bluuebunny/crossref_metadata_2025 huggingface dataset:
Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two‐dimensional polyacrylamide gel electrophoresis
Authors: Haebel Sophie , Jensen Charlotte , Roepstorff Peter , Andersen Svend Olav
Published: June 2010

Simultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15‐kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix‐assisted laser desorption ionization mass spectrometry (MALDI MS) time‐course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two‐dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants.
Refined solution structure of human profilin I
Authors: Metzler William J. , Farmer Bennett T. , Constantine Keith L. , Friedrichs Mark S. , Mueller Luciano , Lavoie Thomas
Published: June 2010

Profilin is a ubiquitous eukaryotic protein that binds to both cytosolic actin and the phospholipid phospha‐tidylinositol‐4,5‐bisphosphate. These dual competitive binding capabilities of profilin suggest that profilin serves as a link between the phosphatidyl inositol cycle and actin polymerization, and thus profilin may be an essential component in the signaling pathway leading to cytoskeletal rearrangement.

The refined three‐dimensional solution structure of human profilin I has been determined using multidimensional heteronuclear NMR spectroscopy. Twenty structures were selected to represent the solution conformational ensemble. This ensemble of structures has root‐mean‐square distance deviations from the mean structure of 0.58 Å for the backbone atoms and 0.98 Å for all non‐hydrogen atoms. Comparison of the solution structure of human profilin to the crystal structure of bovine profilin reveals that, although profilin adopts essentially identical conformations in both states, the solution structure is more compact than the crystal structure. Interestingly, the regions that show the most structural diversity are located at or near the actin‐binding site of profilin. We suggest that structural differences are reflective of dynamical properties of profilin that facilitate favorable interactions with actin. The global folding pattern of human profilin also closely resembles that of Acanthamoeba profilin I, reflective of the 22% sequence identity and ∼45% sequence similarity between these two proteins.
An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins
Authors: Sowdhamini R. , Blundell Tom L.
Published: June 2010

With a growing number of structures available in the Brookhaven Protein Data Bank, automatic methods for domain identification are required for the construction of databases. Domains are considered to be clusters of secondary structure elements. Thus, helices and strands are first clustered using intersecondary structural distances between Cα positions, and dendrograms based on this distance measure are used to identify domains. Individual domains are recognized by a disjoint factor, which enables the automatic identification and classification into disjoint, interacting, and conjoint domains. Application to a database of 83 protein families and 18 unique structures shows that the approach provides an effective delineation of boundaries and identifies those proteins that can be considered as a single domain. A quantitative estimate of the interaction between domains has been proposed. The database of protein domains is a useful tool for understanding protein folding, for recognizing protein folds, and for understanding structure‐activity relationships.
Competing interactions contributing to α‐helical stability in aqueous solution
Authors: Bodkin Michael J. , Goodfellow Julia M.
Published: June 2010

The stability of a 15‐residue peptide has been investigated using CD spectroscopy and molecular simulation techniques. The sequence of the peptide was designed to include key features that are known to stabilize α‐helices, including ion pairs, helix dipole capping, peptide bond capping, and aromatic interactions. The degree of helicity has been determined experimentally by CD in three solvents (aqueous buffer, methanol, and trifluoroethanol) and at two temperatures. Simulations of the peptide in the aqueous system have been performed over 500 ps at the same two temperatures using a fully explicit solvent model. Consistent with the CD data, the degree of helicity is decreased at the higher temperature. Our analysis of the simulation results has focused on competition between different side‐chain/side‐chain and side‐chain/main‐chain interactions, which can, in principle, stabilize the helix. The unfolding in aqueous solution occurs at the amino terminus because the side‐chain interactions are insufficient to stabilize both the helix dipole and the peptide hydrogen bonds. Loss of capping of the peptide backbone leads to water insertion within the first peptide hydrogen bond and hence unfolding. In contrast, the carboxy terminus of the α‐helix is stable in both simulations because the C‐terminal lysine residue stabilizes the helix dipole, but at the expense of an ion pair.
An NMR and spin label study of the effects of binding calcium and troponin I inhibitory peptide to cardiac troponin C
Authors: Howarth Jack W. , Krudy George A. , Lin Xin , Putkey John A. , Rosevear Paul R.
Published: June 2010

