bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular modeling indicates that homodimers form the basis for intermediate filament assembly from human and mouse epidermal keratins
Authors: Downing Donald T. 
Published: May 2005

AbstractMammalian epidermal keratin molecules adopt rod‐shaped conformations that aggregate to form cytoplasmic intermediate filaments. To investigate these keratin conformations and the basis for their patterns of molecular association, graphical methods were developed to relate known amino acid sequences to probable spacial configurations. The results support the predominantly α‐helical conformation of keratin chains, interrupted by short non‐α‐helical linkages. However, it was found that many of the linkages have amino acid sequences typical of β‐strand conformations. Space‐filling atomic models revealed that the β‐strand sequences would permit the formation of 2‐chain and 4‐chain cylindrical β‐helices, fully shielding the hydrophobic amino acid chains that alternate with hydrophilic residues in these sequences. Because of the locations of the β‐helical regions in human and mouse stratum corneum keratin chains, only homodimers of the keratins could interact efficiently to form 2‐chain and 4‐chain β‐helices. Tetramers having the directions and degrees of overlap of constituent dimers that have been identified by previous investigators are also predicted from the interactions of β‐helical motifs. Heterotetramers formed from dissimilar homodimers could combine, through additional β‐helical structures, to form higher oligomers having the dimensions seen in electron microscopic studies. Previous results from chemical crosslinking studies can be interpreted to support the concept of homodimers rather than heterodimers as the basis for keratin filament assembly. © 1995 Wiley‐Liss, Inc.
Dynamic structure of human serum transferrin from transient electric birefringence experiments
Authors: van Haeringen Bart , de Lange Frank , van Stokkum Ivo. H. M. , Srai S. Kaila S. , Evans Robert W. , van Grondelle Rienk , Bloemendal Michael 
Published: May 2005

AbstractIn order to investigate the secondary, tertiary, and dynamic structure of the iron‐free (apo) and iron‐saturated (holo) forms of human serum transferrin and its amino (N)‐terminal lobe at the physiologically relevant pHs 7.4 and 5.0, we have combined ultraviolet circular dichroism (CD) spectroscopy with transient‐electric birefringence (TEB) measurements. No significant changes are found in the protein's secondary structure under the different conditions studied. The tertiary structure as monitored by near‐UV CD is affected by iron binding, but does not change upon decrease in pH. In contrast, TEB results indicate dramatic changes in the dynamic structure of transferrin both upon binding of iron and decrease of pH. In apotransferrin freedom of movement is found for the lobes with respect to each other, and for the domains within the lobes. The interlobal flexibility is considerably enhanced at the lower pH. Holotransferrin is found to behave as a rigid molecule. © 1995 Wiley‐Liss, Inc.
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing
Authors: Jones David T. , Miller Robert T. , Thornton Janet M. 
Published: May 2005

AbstractAnalysis of the results of the recent protein structure prediction experiment for our method shows that we achieved a high level of success, Of the 18 available prediction targets of known structure, the assessors have identified 11 chains which either entirely match a previously known fold, or which partially match a substantial region of a known fold. Of these 11 chains, we made predictions for 9, and correctly assigned the folds in 5 cases. We have also identified a further 2 chains which also partially match known folds, and both of these were correctly predicted. The success rate for our method under blind testing is therefore 7 out of 11 chains. A further 2 folds could have easily been recognized but failed due to either overzealous filtering of potential matches, or to simple human error on our part. One of the two targets for which we did not submit a prediction, prosubtilisin, would not have been recognized by our usual criteria, but even in this case, it is possible that a correct prediction could have been made by considerin a combination of pairwise energy and solvation energy Z‐scores. Inspection of the threading alignments for the (αβ)8 barrels provides clues as to how fold recognition by threading works, in that these folds are recognized by parts rather than as a whole. The prospects for developing sequence threading technology further is discussed. © 1995 Wiley‐Liss, Inc.
The phospho‐β‐galactosidase and synaptotagmin predictions
Authors: Benner Steven A. , Gerloff Dietlind , Chelvanayagam Gareth 
Published: May 2005

