bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revised 2.3 Å structure of porcine pepsin: Evidence for a flexible subdomain
Authors: Abad‐Zapatero Cele , Rydel Timothy J. , Erickson John 
Published: May 2005

AbstractA revised three‐dimensional crystal structure of ethanol‐inhibited porcine pepsin refined to an R‐factor of 0.171 at 2.3 Å resolution is presented and compared to the refined structures of the fungal aspartic proteinases: penicillopepsin, rhizopuspepsin, and endothiapepsin. Pepsin is composed of two nearly equal N and C domains related by an intra dyad. The overall polypeptide fold and active site structures are homologous for pepsin and the fungal enzymes. The weak inhibition of pepsin by ethanol can be explained by the presence of one or more ethanol molecules, in the vicinity of the active site carboxylates, which slightly alter the hydrogen‐bonding network and which may compete with substrate binding in the active site. Structural superposition analysis showed that the N domains aligned better than the C‐domains for pepsin and the fungal aspartic proteinases: 107–140 Cα pairs aligned to 0.72–0.85 Å rms for the N domains; 64–95 Cα pairs aligned to 0.78–1.03 Å rms for the C domains. The major structural difference between pepsin and the fungal enzymes concerns a newly described subdomain whose conformation varies markedly among these enzyme structures. The subdomain in pepsin comprises nearly 100 residues and is composed of two contiguous segments within the C domain (residues 192–212 and 223–299). The subdomain is connected, or “hinged,” to a mixed β‐sheet that forms one of the structurally invariant, active site ψ‐loops. Relative subdomain displacements as large as a 21.0° rotation and a 5.9 Å translation were observed among the different enzymes. There is some suggestion in pepsin that the subdomain may be flexible and perhaps plays a structural role in mediating substrate binding, determining the substrate specificity, or in the activation of the zymogen.
Helix packing of leucine‐rich peptides: A parallel leucine ladder in the structure of Boc‐Aib‐Leu‐Aib‐Aib‐Leu‐Leu‐Leu‐Aib‐Leu‐Aib‐OMe
Authors: Karle Isabella L. , Flippen‐Anderson Judith L. , Sukumar M. , Balaram P. 
Published: May 2005

AbstractThe packing of peptide helices in crystals of the leucine‐rich decapeptide Boc‐Aib‐Leu‐Aib‐Aib‐Leu‐Leu‐Leu‐Aib‐Leu‐Aib‐OMe provides an example of ladder‐like leucylleucyl interactions between neighboring molecules. The peptide molecule forms a helix with five 5→1 hydrogen bonds and two 4→1 hydrogen bonds near the C terminus. Three head‐to‐tail NH ċ O = C hydrogen bonds between helices form continuous columns of helices in the crystal. The helicial columns associate in an antiparallel fashion, except for the association of Leu ċ Leu side chains, which occurs along the diagonal of the cell where the peptide helices are parallel. The peptide, with formula C56H102N10O13, crystallizes in space group P212121 with Z = 4 and cell parameters a = 16.774(3) Å, b = 20.032(3) Å and c = 20.117(3) Å; overall agreement factor R = 10.7% for 2014 data with |Fobs| < 3σ(F); resolution 1.0 Å.
Protease pro region required for folding is a potent inhibitor of the mature enzyme
Authors: Baker David , Silen Joy L. , Agard David A. 
Published: May 2005

Abstractα‐Lytic protease, an extracellular bacterial serine protease, is synthesized with a large pro region that is required in vivo for the proper folding of the protease domain. To allow detailed mechanistic study, we have reconstituted pro region‐dependent folding in vitro. The pro region promotes folding of the protease domain in the absence of other protein factors or exogenous energy sources. Surprisingly, we find that the pro region is a high affinity inhibitor of the mature protease. The pro region also inhibits the closely related Streptomyces griseus protease B, but not the more distantly related, yet structurally similar protease, elastase. Based on these data, we suggest a mechanism in which pro region binding reduces the free energy of a late folding transition state having native‐like structure.
Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure
Authors: Arnold Gregory E. , Dunker A. Keith , Johns Susan J. , Douthart Richard J. 
Published: May 2005

