while if ϵ > 0 then, as proved by Ajtai, Komlós, and Szemerédi, a typical Qt has a “giant” component with at least α(ϵ)N vertices, where α(ϵ) > 0. In this note we give essentially best possible results concerning the emergence of this giant component close to the time of phase transition. Our results imply that if η > 0 is fixed and t ⩽ (1 − n−η) N/2, then all components of a typical Qt have at most nβ(η) vertices, where β(η) > 0. More importantly, if 60(log n)3/n ⩽ ϵ = ϵn = o(1), then the largest component of a typical Qt has about 2ϵN vertices, while the second largest component has order O(nϵ−2). Loosely put, the evolution of a typical Qn process is such that shortly after time N/2 the appearance of each new edge results in the giant component acquiring 4 new vertices.
Volumes Spanned by Random Points in the Hypercube
Authors: Dyer M. E. , Füredi Z. , McDiarmid C.
Published: May 2007

Consider the hypercube [0, 1]n in Rn. This has 2n vertices and volume 1. Pick N = N(n) vertices independently at random, form their convex hull, and let Vn be its expected volume. How large should N(n) be to pick up significant volume? Let k=2/√≈1.213, and let ϵ > 0. We shall show that, as n→∞, Vn→0 if N(n)⩽(k−ϵ)n →1 if N(n) ⩾ (k + ϵ)n. A similar result holds for sampling uniformly from within the hypercube, with constant .
The Forwarding Indices of Random Graphs
Authors: Fernandez de la Vega W. , Gordones L. Marquez
Published: May 2007

A routing R of a graph G is a set of n(n − 1) elementary paths R(u, v) specified for all ordered pairs (u, v) of vertices of G. The vertex‐forwarding index ξ(G) of G, is defined by

magnified image

Where ξ(G, R) is the maximum number of paths of the routing R passing through any vertex of G and the minimum is taken over all the routings of G. Let Gp denote the random graph on n vertices with edge probability p and let m = np. It is proved among other things that, under natural growth conditions on the function p = p(n), the ratio

magnified image

Tends to 1 in probability as n tends to infinity.
Almost all cubic graphs are Hamiltonian
Authors: Robinson R. W. , Wormald N. C.
Published: May 2007

In a previous article the authors showed that at least 98.4% of large labelled cubic graphs are hamiltonian. In the present article, this is improved to 100% in the limit by asymptotic analysis of the variance of the number of Hamilton cycles with respect to populations of cubic graphs with fixed numbers of short odd cycles.
Probabilistic construction of proportional graphs
Authors: Janson Svante , Spencer Joel
Published: May 2007

Proportional graphs are constructed for any rational p ϵ (0, 1) by a probabilistic method: it is shown that a certain random graph may with positive probability be adjusted so as to become proportional. The construction uses a novel type of random graph, where the number of edges is fixed but, nevertheless, the edges appear independently in rather large sets of possible edges.
Parallel simulated annealing
Authors: Mazza Christian
Published: May 2007

This article introduces the notion of restricted parallelism for networks, a generalization of the unlimited parallelism for Boltzmann machines. The convergence of the annealing algorithm in the restricted parallel form is established, for an arbitrary network.
On the Travelling Salesperson Problem in Many Dimensions
Authors: Rhee Wansoo T.
Published: May 2007

Consider d ⩾ 2, and m points X1, …, Xm that are independent uniformly distributed in [0, 1]d. It is well known that the length Tm of the shortest tour through X1, …, Xm satisfies limm→∞ E(Tm)/m1−1/d = β(d) for a certain number β(d). We show that for some numerical constant K,

.
Counting the Number of Hamilton Cycles in Random Digraphs
Authors: Frieze Alan , Suen Stephen
Published: May 2007

We show that there exists a a fully polynomial randomized approximation scheme for counting the number of Hamilton cycles in almost all directed graphs.
Chain Lengths in Certain Random Directed Graphs
Authors: Newman Charles M.
Published: May 2007