AbstractTwo bona fide consensus predictions of secondary and tertiary structure in a protein family, made and announced before experimental structures were known, are evaluated in light of the subsequently determined experimental structures. The first, for phospho‐β‐galactosidase, identified the core strands of an 8‐fold α–β barrel, and identified the 8‐fold α–β barrel itself, which was found in the subsequently determined experimental structure to be the core folding domain. The second, for synaptotagmin, identified seven out of eight β‐strands in the structure correctly, missing only a noncore strand. Three preferred “topologies” were selected from several hundred thousand possible topologies of these seven predicted strands using a rule‐based analysis. The subsequently determined experimental structure showed that these seven strands in synaptotagmin adopt one of the three preferred topologies. We were unable, however, to identify the correct topology from among these three topologies. © 1995 Wiley‐Liss, Inc.
An automated method for dynamic ligand design
Authors: Miranker Andrew , Karplus Martin 
Published: May 2005

AbstractAn automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site. © 1995 Wiley‐Liss, Inc.
Hinge‐bending motion in citrate synthase arising from normal mode calculations
Authors: Marques Osni , Sanejouand Yves‐Henri 
Published: May 2005

AbstractA normal mode analysis of the closed form of dimeric citrate synthase has been performed. The largest‐amplitude collective motion predicted by this method compares well with the crystallographically observed hinge‐bending motion. Such a result supports those obtained previously in the case of hinge‐bending motions of smaller systems, such as lysozyme or hexokinase. Taken together, all these results suggest that low‐frequency normal modes may become useful for determining a first approximation of the conformational path between the closed and open forms of these proteins. © 1995 Wiley‐Liss, Inc.
Preliminary X‐ray crystallographic analysis of Tritrichomonas foetus inosine‐5′‐monophosphate dehydrogenase
Authors: Whitby Frank G. , Huete‐Perez Jorge , Luecke Hartmut , Wang C. C. 
Published: May 2005

AbstractInosine‐5′‐monophosphate dehydrogenase (IMPDH) from the protozoan parasite Tritrichomonas foetus has been expressed in E. coli and crystallized. Crystals were grown to 0.1 mm in each dimension in 18 to 72 h using ammonium sulfate and low‐molecular‐weight polyethylene glycols. The crystals belong to the cubic space group P432 with unit cell edge = 157.25 Å. The enzyme is a homotetramer with each monomer having a molecular weight of 55,534 Da. There is one monomer per asymmetric unit, based on a volume/mass ratio of 2.7 Å3/Da and self‐rotation analysis. The crystals are adequately stable to allow a complete data set to be collected from a single crystal. Complete native data sets have been collected to 2.3 Å resolution at 4°C using synchrotron radiation. High‐quality complete data extending to 3.0 Å resolution have been collected from crystals of four putative derivatives, and the data appear to be isomorphous with that of the native crystals in each case. Efforts to solve the derivatives for use in MIR phasing are underway. © 1995 Wiley‐Liss, Inc.
Purification, crystallization, and preliminary X‐ray analysis of Bacillus subtilis ferrochelatase
Authors: Hansson Mats , Al‐Karadaghi Salam 
Published: May 2005

AbstractBacillus subtilis ferrochelatase (EC 4.99.1.1), the final enzyme in protoheme IX biosynthesis, was produced with an inducible T7 RNA polymerase expression system in Escherichia coli and purified from the soluble cell fraction. It was crystallized from polyethylene glycol solution using the microseeding technique. The crystals diffract to a minimum Bragg spacing of 2.1 Å. The space group is P42 with unit cell dimensions a = b = 50.2 Å, c = 120.1 Å. © 1995 Wiley‐Liss, Inc.
Relativistic atomic structure theory: Some recent work
Authors: Grant I. P. 
Published: May 2005