AbstractThe conditional probability, P(σ|x), is a statement of the probability that the value of σ will be found given the prior information that a value of x has been observed. Here σ represents any one of the secondary structure types, α, β, τ, and ρ for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N‐cap and C‐cap values; (4) Chou–Fasman conformational parameters for helix, Pα, for sheet, Pβ, and for turn, Pτ; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, Iα, for sheet, Iβ, for turn, I,τ, and for random structure, Iρ.Plots of P (σ|x) vs. x are demonstrated to provide information about the correlation between structure and attribute, σ and x. The separations between different P (σ|x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P (α|x), P (β|x), P (τ|x) and P (ρ|x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix > Pα » N‐cap > C‐cap ≈ Iα ≈ Iτ. The information value for turns, Iτ, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: Iβ » Pβ ≈ hydropathy > Iρ ≈ hydrophobic moment assuming sheet.Three attributes, at their low values, were found to give significant discrimination for the absence of helix: Iα ≈ Pα ≈ hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: Pβ » Iτ ≈ hydropathy. Indications of the absence of σ could be as useful for some applications as the indication of the presence of σ.
Structures of the “open” and “closed” state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: Implications for the reaction mechanism
Authors: Noble Martin E. M. , Zeelen Johan Ph. , Wierenga Rik K. 
Published: May 2005

AbstractThe structure of trypanosomal triosephosphate isomerase (TIM)has been solved at a resolution of 2.1Å in a new crystal form grown at pH 8.8 from PEG6000. In this new crystal form (space group C2, cell dimensions 94.8 Å, 48.3 Å, 131.0 Å, 90.0°, 100.3°, 90.0°), TIM is present in a ligand‐free state. The asymmetric unit consists of two TIM subunits. Each of these subunits is part of a dimer which is sitting on a crystallographic twofold axis, such that the crystal packing is formed from two TIM dimers in two distinct environments. The two constituent monomers of a given dimer are, therefore, crystallographically equivalent. In the ligand‐free state of TIM in this crystal form, the two types of dimer are very similar in structure, with the flexible loops in the “Open” conformation. For one dimer (termed molecule‐1), the flexible loop (loop‐6) is involved in crystal contacts. Crystals of this type have been used in soaking experiments with 0.4 M ammonium sulphate (studied at 2.4 Å resolution), and with 40 μM phosphoglycolohydroxamate (studied at 2.5 Å resolution). It is found that transfer to 0.4 M ammonuum sulphate (equal to 80 times the Ki of sulphate for TIM), gives rise to significant sulphate binding at the active site of one dimer (termed molecule‐2), and less significant binding at the active site of the other. In neither dimer does sulphate induce a “closed” conformation. In a mother liquor containing 40 μM phosphoglycolohydroxamate (equal to 10 times the Ki of phosphoglycolohydroxamate for TIM), an inhibitor molecule binds at the active site of only that dimer of which the flexible loop is free from crystal contacts (molecule‐2). In this dimer, it induces a closed conformation. These three structures are compared and discussed with respect to the mode of binding of ligand in the active site as well as with respect to the conformational changes resulting from ligand binding. © 1993 Wiley‐Liss, Inc.
Dynamic properties of some β‐chain mutant hemoglobins
Authors: Militello V. , Cupane A. , Leone M. , Brinigar W. S. , Lu A.‐L. , Fronticelli C. 
Published: May 2005

AbstractThe thermal behavior of the Soret band relative to the carbonmonoxy derivatives of some β‐chain mutant hemoglobins is studied in the temperature range 300–10 K and compared to that of wild‐type carbonmonoxy hemoglobin. The band profile at various temperatures is modeled as a Voigt function that accounts for homogeneous broadening and for the coupling with high‐ and low‐frequency vibrational modes, while inhomogeneous broadening is taken into account with a gaussian distribution of purely electronic transition frequencies. The various contributions to the overall bandwidth are singled out With this analysis and their temperature dependence, in turn, gives information on structural and dynamic properties of the system studied. In the wildtype and mutant hemoglobins, the values of homogeneous bandwidth and of the coupling constants to high‐frequency vibrational modes are not modified with respect to natural human hemoglobin, thus indicating that the local electronic and vibrational properties of the heme–CO complex are not altered by the recombinant procedures. On the contrary, differences in the protein dynamic behavior are observed. The most relevant are those relative to the “polar isosteric” βVal‐67(Ell) →Thr substitution, localized in the heme pocket, which results in decreased coupling with low‐frequency modes and increased anharmonic motions. Mutations involving residue βLys‐144(HC1) at the C‐terminal and residue βCys‐112(G14) at the α1β1 interface have a smaller effect consisting in an increased coupling with low‐frequency modes. Mutations at the β‐N‐terminal and at the α1β2 interface have no effect on the dynamic properties of the heme pocket. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction studies of leishmanolysin, the major surface metalloproteinase from Leishmania major
Authors: Schlagenhauf Edith , Etges Robert , Metcalf Peter 
Published: May 2005