We study the random directed graph with vertex set {1, …, n} in which the directed edges (i, j) occur independently with probability cn/n for i<j and probability zero for i ⩽ j. Let Mn (resp., Ln) denote the length of the longest path (resp., longest path starting from vertex 1). When cn is bounded away from 0 and ∞ as n→∞, the asymptotic behavior of Mn was analyzed in previous work of the author and J. E. Cohen. Here, all restrictions on cn are eliminated and the asymptotic behavior of Ln is also obtained. In particular, if cn/ln(n)→∞ while cn/n→0, then both Mn/cn and Ln/cn are shown to converge in probability to the constant e.
Refined Approximations for the Ewens Sampling Formula
Authors: Barbour A. D.
Published: May 2007

The Ewens sampling formula is a family of probability distributions over the space of cycle types of permutations ofnobjects, indexed by a real parameter θ. In the case θ = 1, where the distribution reduces to that induced by the uniform distribution on all permutations, the joint distributions of the numbers of cycles of lengths less thanb = o(n)is extremely well approximated by a product of Poisson distributions, having mean 1/jfor cycle lengthj: the error is super‐exponentially small withnb−1. For θ ≠ 1. the analogous approximation, with means adjusted to θ/j, is good, but with error only linear inn−1b. In this article, it is shown that, by choosing the means of the Poisson distributions more carefully, an error quadratic inn−1bcan be achieved, and that essentially nothing better is possible.
1‐Pancyclic Hamilton Cycles in Random Graphs
Authors: Cooper C.
Published: May 2007

We consider a generalization of the pancyclic property. A graph G is defined to be 1‐pancyclic if there is some Hamilton cycle H in G such that we can find a cycle Cs of length s (3 ⩽ s ⩽ n − 1) using only the edges of H and one other edge es. We show that the threshold for Gn,p to be Hamiltonian, is the threshold for the 1‐pancyclic property.
Simple Constructions of Almost k‐wise Independent Random Variables
Authors: Alon Noga , Goldreich Oded , Håstad Johan , Peralta René
Published: May 2007

We present three alternative simple constructions of small probability spaces onnbits for which anykbits are almost independent. The number of bits used to specify a point in the sample space is (2 +o(1)) (log logn+k/2 + logk+ log 1/ϵ), where ϵ is the statistical difference between the distribution induced on anykbit locations and the uniform distribution. This is asymptotically comparable to the construction recently presented by Naor and Naor (our size bound is better as long as ϵ < 1/(klogn)). An additional advantage of our constructions is their simplicity.
Generalized Digital Trees and Their Difference—Differential Equations
Authors: Flajolet Philippe , Richmond Bruce
Published: May 2007

Consider a tree partitioning process in which n elements are split into b at the root of a tree (b a design parameter), the rest going recursively into two subtrees with a binomial probability distribution. This extends some familiar tree data structures of computer science like the digital trie and the digital search tree. The exponential generating function for the expected size of the tree satisfies a difference–differential equation of order b,

magnified image

The solution involves going to ordinary (rather than exponential) generating functions, analyzing singularities by means of Mellin transforms and contour integration. The method is of some general interest since a large number of related problems on digital structures can be treated in this way via singularity analysis of ordinary generating functions.
Limit Theorems for Combinatorial Structures via Discrete Process Approximations
Authors: Arratia Richard , Tavaré Simon
Published: May 2007

Discrete functional limit theorems, which give independent process approximations for the joint distribution of the component structure of combinatorial objects such as permutations and mappings, have recently become available. In this article, we demonstrate the power of these theorems to provide elementary proofs of a variety of new and old limit theorems, including results previously proved by complicated analytical methods. Among the examples we treat are Brownian motion limit theorems for the cycle counts of a random permutation or the component counts of a random mapping, a Poisson limit law for the core of a random mapping, a generalization of the Erdös–Turán Law for the log‐order of a random permutation and the smallest component size of a random permutation, approximations to the joint laws of the smallest cycle sizes of a random mapping, and a limit distribution for the difference between the total number of cycles and the number of distinct cycle sizes in a random permutation.
The Variance of Level Numbers in Certain Families of Trees
Authors: Gutjahr W. J.
Published: May 2007