AbstractRecent developments in relativistic atomic structure have been more in terms of program improvement than in fundamental theory. Some comments on both aspects of this work are illustrated by a description of two different recent applications. In the first, we study the contribution of the interaction of relativity and correlation to the 2 3S−2 3P0,1,2 intervals in heliumlike ions, whose theoretical estimation is important for testing QED. The study of satellite structure in the Kβ x‐ray emission spectrum of Ar illustrates a quite different use of the program packages developed at Oxford for investigating configuration interaction. The use of shake theory to predict the initial states, populated along with the primary vacancy giving rise to the diagram line, gives a satellite line intensity distribution which agrees very well with recent experimental spectra.
Isospin basis for atoms in relativistic approximation
Authors: Šimonis V. Č. , Kaniauskas J. M. , Rudzikas Z. B. 
Published: May 2005

AbstractThe isospin basis is put into operation for investigation of atomic configurations, having two shells of equivalent electrons, characterized by the same orbital (LS coupling) or total (jj coupling) angular momenta of each electron. Tensorial properties of both the operators and the wave functions are studied in this basis. The two‐particle operator is expressed in terms of the tensors irreducible in the isospin space. The problem of the additional classification of the levels is considered. The accuracy of the quantum numbers of the isospin basis in jj coupling scheme is discussed.
1/Z perturbation theory for calculation of line strengths in the neon isoelectronic sequence
Authors: Pokleba A. K. , Safronova U. I. 
Published: May 2005

AbstractThe line strengths of 2–2 and 3–3 transitions (2s22p53s–2s22p53p–2s22p53d, 2s2s2p63s–2s2p63p‐2s2p63d, 2s22p53l‐2s2p63l) have been calculated for the Ne isoelectronic sequence (Z = 14 ÷ 100). The calculation has been carried out in intermediate coupling. Relativistic corrections have been included through the Breit operator. Perturbation theory in 1/Z has been used to account for electronic interactions.
Core polarization and relativistic effects competition in the first ionization potentials for some systems in the Cu, Ag, and Au isoelectronic sequences
Authors: Migdalek J. , Baylis W. E. 
Published: May 2005

AbstractSingle‐configuration relativistic Hartree–Fock values of the first ionization potentials for Cu through Kr7+, Ag through I6+, and Au through Pb3+ are computed in “frozen” and “relaxed core” approximations with and without allowance for core polarization. Effects of polarization of the atomic core by the valence electron are included by introducing a polarization potential in the one‐electron Hamiltonian of the valence electron. The core polarization potential depends on two parameters, the static dipole polarizability of the core α and the cut‐off radius r0, which are chosen independently of the ionization potential data. It is demonstrated that by including the core polarization potential with α and r0 parameters, which are simply chosen instead of being empirically fitted, it is still possible to account, on the average, for at least 70% of the discrepancy between the single‐configuration relativistic Hartree–Fock ionization potentials and the experiment, a discrepancy usually ascribed to the contribution of valence‐core electron correlations, and to bring the theoretical ionization potentials to an average agreement with experiment of around 1%. It can be concluded from this study that for low and medium Z elements the core polarization dominates for neutral systems or systems in low ionization stages, whereas for highly ionized systems the relativistic effects prevail. For heavy elements, however, the core polarization influence is comparable to the relativistic one only for neutral systems, whereas for ions the relativistic effects are overwhelmingly predominant.
Basis set expansion of the dirac operator without variational collapse
Authors: Kutzelnigg Werner 
Published: May 2005

AbstractThe eigenstates of the matrix representation of the Dirac operator for c → ∞ do not approach their nonrelativistic counterparts in the same basis. This wrong “Schrödinger limit” is shown to be the main reason for the phenomenon known as “variational collapse.” After a short review of existing proposals to overcome the “variational collapse,” a systematic study of the possible ways to avoid it is given. All discussed approaches are analyzed in terms of various criteria that one wants to fulfill. The most promising approach consists of a free‐particle Foldy–Wouthuysen (FW) transformation on operator level and a back transformation on matrix level (approaches C2 and C3). This implies a modification of the free‐electron part of the matrix representation of the Dirac operator and leads to the correct Schrödinger limit (and if one wishes even the correct Pauli limit) in the same basis (and to the exact results for a complete basis). The potential energy is unchanged, which makes the application to n ‐electron systems straightforward. Projection of the Dirac operator to positive energy states does not remove the variational collapse unless this is done in a very special way.
Relativistic calculations of dissociation energies and related properties
Authors: Pitzer Kenneth S. 
Published: May 2005