AbstractThe membrane‐bound GPI‐anchored zinc metalloproteinase leishmanolysin purified from Leishmania major promastigotes has been crystallized in its mature form. Two crystal forms of leishmanolysin have been grown by the vapor diffusion method using 2‐methyl‐2,4‐pentanediol as the precipitant. Macroseeding techniques were employed to produce large single crystals. Protein microhet‐erogeneity in molecular size and charge was incorporated into both crystal forms. The tetragonal crystal form belongs to the space group P41212 or the enantiomorph P43212, has unit cell parameters of a = b = 63.6 Å, c = 251.4 Å, and contains one molecule per asymmetric unit. The second crystal form is monoclinic, space group C2, with unit cell dimensions a = 107.2 Å, b = 90.6 Å, c = 70.6 Å, β = 110.6°, and also contains one molecule per asymmetric unit. Both crystal forms diffract X‐rays beyond 2.6 Å resolution and are suitable for X‐ray analysis. Native diffraction data sets have been collected and the structure determination of leishmanolysin using a combination of the isomorphous replacement and the molecular replacement methods is in progress. © 1995 Wiley‐Liss, Inc.
Crystallization and preliminary X‐ray diffraction studies of the cartilage link protein from bovine trachea
Authors: Jedrzejas Marek J. , Baker John R. , Luo Ming 
Published: May 2005

AbstractCartilage extracellular matrix link protein, having molecular mass of approximately 40 kDa, is a metalloprotein that binds divalent cations and is only soluble in low ionic strength solutions. The link protein was purified from bovine trachea and has been crystallized by a vapor diffusion method using PEG 3350 as precipitant. The crystal symmetry is P1, and the unit cell dimensions are a = 43.55, b = 53.11, c = 60.10 Å, α = 90.44, β = 106.21, γ = 101.51°. The VM of 1.8 Å3/Da is consistent with the presence of two molecules of the link protein in the asymmetric unit. The crystals diffract X‐rays from a synchrotron source to 1.7 Å resolution. © 1995 Wiley‐Liss, Inc.
Massive cluster impact mass spectrometry: A new desorption method for the analysis of large biomolecules
Authors: Mahoney J. F. , Perel J. , Ruatta S. A. , Martino P. A. , Husain S. , Cook Kelsey , Lee T. D. 
Published: May 2005

AbstractA new ion desorption method is described that utilizes a primary beam of massive, multiply charged cluster ions to generate secondary ions of peptides in a glycerol matrix. The massive cluster ion beam is generated via electrohydrodynamic emission using a 1.5 M solution of ammonium acetate in 30% aqueous glycerol. Negaitve ion spectra of peptides obtained using this technique show greatly decreased relative intensities for fragment ions and ‘chemical noise’ background when compared to spectra obtained using a xenon atom primary beam. The near absence of fragmets derived from radiation damage to the sample solution is attributed to the impact of primary particles with energies less than 1 eV/nucleon.
A mass spectrometric investigation of mono‐, di‐ and trimethylenebis (disphenylphosphine)‐ Pt(II)‐cis‐dichloro and ‐dicyano derivatives
Authors: Vianello Sebastiano , Bonivento Massimiliano , Cattalini Lucio , Curcuruto Ornella , Traldi Pietro , Chapman J. R. 
Published: May 2005