The paramagnetic relaxation reagent, 4‐hydroxy‐2,2,6,6‐tetramethylpiperidinyl‐1‐oxy (HyTEMPO), was used to probe the surface exposure of methionine residues of recombinant cardiac troponin C (cTnC) in the absence and presence of Ca2+ at the regulatory site (site II), as well as in the presence of the troponin I inhibitory peptide (cTnIp). Methyl resonances of the 10 Met residues of cTnC were chosen as spectral probes because they are thought to play a role in both formation of the N‐terminal hydrophobic pocket and in the binding of cTnIp. Proton longitudinal relaxation rates (R1's) of the [13C‐methyl] groups in [13C‐methyl]Met‐labeled cTnC(C35S) were determined using a T1 two‐dimensional heteronuclear single‐ and multiple‐quantum coherence pulse sequence. Solvent‐exposed Met residues exhibit increased relaxation rates from the paramagnetic effect of HyTEMPO. Relaxation rates in 2Ca2+‐loaded and Ca2+‐saturated cTnC, both in the presence and absence of HyTEMPO, permitted the topological mapping of the conformational changes induced by the binding of Ca2+ to site II, the site responsible for triggering muscle contraction. Calcium binding at site II resulted in an increased exposure of Met residues 45 and 81 to the soluble spin label HyTEMPO. This result is consistent with an opening of the hydrophobic pocket in the N‐terminal domain of cTnC upon binding Ca2+ at site II. The binding of the inhibitory peptide cTnlp, corresponding to Asn 129 through Ile 149 of cTnl, to both 2Ca2+‐loaded and Ca2+‐saturated cTnC was shown to protect Met residues 120 and 157 from HyTEMPO as determined by a decrease in their measured R1 values. These results suggest that in both the 2Ca2+‐loaded and Ca2+‐saturated forms of cTnC, cTnlp binds primarily to the C‐terminal domain of cTnC.
Engineering the substrate specificity of rhizopuspepsin: The role of Asp 77 of fungal aspartic proteinases in facilitating the cleavage of oligopeptide substrates with lysine in P1
Authors: Todd Lowther W. , Dunn Ben M. , Majer Pavel
Published: June 2010

Rhizopuspepsin and other fungal aspartic proteinases are distinct from the mammalian enzymes in that they are able to cleave substrates with lysine in the P1 position. Sequence and structural comparisons suggest that two aspartic acid residues, Asp 30 and Asp 77 (pig pepsin numbering), may be responsible for generating this unique specificity. Asp 30 and Asp 77 were changed to the corresponding residues in porcine pepsin, Ile 30 and Thr 77, to create single and double mutants. The zymogen forms of the wild‐type and mutant enzymes were overexpressed in Escherichia coli as inclusion bodies. Following solubilization, denaturation, refolding, activation, and purification to homogeneity, structural and kinetic comparisons were made. The mutant enzymes exhibited a high degree of structural similarity to the wild‐type recombinant protein and a native isozyme. The catalytic activities of the recombinant proteins were analyzed with chromogenic substrates containing lysine in the P1, P2, or P3 positions. Mutation of Asp 77 resulted in a loss of 7 kcal mol−1 of transition‐state stabilization energy in the hydrolysis of the substrate containing lysine in P1. An inhibitor containing the positively charged P1‐lysine side chain inhibited only the enzymes containing Asp 77. Inhibition of the Asp 77 mutants of rhizopuspepsin and several mammalian enzymes was restored upon acetylation of the lysine side chain. These results suggest that an exploitation of the specific electrostatic interaction of Asp 77 in the active site of fungal enzymes may lead to the design of compounds that preferentially inhibit a variety of related Candida proteinases in immunocompromised patients.
Secondary and tertiary structure of the A‐state of cytochromecfrom resonance Raman spectroscopy
Authors: Jordan Trace , Eads Janina C. , Spiro Thomas G.
Published: June 2010

Ferricytochromeccan be converted to the partially folded A‐state at pH 2.2 in the presence of 1.5 M NaCl. The structure of the A‐state has been studied in comparison with the native and unfolded states, using resonance Raman spectroscopy with visible and ultraviolet excitation wavelengths. Spectra obtained with 200 nm excitation show a decrease in amide II intensity consistent with loss of structure for the 50s and 70s helices. The 230‐nm spectra contain information on vibrational modes of the single Trp 59 side chain and the four tyrosine side chains (Tyr 48, 67, 74, and 97). The Trp 59 modes indicate that the side chain remains in a hydrophobic environment but loses its tertiary hydrogen bond and is rotationally disordered. The tyrosine modes Y8b and Y9a show disruption of tertiary hydrogen bonding for the Tyr 48, 67, and 74 side chains. The high‐wavenumber region of the 406.7‐nm resonance Raman spectrum reveals a mixed spin heme iron atom, which arises from axial coordination to His 18 and a water molecule. The low‐frequency spectral region reports on heme distortions and indicates a reduced degree of interaction between the heme and the polypeptide chain. A structural model for the A‐state is proposed in which a folded protein subdomain, consisting of the heme and the N‐terminal, C‐terminal, and 60s helices, is stabilized through nonbonding interactions between helices and with the heme.
Identification of the binding and activating sites of the sphingolipid activator protein, saposin C, with glucocerebrosidase
Authors: Weiler Solly , Tomich John M. , Kishimoto Yasuo , O'Brien John S. , Barranger John A.
Published: June 2010