For the families of t‐ary trees and planted plane trees, the variance of the level numbers (i.e., the depths of specified endnodes) is determined. We apply different types of techniques, such as singularity analysis (Kirschenhofer's diagonalization method) or a probabilistic approach using weak convergence and uniform integrability. In the case of binary trees, an exact variance formula for finite tree size is established; in the other cases, asymptotic equivalents are derived. Also some results on higher moments are presented.
Coloring Clique‐free Graphs in Linear Expected Time
Authors: Prömel Hans Jürgen , Steger Angelika
Published: May 2007

This article presents a linear expected time algorithm to color every graph which does not contain a clique on l + 1 vertices as a subgraph with a minimal number of colors. This extends a result of Dyer and Frieze for l‐colorable graphs. For the proof we develop a new method which allows us to precisely estimate the number of graphs with certain structural properties.
Local Limit Theorems for Sums of Power Series Distributed Random Variables and for the Number of Components in Labelled Relational Structures
Authors: Mutafchiev Lyuben R.
Published: May 2007

A Local limit theorem for the distribution of the number of components in random labelled relational structures of size n (e.g., a type of random graphs on n vertices, random permutations of n elements, etc.) is proved as n→∞. The case when the corresponding exponential generating functions diverge at their radii of convergence is considered.
A Canonical Ramsey Theorem
Authors: Eaton Nancy , Rödl Vojtěch
Published: May 2007

Say a graph H selects a graph G if given any coloring of H, there will be a monochromatic induced copy of G in H or a completely multicolored copy of G in H. Denote by s(G) the minimum order of a graph that selects G and set s(n) = max {s(G): |G| = n}. Upper and lower bounds are given for this function. Also, consider the Folkman function fr(n) = max{min{|V(H)|: H → (G)1r}: |V(G)| = n}, where H → (G)1r indicates that H is vertex Ramsey to G, that is, any vertex coloring of H with r colors admits a monochromatic induced copy of G. The method used provides a better upper bound for this function than was previously known. As a tool, we establish a theorem for projective planes.
Markov chains on hypercubes: Spectral representations and several majorization relations
Authors: Karlin Samuel , Lindqvist Bo , Yao Yi‐Ching
Published: May 2007

Various Markov chains on hypercubes ℒ︁are considered and their spectral representations are presentend in terms of Kronecker products. Special attention is given to random walks on the graphs 𝒮(l = 1,n − 2), where the vertex set is ℒ︁ and two vertices are connected if and only if their Hamming distance is at most l. It is shown that λ(𝒮1)>λ(𝒮1)>λ(𝒮n−1)>λ(𝒮n),l=2,…,n−2, where λ (𝒮I) is the specturum of the random walk on 𝒮I, and > denotes the majorization ordering. A similar majorization relation is established for graphs V1 where two veritces are connected if and only if their Hamming distance is exactly l. Some applications to mean times of these random walks are given. © 1993 John Wiley & Sons, Inc.
How homogeneous can the last appearing pattern be?
Authors: Móri Tamás F.
Published: May 2007

Given a sequence of indepent, uniformly distributed random letters coming from a finite alphabet, we are interested in the word (pattern) which is the last to be observed for the first time among all words of length n. We derive anas. result on the homogeneity of this last appearing pattern as a corollary of a more general theorem. © 1993 John Wiley & Sons, Inc.
Multicyclic components in a random graph process
Authors: Janson Svante
Published: May 2007

A limit theorem is obtained for the number of components with more than one cycle that are created during the evolution of a random graph process. In particular, it is shown that the probability that the process never contains more than one such component is about 0.87 © 1993 John Wiley & Sons, Inc.