bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macromolecular crystal growth experiments on international microgravity laboratory – 1
Authors: Day John , McPherson Alexander 
Published: February 2009

AbstractMacromolecular crystal growth experiments, using satellite tobacco mosaic virus (STMV) and canavalin from jack beans as samples, were conducted on a US Space Shuttle mission designated International Microgravity Laboratory — 1 (IML‐1), flown January 22–29, 1992. Parallel experiments using identical samples were carried out in both a vapor diffusion‐based device (PCG) and a liquid‐liquid diffusion‐based instrument (CRYOSTAT). The experiments in each device were run at 20–22 °C and at colder temperatures.Crystals were grown in virtually every trial, but the characteristics of the crystals were highly dependent on the crystallization technique employed and the temperature experience of the sample. In general, very good results, based on visual inspection of the crystals, were obtained in both PCG and CRYOSTAT. Unusually impressive results were, however, achieved for STMV in the CRYOSTAT instrument. STMV crystals grown in microgravity by liquid‐liquid diffusion were more than 10‐fold greater in total volume than any STMV crystals previously grown in the laboratory.X‐ray diffraction data collected from eight STMV crystals grown in CRYOSTAT demonstrated a substantial improvement in diffraction quality over the entire resolution range when compared to data from crystals grown on Earth. In addition, the extent of the diffraction pattern for the STMV crystals grown in space extended to 1.8 Å resolution, whereas the best crystals that were ever grown under conditions of Earth's gravity produced data limited to 2.3 Å resolution.Other observations indicate that the growth of macromolecular crystals is indeed influenced by the presence or absence of gravity. These observations further suggest, consistent with earlier results, that the elimination of gravity provides a more favorable environment for such processes.
Differences in the amino acid distributions of 310‐helices and α‐helices
Authors: Karpen Mary E. , De Haseth Pieter L. , Neet Kenneth E. 
Published: February 2009

AbstractLocal determinants of 310‐helix stabilization have been ascertained from the analysis of the crystal structure data base. We have clustered all 5‐length substructures from 51 nonhomologous proteins into classes based on the conformational similarity of their backbone dihedral angles. Several clusters, derived from 310‐helices and multiple‐turn conformations, had strong amino acid sequence patterns not evident among α‐helices. Aspartate occurred over twice as frequently in the N‐cap position of 310‐helices as in the N‐cap position of α‐helices. Unlike α‐helices, 310‐helices had few C‐termini ending in a left‐handed α conformation; most 310 C‐caps adopted an extended conformation. Differences in the distribution of hydrophobic residues among 310‐ and α‐helices were also apparent, producing amphipathic 310‐helices. Local interactions that stabilize 310‐helices can be inferred both from the strong amino acid preferences found for these short helices, as well as from the existence of substructures in which tertiary interactions replace consensus local interactions. Because the folding and unfolding of α‐helices have been postulated to proceed through reverse‐turn and 310‐helix intermediates, sequence differences between 310‐ and α‐helices can also lend insight into factors influencing α‐helix initiation and propagation.
Purification and properties of the cellular prion protein from Syrian hamster brain
Authors: Pan Keh‐Ming , Stahl Neil , Prusiner Stanley B. 
Published: February 2009

AbstractThe cellular prion protein (PrPC) is encoded by a chromosomal gene, and its scrapie isoform (PrPSc) features in all aspects of the prion diseases. Prior to the studies reported here, purification of PrPC has only been accomplished using immunoaffinity chromatography yielding small amounts of protein. Brain homogenates contain two PrPC forms designated PrPC‐I and ‐II. These proteins were purified from a microsomal fraction by detergent extraction and separated by immobilized Cu2+ ion affinity chromatography. PrPC‐II appears to be generated from PrPC‐I by limited proteolysis of the N‐terminus. Fractions enriched for PrPC‐I were purified further by cation‐exchange chromatography and sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE). Greater than 90% of the final product migrated as a broad band of Mr 33–35 kDa as judged by silver staining after SDS‐PAGE. Digestion of PrPC‐I with peptide‐N‐glycosidase (PNGase) compressed the band and shifted its mobility giving an Mr of 27 kDa. The protocol described should be amenable to large‐scale preparation of PrPC, enabling physical comparisons of PrPC and PrPSc.
Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two‐dimensional NMR spectroscopy
Authors: Wittekind Michael , Rajagopal Ponni , Branchini Bruce R. , Reizer Jonathan , Saier Milton H. , Klevit Rachel E. 
Published: February 2009