Saposin C is a sphingolipid activator protein of 8.5 kDa that activates lysosomal glucocerebrosidase. Previously, we synthesized and characterized a synthetic full‐length human saposin C protein that displays 85% of the activity of the native saposin C. In this study we use shorter synthetic peptides derived from the saposin C sequence to map binding and activation sites. By determining the activity and kinetic constant (Kact) values of these peptides, we have identified two functional domains, each comprising a binding site adjacent to or partially overlapping with an activation site. Domains 1 and 2 are located within amino acid positions 6–34 and 41–60, respectively. The activation sites span residues 27–34 and 41–49, whereas binding sites encompass residues 6–27 and 45–60. Peptides containing the sequences of either domain displayed 90% of the activity of the full‐length synthetic saposin C. Domain 2, however, bound to glucocerebrosidase by at least an order of magnitude more strongly than domain 1. Binding sites within these domains contain sequences that are excellent candidates for forming amphipathic helical structures. Competition assays demonstrated that the binding of one domain to glucocerebrosidase prevents binding of the other domain, and that saposin A and saposin C bind to the same sites on glucocerebrosidase. A model predicting a saposin C:glucocerebrosidase complex with a stoichiometry of 4:2, respectively, is presented.
Human S100b protein: Formation of a tetramer from synthetic calcium‐binding site peptides
Authors: Donaldson Craig , Barber Kathryn R. , Shaw Gary S. , Kay Cyril M.
Published: June 2010

Human brain S100b protein is a unique calcium‐binding protein comprised of two identical 91‐amino acid polypeptide chains that each contain two proposed helix‐loop‐helix (EF‐hand) calcium‐binding sites. In order to probe the assembly of the four calcium‐binding sites in S100b, a peptide comprised of the N‐terminal 46 residues of S100b protein was synthesized and studied by CD and 1H NMR spectroscopies as a function of concentration and temperature. At relatively high peptide concentrations and in the absence of calcium, the peptide exhibited a significant proportion of α‐helix (45%). Decreasing the peptide concentration led to a loss of α‐helix as monitored by CD spectroscopy and coincident changes in the 1H NMR spectrum. These changes were also observed by 1H NMR spectroscopy as a function of temperature where it was observed that the Tm of the peptide was lowered approximately 14 °C with a 17‐fold decrease in peptide concentration. Sedimentation equilibrium studies were used to determine that the peptide formed a tetramer in solution in the absence of calcium. It is proposed that this tetrameric fold also occurs in S100b and is a result of the interaction of portions of all four calcium‐binding sites.
Structural motifs for pyridoxal‐5′‐phosphate binding in decarboxylases: An analysis based on the crystal structure of the Lactobacillus 30a ornithine decarboxylase
Authors: Momany Cory , Ghosh Ratna , Hackert Marvin L.
Published: June 2010

Two of the five domains in the structure of the ornithine decarboxylase (OrnDC) from Lactobacillus 30a share similar structural folds around the pyridoxal‐5′‐phosphate (PLP)‐binding pocket with the aspartate aminotransferases (AspATs). Sequence comparisons focusing on conserved residues of the aligned structures reveal that this structural motif is also present in a number of other PLP‐dependent enzymes including the histidine, dopa, tryptophan, glutamate, and glycine decarboxylases as well as tryptophanase and serine‐hydroxymethyl transferase. However, this motif is not present in eukaryotic OrnDCs, the diaminopimelate decarboxylases, nor the Escherichia coli or oat arginine decarboxylases. The identification and comparison of residues involved in defining the different classes are discussed.
Backbone dynamics of the oligomerization domain of p53 determined from 15N NMR relaxation measurements
Authors: Clubb Robert T. , Omichinski James G. , Gronenborn Angela M. , Marius Clore G. , Sakaguchi Kazuyazu , Appella Ettore
Published: June 2010

The backbone dynamics of the tetrameric p53 oligomerization domain (residues 319–360) have been investigated by two‐dimensional inverse detected heteronuclear 1H‐15N NMR spectroscopy at 500 and 600 MHz. 15N T1, T2, and heteronuclear NOEs were measured for 39 of 40 non‐proline backbone NH vectors at both field strengths. The overall correlation time for the tetramer, calculated from the T1/T2 ratios, was found to be 14.8 ns at 35 °C. The correlation times and amplitudes of the internal motions were extracted from the relaxation data using the model‐free formalism (Lipari G, Szabo A, 1982, J Am Chem Soc 104:4546–4559). The internal dynamics of the structural core of the p53 oligomerization domain are uniform and fairly rigid, with residues 327–354 exhibiting an average generalized order parameter (S2) of 0.88 ± 0.08. The N‐ and C‐termini exhibit substantial mobility and are unstructured in the solution structure of p53. Residues located at the N‐ and C‐termini, in the β‐sheet, in the turn between the α‐helix and β‐sheet, and at the C‐terminal end of the α‐helix display two distinct internal motions that are faster than the overall correlation time. Fast internal motions (±20 ps) are within the extreme narrowing limit and are of uniform amplitude. The slower motions (0.6–2.2 ns) are outside the extreme narrowing limit and vary in amplitude. Four residues at the tetramer interface exhibit a small degree of conformational averaging as evidenced by 15N line broadening, possibly due to sliding or rolling of the helices at the interface of the two dimers that form the tetramer.
Predicting the helix packing of globular proteins by self‐correcting distance geometry
Authors: Mumenthaler C.H. , Braun W.
Published: June 2010

A new self‐correcting distance geometry method for predicting the three‐dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 Å to 3.1 Å for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.
Multimeric intermediates in the pathway to the aggregated inclusion body state for P22 tailspike polypeptide chains
Authors: Speed Margaret A. , Wang Daniel I.C. , King Jonathan
Published: June 2010