AbstractThe mass spectrometric behaviour of mono‐, di‐ and trimethylenebis(diphenylphosphine)‐Pt(II)‐cis‐dichloro and ‐dicyano drivatives has been studied with the aid of two different ionization techniques (electron ionization and fast‐atom bombardment) and metastable ion studies, with the aim of finding the most suitable mass spectrometric technique for determining the real monomeric or dimeric structure of such compounds. Electron ionization mass spectrometry led to the best results in terms of molecular ion identification and production of fragment ions well‐related to the original structure. On the contrary, fast‐atom bombardment led to the formation of dimeric species for Pt{1,2‐bis(diphenylphosphino)methane}Cl2 and Pt{1,2‐bis(diphenylphosphino)methane}(CN)2 due to the high reactivity of the monomeric molecules in the condensed phase.
Methane chemical ionization of pesticides by ion‐trap technology: Spectral characteristics and data precision
Authors: Cairns Thomas , Chiu Kin. S. , Siegmund Emil 
Published: May 2005

AbstractExamination of the methane chemical ionization (CI) spectra produced in an ion trap under automatic reaction control has revealed a strong concentration dependence phenomenon even at trace levels (ppm). The spectra produced during the elution profile of various pesticides via capillary gas‐chromatographic introduction have indicated a large percentage of an electron ionization (EI) spectral component superimposed on the CI spectrum. This duplicity of spectral character can be an important asset for confirmation of presence and it does not present a problem of obtaining acceptable precision and accuracy on quantification of pesticide residues. Identification of residues using the standard spectral library databased derived from other sources might require careful scrutiny before acceptance.
Theory of coupling axial and radial ion motion in an ion cyclotron resonance cell during off‐resonance excitation
Authors: Mordehai Alex V. , Henion Jack D. 
Published: May 2005

AbstractAn analytic theory of nonlinear effects in the Z‐oscillation (axial motion) during off‐resonance excitation is proposed. This theory is fbased on a representation of electric potential in an ion cyclotron resonance cell in the fourth‐order approximation. Z‐oscillation is considered as a parametric oscillation with a defined motion in the plane of the magnetic field. It is shown that a peculiarity of ion motion due tocoupling of axial and radial motions can be understood in terms of the stability of the Mathieu equation common to the dthree‐dimensional quadrupole ion trap (quistor). Analytic expressions relating parameters (A, Q) of the dMathieu equation to the coefficients of electric potential expansion in the cell are obtained. The strongest coupling effects arise when the frequency of excitation differs from the base cyclotron frequency bytwice the value of the effective frequency of Z‐oscillation that correof parametric resonance in Z‐oscillations.
Thermal degradation of O‐acyl oximes under electron impact ionization conditions
Authors: Horiyama Shizuyo , Suwa Kiyoko , Yamaki Masae , Kataoka Hiromi , Katagi Toyoshi , Takayama Mitsuo 
Published: May 2005

AbstractThermal degradation of O‐acyl oximes under electron impact ionization (EI) conditions has been examined. The EI mass spectra gave fragment ions originating from thermal degradation, as well as molecular ions M+· and normal fragment ions due to unimolecular decomposition of the M+· ions. The fragment ions due to thermal degradation of O‐acyl oximes were identified by using fast‐atom bombardment (FAB) mass spectrometry with a liquid matrix together with the collision‐induced dissociation (CID) technique. While the FAB mass spectra of O‐acyl oximes gave, preferentially, M+· ions together with some characteristic fragment ions, as well as the molecular related ions [M+H]+ and [M−H]+, the spectra showed little evidence of the fragment ions which may originate from thermal degradation, under EI conditions. The CID spectra of selected M+· ions formed by electron impact also showed little of such fragment ions. The thermal degradation was directly confirmed by measuring the FAB mass spectra of O‐acyl oximes that had been heated in a sealed sample tube.
Ion‐Optical solutions in time‐of‐flight mass spectrometry
Authors: Ioanoviciu Damaschin 
Published: May 2005

AbstractTime‐of‐flight mass spectrometers are able to cover mass ranges to around a half a million Da. The mass resolution of these instruments has been improved drastically by incorporation of electrostatic mirrors. The ion‐optical solutions enabling these achievements and other promising features are discussed in terms of: First‐ and second‐order space focusing in time for linear drift time‐of‐flight mass spectrometers; velocity focusing by time lag; ion‐packet bunching in post‐source impulse focusing; first‐ and second‐order energy focusing in time, in single‐ and double‐stage homogeneous electrostatic mirrors with normal and oblique ion incidence; gridless designs; perfect time focusing in parabolic potential and axial symmetry; cylindrical ion mirrors and toroidal electrostatic deflectors as time‐of‐flight mass analyzers; three electrostatic sector geometry applied in secondary ion microscopy and four toroidal sector systems for tandem mass spectrometry; poloidal electrostatic sectors. Estimation of time‐of‐flight mass spectrometer performance limits is discussed and the stable as well as the metastable peak shapes found in time‐of‐flight mass spectra.
Delayed extraction matrix‐assisted laser desorption time‐of‐flight mass spectrometry
Authors: Vestal M. L. , Juhasz P. , Martin S. A. 
Published: May 2005