AbstractThe solution structure of the phosphocarrier protein, HPr, from Bacillus subtilis has been determined by analysis of two‐dimensional (2D) NMR spectra acquired for the unphosphorylated form of the protein. Inverse‐detected 2D (1H‐15N) heteronuclear multiple quantum correlation nuclear Overhauser effect (HMQC NOESY) and homonuclear Hartmann‐Hahn (HOHAHA) spectra utilizing 15N assignments (reported here) as well as previously published 1H assignments were used to identify cross‐peaks that are not resolved in 2D homonuclear 1H spectra. Distance constraints derived from NOESY cross‐peaks, hydrogen‐bonding patterns derived from 1H–2H exchange experiments, and dihedral angle constraints derived from analysis of coupling constants were used for structure calculations using the variable target function algorithm, DIANA. The calculated models were refined by dynamical simulated annealing using the program X‐PLOR. The resulting family of structures has a mean backbone rmsd of 0.63 Å (N, Cα, C', O atoms), excluding the segments containing residues 45–59 and 84–88. The structure is comprised of a four‐stranded antiparallel β‐sheet with two antiparallel α‐helices on one side of the sheet. The active‐site His 15 residue serves as the N‐cap of α‐helix A, with its Nδ1 atom pointed toward the solvent to accept the phosphoryl group during the phosphotransfer reaction with enzyme I. The existence of a hydrogen bond between the side‐chain oxygen atom of Tyr 37 and the amide proton of Ala 56 is suggested, which may account for the observed stabilization of the region that includes the β‐turn comprised of residues 37–40. If the βαββαβ(α) folding opology of HPr is considered with the peptide chain polarity reversed, the protein fold is identical to that described for another group of βαββαβ proteins that include acylphosphatase and the RNA‐binding domains of the U1 snRNP A and hnRNP C proteins.
Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2
Authors: Bassolino‐Klimas Donna , Bruccoleri Robert E. , Subramaniam Shankar 
Published: February 2009

AbstractA model structure has been constructed for a monoclonal anti‐dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey, T., & McConnell, H.M., 1984, Biochemistry 23, 1138–1142). Its amino acid sequence shows striking homology with the anti‐lysozyme Fab fragments HyHel5 (83%) and HyHel10 (73%). Based on this homology, a model for the ANO2 variable heavy and variable light chain framework was constructed using a hybrid of the HyHel5 light chain and the HyHel10 heavy chain backbone, omitting the hypervariable loops. These coordinates were used as scaffolds for the model building of ANO2.The CONGEN conformational sampling algorithm (Bruccoleri, R.E. & Karplus, M., 1987, Biopolymers 26, 127–196) was used to model the six hypervariable loops that contain the antigen‐combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent‐accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the β‐barrel, namely, L2‐H1‐L3‐H2‐H3‐L1. The model structures thus obtained were compared to the high resolution X‐ray structure (Brünger, A.T., Leahy, D.J., Hynes, T.R., & Fox, R.O., 1991, J. Mol. Biol. 221, 239–256).
A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives
Authors: Doolittle Russell F. 
Published: February 2009