The failure of newly synthesized polypeptide chains to reach the native conformation due to their accumulation as inclusion bodies is a serious problem in biotechnology. The critical intermediate at the junction between the productive folding and the inclusion body pathway has been previously identified for the P22 tailspike endorham‐nosidase. We have been able to trap subsequent intermediates in the in vitro pathway to the aggregated inclusion body state. Nondenaturing gel electrophoresis identified a sequential series of multimeric intermediates in the aggregation pathway. These represent discrete species formed from noncovalent association of partially folded intermediates rather than aggregation of native‐like trimeric species. Monomer, dimer, trimer, tetramer, pentamer, and hexamer states of the partially folded species were populated in the initial stages of the aggregation reaction. This methodology of isolating early multimers along the aggregation pathway was applicable to other proteins, such as the P22 coat protein and carbonic anhydrase II.
Characterization of a quaternary‐structured folding intermediate of an antibody Fab‐fragment
Authors: Lilie Hauke , Jaenicke Rainer , Buchner Johannes
Published: June 2010

Antibody folding is a complex process comprising folding and association reactions. Although it is usually difficult to characterize kinetic folding intermediates, in the case of the antibody Fab fragment, domain‐domain interactions lead to a rate‐limiting step of folding, thus accumulating folding intermediates at a late step of folding. Here, we analyzed a late folding intermediate of the Fab fragment of the monoclonal antibody MAK 33 from mouse (k/IgGl). As a strategy for accumulation of this intermediate we used partial denaturation of the native Fab by guanidinium chloride. This denaturation intermediate, which can be populated to about 90%, is indistinguishable from a late‐folding intermediate with respect to denaturation and renaturation kinetics. The spectroscopic analysis reveals a native‐like secondary structure of this intermediate with aromatic side chains only slightly more solvent exposed than in the native state. The respective partner domains are weakly associated. From these data we conclude that the intramolecular association of the two chains during folding, with all domains in a nativelike structure, follows a two‐step mechanism. In this mechanism, presumably hydrophobic interactions are followed by rearrangements leading to the exact complementarity of the contact sites of the respective domains.
Crystal structure of human pepsin and its complex with pepstatin
Authors: Fujinaga Masao , Chernaia Maia M. , Mosimann Steve C. , James Michael N.G. , Tarasova Nadya I.
Published: June 2010

The three‐dimensional crystal structure of human pepsin and that of its complex with pepstatin have been solved by X‐ray crystallographic methods. The native pepsin structure has been refined with data collected to 2.2 Å resolution to an R‐factor of 19.7%. The pepsin:pepstatin structure has been refined with data to 2.0 Å resolution to an R‐factor of 18.5%. The hydrogen bonding interactions and the conformation adopted by pepstatin are very similar to those found in complexes of pepstatin with other aspartic proteinases. The enzyme undergoes a conformational change upon inhibitor binding to enclose the inhibitor more tightly. The analysis of the binding sites indicates that they form an extended tube without distinct binding pockets. By comparing the residues on the binding surface with those of the other human aspartic proteinases, it has been possible to rationalize some of the experimental data concerning the different specificities. At the S1 site, valine at position 120 in renin instead of isoleucine, as in the other enzymes, allows for binding of larger hydrophobic residues. The possibility of multiple conformations for the P2 residue makes the analysis of the S2 site difficult. However, it is possible to see that the specific interactions that renin makes with histidine at P2 would not be possible in the case of the other enzymes. At the S3 site, the smaller volume that is accessible in pepsin compared to the other enzymes is consistent with its preference for smaller residues at the P3 position.
Crystallization and preliminary X‐ray diffraction studies on recombinant isopenicillin N synthase from Aspergillus nidulans
Authors: Roach Peter L. , Schofield Christopher J. , Baldwin Jack E. , Clifton Ian J. , Hajdu Janos
Published: June 2010

Recombinant Aspergillus nidulans isopenicillin N synthase was purified from an Escherichia coli expression system. The apoenzyme in the presence of saturating concentrations of MnCl2 could be crystallized by either macro‐ or microseeding, using the hanging drop vapor diffusion technique with polyethylene glycol 8000 as precipitant. The crystals (0.5–1.0 mm overall dimensions) diffract X‐rays to at least 2.0 Å resolution at synchrotrons and belong to space group P212121 with unit cell dimensions of a = 59.2 Å, b = 127.0 Å, and c = 139.6 Å. The asymmetric unit contains one dimer, and the solvent content of the crystals is 60%. The crystals are radiation sensitive.
Crystallization of fragment D from human fibrinogen
Authors: Everse Stephen J. , Pelletier Huguette , Doolittle Russell F.
Published: June 2010

Fragment D from human fibrinogen has been crystallized. The fragment, which is composed of three disulfide‐linked chains (α' β' γ' = 88,000), was generated with either plasmin or mild trypsin digestion. The crystals diffracted out to 3.5 Å; the space group is P21, unit cell dimensions a = 108 Å, b = 48 Å, c = 167 Å, β = 106°. Fragment D was also co‐crystallized with the ligand GPRP‐amide, in which case the space group is consistent with P212121, unit cell dimensions a = 476 Å, b = 82 Å, c = 432 Å.
Interaction of SecB with intermediates along the folding pathway of maltose‐binding protein
Authors: Diamond Deborah L. , Strobel Sharon , Chun Sang‐Yearn , Randall Linda L.
Published: June 2010