AbstractMethods of calculation of potential energy curves or surfaces, including dissociation energies, bond distances, and vibration frequencies, are discussed as well as recently obtained results for several molecules. The ab initio relativistic methods involve the derivation of “shape‐consistent” effective potentials from Dirac–Fock atomic calculations. These effective potentials are averaged and differenced with respect to spin with the differences, p3/2 – p1/2, etc., yielding spin‐orbit operators. The molecular calculations are then set up in a familiar manner through the SCF stage using spin‐averaged effective potentials. The final stage is a configuration‐interaction calculation including the spin‐orbit terms as well as the electron repulsion terms. Calculations that have been made for several low‐lying excited states as well as the ground state for Au2, TlH, Tl2, Sn2, and Pb2 are reviewed. Good agreement is obtained with spectroscopic data and a number of interesting predictions are made.
Electronic structure of molecules using one‐component wave functions and relativistic effective core potentials
Authors: Kahn Luis R. 
Published: May 2005

AbstractA one‐component approach to molecular electronic structure is discussed that includes the dominant relativistic effects on valence electrons and yet allows the use of the traditional quantum‐chemistry techniques. The approach starts with one‐component Cowan–Griffin relativistic orbitals that successfully incorporate the effects of the mass‐velocity and Darwin terms present in more complicated wave functions such as the Dirac–Hartree–Fock. The approach then constructs “relativistic” effective core potentials (RECPS) from these orbitals, and uses these to bring the relativistic effects into the molecular electronic calculations. The use of effective one‐electron spin‐orbit operators in conjunction with these one‐component wave functions to include the effects of spin‐orbit coupling is discussed. Applications to molecular systems involving heavy atoms and comparisons with available spectroscopic data on molecular geometries and excitation energies are presented. Finally, a new approach to the construction of RECPS encompassing the Hamiltonian and shapeconsistent approach is presented together with a novel analysis of the long‐range behavior of the RECPS.
Electronic structure of the PdCl42− and PtCl42−ions
Authors: Larsson Sven , Olsson Lars‐Fride , Rosén Arne 
Published: May 2005

AbstractThe electronic spectra of PdCl42− and PtCl42− are studied by quantum‐chemical methods with the ultimate object being to understand the differences in reactivity for Pt(II) and Pd(II) complexes. Nonrelativistic ab initio UHF, DV ‐ Xα, and MSXα methods give very similar assignments of the spectra for PdCl42−. The d–d spectrum for PtCl42−, which is very different from the d–d spectrum of PdCl42−, agrees qualitatively with the spectra obtained using the relativistic extended‐Hückel (REX) and Dirac–Slater (DS) methods. Although the latter two methods disagree somewhat in the interpretation of the high intensity bands in PtCl42−, it appears reasonable to interpret at least one of the lines as a 5d → 6p transition.
Electronegativity equalization and the electronic structure of polyhedral clusters of main‐group atoms
Authors: Lohr Lawrence L. 
Published: May 2005

AbstractThe concept of the equalization of atomic electronegativities accompanving molecule formation is applied to a study of the electronic structure of polyhedral clusters of main‐group atoms such as Ge, Sn, Pb, Tl, and Bi. Emphasis is placed upon charged clusters such as Sn9−x Pb(x = 0 → 9), Sn9‐xGe, Sn8−xPbx Tl5−, Sn2Bi, SnTe, etc. The role of the relativistic spin‐orbit splitting of an np shell into np1/2 and np3/2 subshells in modifying atomic and hence molecular electronegativities is discussed. Correlations are made between calculated charge distributions and observed199 Sn NMR chemical shifts for clusters of a given size and charge. It is concluded that a useful picture of charge distributions in these clusters may be obtained from electronegativity equalization considerations.
Butyl nitrite: A novel chemical ionization reagent compound
Authors: Moncur J. H. , Brown R. S. , Ibrahim S. , Wilson J. M. , Jennings Keith R. 
Published: May 2005