AbstractVertebrate fibrinogen is a complex multidomained protein, the structure of which has been inferred mainly from electron microscopy and amino acid sequence studies. Among its most prominent features are two terminal globules, moieties that are mostly composed of the carboxyl‐terminal two‐thirds of the β and γ chains. Sequences homologous to the latter segments are found in several other animal proteins, always as the carboxyl‐terminal contributions. An alignment of 15 amino acid sequences from various fibrinogens and related proteins has been used to make judgments about secondary structure. The nature of amino acids at each position in the alignment was used to distinguish α helices and β structure on the one hand from loops and turns on the other, and the resulting assignments compared with predictions of secondary structure by other methods. Additionally, constraints imposed by the locations of cystines, carbohydrate attachment residues, and proteinase‐sensitive points provided further insights into the general organization of the postulated secondary structures. Other ancillary data, including the effects of bound calcium and the locations of labeled or variant residues, were also considered. An intriguing similarity to a portion of the recently reported structure of a calcium‐dependent lectin is noted.
A database of protein structure families with common folding motifs
Authors: Holm Liisa , Ouzounis Christos , Sander Chris , Tuparev Georg , Vriend Gert 
Published: February 2009

AbstractThe availability of fast and robust algorithms for protein structure comparison provides an opportunity to produce a database of three‐dimensional comparisons, called families of structurally similar proteins (FSSP). The database currently contains an extended structural family for each of 154 representative (below 30% sequence identity) protein chains. Each data set contains: the search structure; all its relatives with 70–30% sequence identity, aligned structurally; and all other proteins from the representative set that contain substructures significantly similar to the search structure. Very close relatives (above 70% sequence identity) rarely have significant structural differences and are excluded. The alignments of remote relatives are the result of pairwise all‐against‐all structural comparisons in the set of 154 representative protein chains. The comparisons were carried out with each of three novel automatic algorithms that cover different aspects of protein structure similarity. The user of the database has the choice between strict rigid‐body comparisons and comparisons that take into account interdomain motion or geometrical distortions; and, between comparisons that require strictly sequential ordering of segments and comparisons, which allow altered topology of loop connections or chain reversals. The data sets report the structurally equivalent residues in the form of a multiple alignment and as a list of matching fragments to facilitate inspection by three‐dimensional graphics. If substructures are ignored, the result is a database of structure alignments of full‐length proteins, including those in the twilight zone of sequence similarity. The database makes explicitly visible architectural similarities in the known part of the universe of protein folds and may be useful for understanding protein folding and for extracting structural modules for protein design. The data sets are available via Internet.
Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein
Authors: He Jing J. , Quiocho Florante A. 
Published: February 2009

AbstractElectrostatic interactions are among the key factors determining the structure and function of proteins. Here we report experimental results that illuminate the functional importance of local dipoles to these interactions. The refined 1.7‐Å X‐ray structure of the liganded form of the sulfate‐binding protein, a primary sulfate active transport receptor of Salmonella typhimurium, shows that the sulfate dianion is completely buried and bound by hydrogen bonds (mostly main‐chain peptide NH groups) and van der Waals forces. The sulfate is also closely linked, via one of these peptide units, to a His residue. It is also adjacent to the N‐termini of three α‐helices, of which the two shortest have their C‐termini “capped” by Arg residues. Site‐directed mutagenesis of the recombinant Escherichia coli sulfate receptor had no effect on sulfate‐binding activity when an Asn residue was substituted for the positively charged His and the two Arg (changed singly and together) residues. These results, combined with other observations, further solidify the idea that stabilization of uncompensated charges in a protein is a highly localized process that involves a collection of local dipoles, including those of peptide units confined to the first turns of helices. The contribution of helix macrodipoles appears insignificant.
Identification of cysteine ligands in metalloproteins using optical and NMR spectroscopy: Cadmium‐substituted rubredoxin as a model [Cd(CysS)4]2‐ center
Authors: Henehan Colin J. , Pountney Dean L. , Vašák Milan , Zerbe Oliver 
Published: February 2009