SecB, a molecular chaperone involved in protein export in Escherichia coli, displays the remarkable ability to selectively bind many different polypeptide ligands whose only common feature is that of being nonnative. The selectivity is explained in part by a kinetic partitioning between the folding of a polypeptide and its association with SecB. SecB has no affinity for native, stably folded polypeptides but interacts tightly with polypeptides that are nonnative. In order to better understand the nature of the binding, we have examined the interaction of SecB with intermediates along the folding pathway of maltose‐binding protein. Taking advantage of forms of maltose‐binding protein that are altered in their folding properties, we show that the first intermediate in folding, represented by the collapsed state, binds to SecB, and that the polypeptide remains active as a ligand until it crosses the final energy barrier to attain the native state.
On the role of Glu‐68 in alcohol dehydrogenase
Authors: Ryde Ulf
Published: June 2010

Theoretical computations (molecular dynamics and combined quantum chemical and molecular mechanical geometry optimizations) have been performed on horse liver alcohol dehydrogenase. The results provide evidence that Glu‐68, a highly conserved residue located 0.47 nm from the catalytic zinc ion, may intermittently coordinate to the zinc ion. Structures with Glu‐68 coordinated to the zinc ion are almost as stable as structures with Glu‐68 at the crystal position and the barrier between the two configurations of Glu‐68 is so low that it can readily be bypassed at room temperature. There is a cavity behind the zinc ion that seems to be tailored to allow such coordination of Glu‐68 to the zinc ion. It is suggested that Glu‐68 may facilitate the exchange of ligands in the substrate site by coordinating to the zinc ion when the old ligand dissociates.
Comparison of methods for searching protein sequence databases
Authors: Pearson William R.
Published: June 2010

We have compared commonly used sequence comparison algorithms, scoring matrices, and gap penalties using a method that identifies statistically significant differences in performance. Search sensitivity with either the Smith‐Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45–55, and optimized gap penalties instead of the conventional PAM250 matrix. More dramatic improvement can be obtained by scaling similarity scores by the logarithm of the length of the library sequence (ln()‐scaling). With the best modern scoring matrix (BLOSUM55 or J093) and optimal gap penalties (‐12 for the first residue in the gap and —2 for additional residues), Smith‐Waterman and FASTA performed significantly better than BLASTP. With ln()‐scaling and optimal scoring matrices (BLOSUM45 or Gonnet92) and gap penalties (‐12, ‐1), the rigorous Smith‐Waterman algorithm performs better than either BLASTP and FASTA, although with the Gonnet92 matrix the difference with FASTA was not significant. Ln()‐scaling performed better than normalization based on other simple functions of library sequence length. Ln()‐scaling also performed better than scores based on normalized variance, but the differences were not statistically significant for the BLOSUM50 and Gonnet92 matrices. Optimal scoring matrices and gap penalties are reported for Smith‐Waterman and FASTA, using conventional or ln()‐scaled similarity scores. Searches with no penalty for gap extension, or no penalty for gap opening, or an infinite penalty for gaps performed significantly worse than the best methods. Differences in performance between FASTA and Smith‐Waterman were not significant when partial query sequences were used. However, the best performance with complete query sequences was obtained with the Smith‐Waterman algorithm and ln()‐scaling.
Automatic recognition of hydrophobic clusters and their correlation with protein folding units
Authors: Zehfus Micheal H.
Published: June 2010

A method is described to objectively identify hydrophobic clusters in proteins of known structure. Clusters are found by examining a protein for compact groupings of side chains. Compact clusters contain seven or more residues, have an average of 65% hydrophobic residues, and usually occur in protein interiors. Although smaller clusters contain only side‐chain moieties, larger clusters enclose significant portions of the peptide backbone in regular secondary structure. These clusters agree well with hydrophobic regions assigned by more intuitive methods and many larger clusters correlate with protein domains. These results are in striking contrast with the clustering algorithm of J. Heringa and P. Argos (1991, J Mol Biol 220:151–171). That method finds that clusters located on a protein's surface are not especially hydrophobic and average only 3–4 residues in size.

Hydrophobic clusters can be correlated with experimental evidence on early folding intermediates. This correlation is optimized when clusters with less than nine hydrophobic residues are removed from the data set. This suggests that hydrophobic clusters are important in the folding process only if they have enough hydrophobic residues.
Optimization of homoepitaxially grown AlGaN/GaN heterostructures
Authors: Grenko J. A. , Ebert C. W. , Reynolds C. L. , Duscher G. J. , Barlage D. W. , Johnson M. A. L. , Preble E. A. , Paskova T. , Evans K. R.
Published: June 2010