AbstractA new delayed extraction matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight (TOF) mass spectrometer system is described which provides dramatically improved performance over that obtained with identical TOF analyzers operated with constant electrical fields. In this system the ions formed by MALDI are produced in a weak electrical field, and subsequently extracted by application of a high voltage pulse after a predetermined time delay. Three parameters can be independently adjusted to optimize the performance. These include the field magnitude and direction during and immediately following ion production, the magnitude of the extraction field, and the time delay between the laser pulse and application of the extraction field. Theoretical equations are presented which guide the selection of these parameters to optimize the performance.Results are presented from three TOF analyzers of similar design, but ranging in size from a 1.3 m linear analyzer to a 6.4 m reflector. In all cases delayed extraction provides substantially improved resolution over that obtained from static operation. In the smallest linear analyzer resolution of M/ΔM (full width at half maximum) of 4000 is demonstrated for angiotensin I, and with the largest reflecting analyzer, the isotope peaks of bovine insulin are resolved nearly to baseline. With larger proteins, the isotopic peaks are not resolved, but resolution approaching the width of the isotopic envelope is obtained. Resolution improvement is demonstrated for proteins up to 30 kDa. In addition to improved resolution, delayed extraction is shown to improve the quality of MALDI mass spectra by suppressing matrix background, reducing chemical noise, and minimizing the effect of laser intensity on performance.
The characterization of proteins and peptides by automated methods
Authors: Bonner Ron , Shushan Bori 
Published: May 2005

AbstractA suite of software programs called the BioToolBox is described. The primary purpose of the BioToolBox is to facilitate the characterisation of proteins and peptides using data acquired by IonSpraTM mass spectrometry and tandem mass spectrometry. As an example, the characterization of a 50 KDa protein (transcription termination factor‐rho) is described. The programs which comprise the BioToolBox produce complementary information which is exchanged between the software modules.
The contribution of bremsstrahlung to radiation damage by ESCA
Authors: Wagner C. D. 
Published: May 2005

AbstractThere has been a widely‐held belief that the radiation damage occasionally observed in analysis by ESCA is largeldue to the bremsstrahlung component of the radiation from electron impact on the aluminum or magnesium X‐ray anodes. Analysis of the distribution of photons detected from 15kV electrons on aluminum shows that no more than 3% of the radiation damage can come from the bremsstrahlung component.
On the influence of sample temperature on depth resolution in sputtering
Authors: Kühlein Maria , Jäger Ingomar 
Published: May 2005

AbstractEvaporated silver layers of varying thickness on poly‐crystalline copper substrates were sputtered off at different temperatures. The relation between depth resolution and sample temperature at different layer thickness was investigated. It turned out that raising the temperature from 298 K to 423 K results in a significant improvement of Δz whereas at 498 K the depth resolution is—although better than at 298 K—poorer again. Within the investigated range of depth Δz varies like Δz ∞ z5/6 for all temperatures thus indicating a strong deviation from the SLS model.
Developing trends in the application of XPS in the USA
Authors: Wagner C. D. , Joshi A. 
Published: May 2005

AbstractSome recent developments in XPS in the United States are briefly described. Two new instruments have been introduced, one a ‘Small Spot ESCA’, providing analyses of <1 mm area with monochromatized x‐rays, the other a conveniently engineered hemispherical analyser with very high data gathering speed and good resolution. Studies of energies of Auger lines along with those of photoelectron lines elucidate the role of screening energy in chemical shifts. Neighboring molecules, and especially neighboring conductive surfaces can provide screening energies of more than an electron volt. Effects on thin films and highly dispersed phases are beginning to emerge. Accurate data on energies and energy differences of shallow core levels and valence bands are providing information on band bending and chemical shifts at interfaces, information of great value in the semiconductor industry. Low energy monochromatized photons from synchrotron sources have provided data on shifts in core levels between surface atoms and bulk atoms. Applications in surface science are just beginning.