AbstractOptical and NMR methods are presented for the identification of cysteine ligands in Cd‐substituted metalloproteins, in particular those containing zinc‐fingerlike motifs, using Cd‐substituted Desulfovibrio gigas rubredoxin (Cd‐Rd) as a model [Cd(CysS)4]2‐ complex. The 113Cd NMR spectrum of Cd‐Rd contains a single 113Cd resonance with a chemical shift position (723.6 ppm) consistent with tetrathiolate metal coordination. The proton chemical shifts of the four cysteine ligands were obtained from one‐dimensional heteronuclear (1H‐113Cd) multiple quantum coherence (HMQC) and total coherence spectroscopy (TOCSY)‐relayed HMQC experiments. In addition, sequential assignments were made for two short cysteine‐containing stretches of the polypeptide chain using a combination of homonuclear proton correlated spectroscopy, TOCSY, and nuclear Overhauser effect spectroscopy experiments, enabling sequence‐specific heteronuclear 3J(1Hβ‐113Cd) coupling constants for each cysteine to be determined. The magnitude of these couplings (0–38 Hz) follows a Karplus‐like dependence with respect to the H
β
‐C
β
‐S
γ
‐Cd dihedral angles, inferred from the crystal structure of the native protein. The difference absorption envelope (Cd‐Rd vs. apo‐Rd) reveals three distinct transitions with Gaussian‐resolved maxima located at 213, 229, and 245 nm, which are paralleled by dichroic features in the corresponding difference CD and magnetic CD spectra. Based on the optical electronegativity theory of Jørgensen, the lowest energy transition has been attributed to a CysS‐Cd(II) charge‐transfer excitation (245, 26,000 M−1 cm−1) with a molar extinction coefficient per cysteine of 6,500 M−1 cm−1. It is proposed that the intensity of this band can be used as a sensitive measure of the number of cysteine ligands present in Cd(CysS)4‐n
X
n
centers.
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant
Authors: Merlino Antonello , Avella Giovanna , Di Gaetano Sonia , Arciello Angela , Piccoli Renata , Mazzarella Lelio , Sica Filomena 
Published: February 2009

AbstractA specialized class of RNases shows a high cytotoxicity toward tumor cell lines, which is critically dependent on their ability to reach the cytosol and to evade the action of the ribonuclease inhibitor (RI). The cytotoxicity and antitumor activity of bovine seminal ribonuclease (BSRNase), which exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer, are peculiar properties of the swapped form. A dimeric variant (HHP2‐RNase) of human pancreatic RNase, in which the enzyme has been engineered to reproduce the sequence of BSRNase helix‐II (Gln28→Leu, Arg31→Cys, Arg32→Cys, and Asn34→Lys) and to eliminate a negative charge on the surface (Glu111→Gly), is also extremely cytotoxic. Surprisingly, this activity is associated also to the unswapped form of the protein. The crystal structure reveals that on this molecule the hinge regions, which are highly disordered in the unswapped form of BSRNase, adopt a very well‐defined conformation in both subunits. The results suggest that the two hinge peptides and the two Leu28 side chains may provide an anchorage to a transient noncovalent dimer, which maintains Cys31 and Cys32 of the two subunits in proximity, thus stabilizing a quaternary structure, similar to that found for the noncovalent swapped dimer of BSRNase, that allows the molecule to escape RI and/or to enhance the formation of the interchain disulfides.
Morphological, electrical and optical properties of sputtered Mo thin films on flexible substrates
Authors: Bollero A. , Andrés M. , García C. , Abajo J. de , Gutiérrez M. T. 
Published: February 2009

AbstractMolybdenum (Mo) films were deposited onto Kapton® substrates with different thickness by dc‐magnetron sputtering in order to be used as back contact layer in flexible solar cells. The morphology, electrical resistance and reflectance of the films have been studied as a function of the deposition parameters and the thickness of the polymer films. The lowest resistivity and highest reflectance have been obtained for those films deposited at a reduced working gas pressure of 0.6 Pa. The evolution of these properties is shown to be strongly dependent on the microstructure of the films. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrodeposition behavior of noble metals in ordered macroporous silicon
Authors: Matsumoto Tasuku , Kobayashi Katsutoshi , Fukami Kazuhiro , Sakka Tetsuo , Ogata Yukio H. 
Published: February 2009