We report on the growth of Al0.25Ga0.75N/GaN heterostructures on low dislocation density semi‐insulating c‐axis GaN substrates by metalorganic vapor phase epitaxy (MOVPE). A room temperature (RT) Hall mobility (µRT) up to 2065 cm2 V−1 s−1 at sheet density (ns) of 8.25 × 1012 cm−2 has been measured. This work compliments prior studies in which we observed a buffer‐induced modulation of the RT two‐dimensional electron gas (2DEG) ns and µRT by varying the GaN buffer layer thickness. Here, we focus on the optimization of the heterostructure 2DEG properties by elimination of silicon doping in the Al0.25Ga0.75N barrier and unintentional Al in the not‐intentionally doped (n.i.d.) GaN buffer layer. The 15% improvement in µRT and ns relative to previous results is consistent with those predicted by Poisson solver calculations. Use of thick GaN buffers has minimized the theoretical mobility reduction based on intersubband scattering and has enabled us to determine the 2DEG sheet density associated with the polarization field ($n_{{\rm s}}^{{\rm polar}} $) to be ∼5 × 1012 cm−2.
SHI irradiation effects on electrical and optical properties of PPy–SnO2 nanocomposite
Authors: Sarmah S. , Kumar A.
Published: June 2010

The films of polypyrrole–tin oxide (PPy–SnO2) nanocomposites were synthesized by chemical oxidative polymerization technique. These films were irradiated with 90‐MeV O7+ ions at the fluences of 5 × 1010, 1 × 1011, 5 × 1011, and 1 × 1012 ions/cm2. X‐ray diffraction studies show that microstrain and domain crystallite size of SnO2 nanoparticles in PPy matrix increase with the increase of ion fluence, resulting in highly ordered PPy–SnO2 nanocomposites. TGA analysis shows that the SnO2 nanoparticles inhibit the degradation of PPy, thereby enhancing the thermal stability of the PPy–SnO2 nanocomposites. DC electrical conductivity is found to increase with the increase of fluence and conduction mechanism follows a one‐dimensional variable‐range hopping model. AC electrical conductivity also increases with the increase of ion fluence and obeys correlated barrier‐hopping model. I–V characteristics of the PPy–SnO2 nanocomposites exhibit Schottky barrier formation at the PPy/SnO2 interface. The photoluminescence intensity of the PPy–SnO2 nanocomposite increases with the increase of ion fluence, which can be attributed to the thermal detrapping of charge carriers owing to the enormous energy transfer during swift, heavy‐ion irradiation.
Characterization of chemical bath deposited buffer layers for thin film solar cell applications
Authors: Dwyer D. , Sun R. , Efstathiadis H. , Haldar P.
Published: June 2010

Cadmium sulfide (CdS), indium sulfide (In2S3) and zinc sulfide (ZnS) thin films have been deposited by chemical bath deposition (CBD) for buffer layer applications in Cu–chalcopyrite‐based thin film solar cells. Films were characterized by scanning electron microscopy (SEM), UV–Vis transmission, X‐ray photoelectron spectroscopy (XPS), grazing‐incidence X‐ray diffraction (GIXRD), and spectroscopic ellipsometry. Results indicate CdS can be deposited with low oxygen content and high light transmission over 245–1700 nm. CBD‐ZnS and CBD‐InS both exhibit 5–10% less light transmission than CdS in the same thickness range. In terms of light transmission and degree of impurities CdS appears to be a better buffer material than CBD‐ZnS or CBD‐InS.
Large thermally induced nonlinear refraction of gold nanoparticles stabilized by cyclohexanone
Authors: Sarkhosh Leila , Aleali Hoda , Karimzadeh Rouhollah , Mansour Nastaran
Published: June 2010

Stabilized gold nanoparticle (AuNP) colloids have been fabricated by nanosecond pulsed laser ablation of a pure gold plate in cyclohexanone. The AuNPs colloid exhibits a UV–Vis absorption spectrum with a surface plasmon absorption peak at about 540 nm. Scanning electron microscopy has shown the formation of spherical AuNPs with average size about 53 nm. The shift of 24 cm−1 is observed in the carbonyl band of the colloid using FTIR spectroscopy. This shift indicates that the monomer carbonyl group of cyclohexanone interacts with the surface of the AuNPs and leads to stabilizing the colloid. A large nonlinear refractive index of −2.92 × 10−7 cm2/W is measured using the Z‐scan technique under continuous wave laser irradiation at 532 nm. Our results show that the large induced nonlinear refraction is attributed to the surface plasmon resonance (SPR) enhancement effect of AuNPs, high thermo‐optic coefficient and low thermal conductivity of cyclohexanone. Observation of far‐field diffraction ring patterns confirm a thermally induced negative lens effect and spatial self‐phase modulation in the laser beam as it traverses the colloids.
On strain state and pseudo‐moiré TEM contrast of InSb quantum dots coherently grown on InAs surface
Authors: Bert N. A. , Freidin A. B. , Kolesnikova A. L. , Korolev I. K. , Romanov A. E.
Published: June 2010