AbstractA Kratos MS‐25RFA medium resolution mass spectrometer and a Concept IS high resolution mass spectrometer were used to analyse a range of highly substituted aromatic alcohols for kinetic studies.
Fast atom bombardment/collisional activation mass spectrometry of β‐D‐mannosyl‐(1→4)‐β‐D‐N‐acetylglucosaminyl (1→N) urea and related compounds
Authors: Heerma W. , Dallinga J. W. , Dorland L. , van Rhee A. M. , van Pelt J. , Duran M. , de Jong E. G. 
Published: May 2005

AbstractA new compound, obtained during the isolation of oligosaccharides from the urine of two brothers affected with inherited β‐mannosidase deficiency, has been investigated using fast atom bombardment ionization and MS/MS techniques. The compound could be characterized as an N‐acetylglucosamine molecule linked to a hexose and a urea molecule.
How are S ions formed in electron collisions with linear SCS?
Authors: Mazumdar S. , Kumar S. V. K. , Marathe V. R. , Mathur D. 
Published: May 2005

AbstractThe energetics of S ion formation in electron dissociative ionization of linear CS2 are investigated experimentally with a crossed‐beam apparatus. Ab initio self‐consistent‐field molecular orbital (SCF MO) calculations of potential energy curves for low‐lying electronic states of this ion have been made in order to explain how stable S ions are formed, initially at the very large internuclear separation of 3.2 Å.
Structural „memory effects”︁ influencing decompositions of glucose alkoxide anions produced from monoterpene glycoside isomers in tandem mass spectrometry
Authors: Cole R. B. , Tabet J. C. , Salles C. , Jallageas J. C. , Crouzet J. 
Published: May 2005

AbstractIsomeric glycoconjugates have been distinguished using desorption negative‐ion chemical ionization/tandem mass spectrometry (DNCI–MS/MS). The structure of the leaving terpene influences the orientation of consecutive decompositions during collisionally activated decomposition (CAD) of [M–H]− ions which pass through a glucose alkoxide intermediate ion. This apparent „memory effect”︁ can be rationalized by considering the production of anion‐induced dipole complexes.
Can aluminium‐clad capillary columns be used for gas chromatography/mass spectrometry on a sector mass spectrometer?
Authors: Bowen David V. , Pullen Francis S. 
Published: May 2005

AbstractAluminium‐clad fused silica capillary columns can be used with magnetic sector mass spectrometers. The column end needs to be pulled back a millimetre or so from the ion source to avoid electrical arcing. The chromatographic integrity is maintained. This brings the benefits of robust construction and high temperature gas chromatography/mass spectrometry to sector mass spectrometers.
Screening by tandem mass spectrometry for trace levels of alkylbenzenes
Authors: Cairns Thomas , Siegmund Emil G. 
Published: May 2005

AbstractProduct ion spectra derived from molecule ions as the precursor ions for 14 alkylbenzenes have been studied under electron ionization and methane chemical ionization. The data have provided a satisfactory screening method for both detection and confirmation of such compounds at low parts per million levels.
High resolution chromatography/tandem mass spectrometry. Analysis of polychlorinated dibenzo‐p‐dioxins and furans
Authors: Fraisse D. , Gonnord M. F. , Becchi M. 
Published: May 2005

AbstractCapabilities of high resolution chromatography/tandem mass spectrometry for quantitation of polychlorinated dibenzo‐p‐dioxins and polychlorinated dibenzo furans have been investigated with a hybrid instrument. Selected‐transition monitoring procedures, collision energy and collision gases have been optimized for maximum sensitivity. The results are compared with those obtained by high resolution chromatography/high resolution mass spectrometry.
Computer‐controlled sequencing of peptides by tandem mass spectrometry
Authors: Herrmann Jörg , Schlunegger Urs Peter 
Published: May 2005

AbstractA fully automated computer‐controlled system was used to generate series of different linked scans at constant B2E and constant neutral loss in the second field‐free region. This system has been shown to be suitable for deriving the amino acid sequence of oligopeptides.