AbstractElectrodeposition of noble metals (Pt, Pd, and Au) in ordered macropores prepared in p‐type Si under dark condition was investigated. Pt deposition proceeded continuously from the pore bottoms, and ordered micro‐rods were obtained. Pd deposition proceeded on the whole pore walls, and discontinuous micro‐tubes were obtained. Au deposition proceeded at 10‐20 μm depth from the pore openings where a high immersion plating rate was observed without applied potential, and short micro‐rods were obtained. At the pore bottoms a small amount of deposition was observed. The different behaviors of electrodeposition depending on the metals were compared and discussed. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
EPR and photoluminescence diagnostics of singlet oxygen generation on porous silicon surface
Authors: Konstantinova E. A. , Demin V. A. , Ryabchikov Yu. V. , Gongalskiy M. B. , Kashkarov P. K. 
Published: February 2009

AbstractElectron paramagnetic resonance and photoluminescence spectroscopy are used to investigate photosensitized generation of singlet oxygen in the porous silicon layers. The singlet oxygen concentration in the samples was estimated at various oxygen pressures. The time of energy transfer from excitons confined in Si nanocrystals to adsorbed O2 molecules on silicon nanocrystal surface and photosensitization efficiency are found to depend on the porosity of the samples. The singlet oxygen generation efficiency increases strongly for porous silicon with high (>80%) porosity. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A conservative scheme for the shallow‐water system on a staggered geodesic grid based on a Nambu representation
Authors: Sommer Matthias , Névir Peter 
Published: February 2009

AbstractA conservative spatial discretization scheme is constructed for a shallow‐water system on a geodesic grid with C‐type staggering. It is derived from the original equations written in Nambu form, which is a generalization of Hamiltonian representation. The term ‘conservative scheme’ refers to one that preserves the constitutive quantities, here total energy and potential enstrophy. We give a proof for the non‐existence of potential enstrophy sources in this semi‐discretization. Furthermore, we show numerically that in comparison with traditional discretizations, such schemes can improve stability and the ability to represent conservation and spectral properties of the underlying partial differential equations. Copyright © 2009 Royal Meteorological Society
Augmenting real data with synthetic data: an application in assessing Radio‐Isotope identification algorithms
Authors: Burr T. , Hamada M. S. , Graves T. L. , Myers S. 
Published: February 2009

AbstractThe performance of Radio‐Isotope IDentification (RIID) algorithms using gamma spectroscopy is increasingly becoming important. For example, sensors at locations that screen for illicit nuclear material rely on isotope identification to resolve innocent nuisance alarms arising from naturally occurring radioactive material. Recent data collections for RIID testing consist of repeat measurements for each of several scenarios to test RIID algorithms. Efficient allocation of measurement resources requires an appropriate number of repeats for each scenario. To help allocate measurement resources in such data collections for RIID algorithm testing, we consider using only a few real repeats per scenario. In order to reduce uncertainty in the estimated RIID algorithm performance for each scenario, the potential merit of augmenting these real repeats with realistic synthetic repeats is also considered. Our results suggest that for the scenarios and algorithms considered, approximately 10 real repeats augmented with simulated repeats will result in an estimate having comparable uncertainty to the estimate based on using 60 real repeats. Published in 2009 by John Wiley & Sons, Ltd.
Coordinate scaling of the kinetic energy in pair density functional theory: A Legendre transform approach
Authors: Cuevas‐Saavedra Rogelio , Ayers Paul W. 
Published: February 2009

AbstractWe show that the kinetic energy functional in pair density functional theory is homogeneous of degree 2 with respect to coordinate scaling. Although this result was already derived by Levy and Ziesche using the constrained search method (Levy and Ziesche, J Chem Phys 2001, 115, 9110), we derive our result using the Legendre transform formulation (Ayers et al., J Chem Phys 2006, 124, 054101). The advantage of this approach is that in the Legendre transform functional, the N‐representability problem is solved by the functional. By contrast, in the Levy–Ziesche approach, the computationally impracticable N‐representability constraints have to be imposed separately. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009