In this article, we report on the theoretical analysis of transmission electron microscopy (TEM) images of surface InSb quantum dots (QDs) coherently grown on InAs substrate. A finite element method (FEM) is used to calculate elastic fields and total displacements in a QD and an adjusted region of the substrate. The effects of QD form factor and QD aspect ratio δ on displacements and TEM images are analyzed. A quasilinear dependence of radial displacements on radial coordinate for spherical, elliptical, and truncated spherical QDs is demonstrated. It has been found that the displacement field does not depend on the shape and aspect ratio for QDs with δ > δc1, and the upper part of a QD remains practically undistorted for QDs with δ ≥ δc2. For InSb/InAs heterosystem these critical values are δc1 ≈ 0.13 and δc2 ≈ 0.33. The total displacements are used for computation of TEM diffraction contrast associated with QDs. To achieve this the Howie–Whelan dynamic approach is utilized. Calculated TEM images of heavily strained QDs demonstrate the picture of pseudo‐moiré with a strong dependence of moiré‐like fringe distance Δ on aspect ratio δ. This dependence gives the possibility to determine the aspect ratio and height of QDs from the results of TEM experiments.
Role of S–Au labile bonding in stochastic switching of molecular conductance studied by STM
Authors: Patrone Lionel , Soullier Jérémie , Martin Pascal
Published: June 2010

We studied by scanning tunneling microscopy (STM) the stochastic switching of terthiophene–thiol (3T) molecules grafted on gold surface. For this purpose, 3T molecules were inserted in a dodecanethiol self‐assembled monolayer (SAM). Results are analyzed and discussed in comparison with similar studies performed by other groups on various molecules. Stochastic switching events are attributed to S–Au bond fluctuation such as a breaking/reforming mechanism.
Preparation and thermoelectric properties of polycrystalline nonstoichiometric Yb14MnSb11 Zintl compounds
Authors: Yu C. , Zhu T. J. , Yang S. H. , Shen J. J. , Zhao X. B.
Published: June 2010

Polycrystalline nonstoichiometric Yb14MnSb11 compounds have been successfully prepared by modified induction melting and spark plasma sintering. The carrier concentration was finely tuned by changing the elemental ratio of Mn to Sb. Excess Mn decreases the electrical conductivity and increases the Seebeck coefficient. The thermal conductivity of all samples was less than 1.0 W m–1 K–1. The maximum ZT value is 0.35 K at 673 K for Yb14Mn1.05Sb11, significantly higher than that of the stoichiometric Yb14MnSb11 polycrystalline sample. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
IxV curves of boron and nitrogen doping zigzag graphene nanoribbons
Authors: Padilha José E. , Pontes Renato B. , Da Silva Antônio J. R. , Fazzio Adalberto
Published: June 2010

We investigate the transport properties (IxV curves and zero bias transmittance) of pristine graphene nanoribbons (GNRs) as well as doped with boron and nitrogen using an approach that combines nonequilibrium Green's functions and density functional theory (DFT) [NEGF‐DFT]. Even for a pristine nanoribbon we verify a spin‐filter effect under finite bias voltage when the leads have an antiparallel magnetization. The presence of the impurities at the edges of monohydrogenated zigzag GNRs changes dramatically the charge transport properties inducing a spin‐polarized conductance. The IxV curves for these systems show that depending on the bias voltage the spin polarization can be inverted. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Delocalization of Dyson orbitals in F−(H2O) and Cl−(H2O)
Authors: Dolgounitcheva O. , Zakrzewski V. G. , Ortiz J. V.
Published: June 2010

Electron propagator calculations accurately predict the vertical electron detachment energies of the title complexes. Corresponding Dyson orbitals closely resemble canonical Hartree–Fock orbitals. Approximations that use diagonal self‐energies in the latter basis, therefore, show promise for applications on larger anionic clusters. Neutral final states correspond to Cl 3p or water 1b1 holes, in accord with recent interpretations of Cl−(H2O) photoelectron spectra. However, for the F case, the Dyson orbitals are delocalized over the F and O centers and compromise interpretations that ascribe F(H2O) or F−(H2O+) charge‐transfer character to the final states. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Theoretical exploration of hydrogen loss from AlH3 and Al2 H6
Authors: Nold Christopher P. , Head John D.
Published: June 2010

Quantum chemistry calculations are used to explore H2 loss from AlH3 and Al2 H6 and provide insight into the hydrogen production mechanism from polyalanes, a candidate material for energy storage. We present optimized structures for AlH3, Al2H4, Al2H5, and Al2H6 and some reaction pathways for their interconversion. We have found two pathways for the reaction Al2H6 → Al2H4 + H2, which have activation barriers lower in energy than for the removal of H2 from AlH3. However, the low‐energy H2 loss pathway from Al2H6 suggests that the noninteracting Al–H bonds in the transition state structure favor having bonding similar to that occurring in AlH3. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Mini‐bandstructure tailoring in π‐conjugated periodic block copolymers using the envelope crystalline‐orbital method
Authors: Mujica‐Martínez C. A. , Arce J. C.
Published: June 2010

A strategy for the systematic design of polymeric superlattices with tailor‐made mini‐bandgaps and carrier mini‐effective masses is described and computationally implemented by means of an envelope crystalline‐orbital method, which is a straightforward adaptation for molecules of the envelope‐function approximation widely used in solid‐state physics. Such strategy relies on the construction of π‐conjugated periodic block copolymers from well‐characterized parent polymers, in such a way that the aforementioned electronic parameters can be predicted from the lengths of the blocks. Illustrative calculations for prototypical (PPPx‐PDAy)n superlattices demonstrate the plausibility of the strategy and the advantages of the computational implementation used. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2532–2540, 2010
Some comments on the problem of decoherence
Authors: Brändas Erkki J.
Published: June 2010

We consider a universally valid superposition principle derived from a general complex symmetric ansatz. The approach concerns open, dissipative systems and its significance for the examination and analysis of system‐environment correlations. In particular, we discuss the concept of decoherence in the ensuing fundamental operator equations, incorporating simultaneously holistic and classical regimes. Despite its reductionist character, the theory applies to both micro‐ and macroscopic systems. Examples are drawn from general relativity, for example, the law of light deflection, the gravitational redshift, the time delay and the perihelion motion of Mercury, and from the macroscopic domain, for example, the emergence of self‐organization in complicated enough systems. The preceding portrayal commends autonomicity and provides legitimate concepts of central importance in biological organization and artificial intelligence. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Free energy landscapes in THF for the wittig reaction of acetaldehyde and triphenylphosphonium ylide
Authors: Alagona Giuliano , Ghio Caterina
Published: June 2010

The B3P86/6‐31G* mechanistic results for the Wittig reaction of triphenylphosphonium ylide and acetaldehyde, in vacuo and in tetrahydrofuran (THF) in the IEF‐PCM framework, led to distinct behaviors. In particular, only a gauche betaine (Bg) was obtained in the gas phase and the relevant barriers were smaller than those found for a realistic system (a bulky chiral aldehyde (Alagona and Ghio, Theor Chem Acc 2009, 123, 337)). Conversely, in THF, both mechanisms (via oxaphosphetanes (OPs) only and via betaines plus OPs were represented with significant TS1/TSb barriers. Furthermore, an additional gauche betaine, named B′g, was located (Alagona and Ghio, Int J Quant Chem 2010, 110, 765). A number of open questions however called for an answer. The main issues addressed in this study are: (i) Can Bg and B′g proceed to products along different reaction paths on the same hypersurface in THF? (ii) If it is not so, can they interconvert into each other? (iii) Might the reaction proceed via an anti betaine‐type intermediate? (iv) Is it possible to find a pathway leading directly to a transition state along the path to products without passing through an OP intermediate, as suggested on the basis of quantum molecular dynamics simulations on trimethylphosphonium ylide in dimethylsulfoxide (Ziegler et al., J Phys Chem A 2005, 109, 5136)? The answers to these questions depend on the fact that the phenyl groups at the phosphonium ylide are of paramount importance for obtaining a correct reaction behavior. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2509–2521, 2010
Approaches for understanding and embedding stakeholder realities in mangrove rehabilitation processes in Southeast Asia: lessons learnt from Mahakam Delta, East Kalimantan
Authors: Powell Neil , Osbeck Maria
Published: June 2010

Using a soft systems narrative, this paper examines the implementation process growing out of a policy environment intended to promote the rehabilitation of mangrove ecosystems. The analysis is based on research conducted 2007–09 in the Mahakam Delta in East Kalimantan, Indonesian Borneo. The rich and diverse natural resource base of the area has turned East Kalimantan into one of the wealthiest areas in Indonesia. The case from Mahakam reveals that there is no stakeholder consensus in terms of problem definitions and management priorities of the coastal delta area. Further, there are no institutional bodies or ‘guardians’ responsible for monitoring and facilitating the long‐term sustainability of mangrove systems. There are also significant power imbalances in the system, not only between stakeholders, but also between the discourses of conservation and production. In order to ensure the long‐term, sustainable governance of mangrove systems, these institutional and geopolitical issues will need to be addressed and adapted accordingly. Through a structured systemic inquiry, this analysis has explored the problem situation related to the sustainability of mangrove systems for coastal environments and people. The research shows the complexity in managing dynamic coastal systems subjected to rapid human induced biophysical changes exacerbated by a non‐conducive policy environment aggravating the impact on the ground.

The absence of this guardian implies that feedback and institutional learning is not inherent, making constructive adaptation of governance and management arrangements in this context unlikely. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
Quality indicators on global software development projects: does ‘getting to know you’ really matter?
Authors: Gotel Olly , Kulkarni Vidya , Say Moniphal , Scharff Christelle , Sunetnanta Thanwadee
Published: June 2010

While the payback from technical training is largely undisputed, and a cost that many organizations are prepared to incur, the benefits of socialization training on global software development projects remains an area of debate. This paper begins to explore whether getting to know those you are working with really matters when it comes to the quality of the software that is produced in global settings. The paper describes how five student teams were put in competition to develop software for a Cambodian client. Each extended team comprised students distributed across a minimum of three locations, drawn from the US, India, Thailand, and Cambodia. Two exercises were conducted with these students during the project, to examine their awareness of the countries of their collaborators and competitors, and to assess their knowledge of their own extended team members. On a weekly basis, the stress levels of the students, along with the communication patterns of each development team, were also recorded. The quality of each team's eventual software product was measured through a final product selection process. The paper reports on the results of these two exercises, examined in conjunction with these additional data, and implications for practice and future studies are discussed. Copyright © 2010 John Wiley & Sons, Ltd.