bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative modeling methods: Application to the family of the mammalian serine proteases
Authors: Greer Jonathan 
Published: May 2005

AbstractComparative modeling methods are described that can be used to construct a three‐dimensional model structure of a new protein from knowledge of its sequence and of the experimental structure and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequence for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
Functional interaction among catalytic residues in subtilisin BPN′
Authors: Carter Paul , Wells James A. 
Published: May 2005

AbstractVariant of the serine protease, subtilisin BPN′, in which the catalytic triad residues (Ser‐221, His‐64, and Asp‐32) are replaced singly or in combination by alanine retain activities with the substrate N‐succinyl‐L‐Ala‐L‐Ala‐L‐Pro‐L‐Phe‐p‐nitroanilide (sAAPF‐pna) that are at at least 103 to 104 above the non‐enzymatic rate [Carter, P., Wells, J.A. Nature (London) 322:564–568, 1988]. A possible source of the residual activity was the hydrogen bond with the Nδ2 of Asn‐155 that helps to stabilize the oxyanion generated in the tetrahedral transition state during amide bond hydrolysis by the wild‐type enzyme. Replacing Asn‐155 by Gly (N155G) lowers the turnover number (kcat) for sAAPF‐pna by 150‐fold with virtually no change in the Michaelis constant (KM). However, upon combining the N155G and S221A mutations to give N155G:S221A, kcat is actually 5‐fold greater than for the S221A enzyme. Thus, the catalytic role of Asn‐155 is dependent upon the presence of Ser‐221. The residual activity of the N155G:S221A enzyme (∼104‐fold above the uncatalyzed rate) is not an artifact because it can be completely inhibited by the third domain of the turkey ovomucoid inhibitor (OMTKY3), which forms a strong 1:1 complex with the active site. the mutations N155G and S221A individually weaken the interaction between subtilisin and OMTKY3 by 1.8 and 2.0 kcal/mol, respectively, and in combination by 2.1 kcal/mol. This is consistent with disruption of stabilizing interactions around the reactive site carbonyl of the OMTKY3 inhibitor. These data suggest that Ser‐221 functions together with Asn‐155 to accelerate amide bond hydrolysis and that other transition state stabilizing interactions account for the residual rate enhancement of 103− to 104−fold. More generally, these studies illustrate the limitations of using site‐directed mutagenesis to probe the energetic importance of a single catalytic group whose function is dependent upon the interaction with others.
Quantitative organization of the known protein x‐ray structures. I. Methods and short‐length‐scale results
Authors: Rackovsky S. 
Published: May 2005

AbstractWe address herein the problem of delineating the relationships between the known protein structures. In order to study this problem, methods have been developed to represent arbitrarily sized fragments of biopolymer backbone, and to compare distributions of such fragments. These methods are applied to a classification of 123 structures representing the entire set of known x‐ray structures. The resulting data are analyzed (on the four‐Cα length scale) to determine both the large‐scale organization of the set of known structures (i.e., the relationships between large groups of structures, each comprised of proteins that are structurally related) and its local structure (i.e., the quantitative degree of similarity between any two specific structures). It is shown that the set of structures from a continuum of structural types, ranging from allhelical to all‐sheet/barrel proteins. It is further demonstrated that the density of protein structures is not uniform across this continuum, but rather that structures cluster in certain regions, separated by regions of lower population. The properties of the various regions of the structural space are determined. The existence is demonstrated of strong quantitative correlations between the contents of different types of four‐Cα fragments within protein structures, which imply significant constraints on the types of architecture that can occur in proteins. Analysis of the distribution of structures demonstrates some hitherto unsuspected similarities and suggests that, in some circumstances, neither structural similarity no sequence homology may be necessary conditions for evolutionary relationship between proteins. It is also suggested that these unsuspected similarities may imply similar folding mechanisms for structures of apparently different global architecture. Cases are also noted in which apparently similar structures may fold by different mechanisms. The connection between structure and dynamic properties is discussed, and a possible role of dynamics in the evolution of protein structures is suggested. The sensitivity of the methods presented herein to anomalies of structure refinement is demonstrated. It is suggested that present results provide a frame‐work for analyzing experimental results on structural similarity obtained using vibrational circular dichroism spectra, which are sensitive to local backbone structure.
A consensus prediction of the secondary structure for the 6‐phospho‐β‐D‐galactosidase superfamily
Authors: Gerloff Dietlind L. , Benner Steven A. 
Published: May 2005

AbstractTwo separate unrefined models for the secondary structure of two subfamilies of the 6‐phospho‐β‐D‐galactosidase superfamily were independently constructed by examining patterns of variation and conservation within homologous protein sequences, assigning surface, interior, parsing, and active site residues to positions in the alignment, and identifying periodicities in these. A consensus model for the secondary structure of the entire superfamily was then built. The prediction tests the limits of an unrefined prediction made using this approach in a large protein with substantial functional and sequence divergence within the family. The protein belongs to the (α–β class), with the core β strands aligned parallel. The supersecondary structural elements that are readily identified in this model is a parallel β sheet built by strands C, D, and E, with helices 2 and 3 connecting strands (C + D) and (D + E), respectively, and an analogous α–β unit (strand G and helix 7) toward the end of the sequence. The resemblance of the supersecondary model to the tertiary structure formed by 8‐fold α–β barrel proteins is almost certainly not coincidental. © 1995 Wiley‐Liss, Inc.
Knowledge‐based modeling of the D‐lactate dehydrogenase three‐dimensional structure
Authors: Vinals Carla , De Bolle Xavier , Depiereux Eric , Feytmans Ernest 
Published: May 2005

AbstractA three‐dimensional structure of the NAD‐dependent D‐lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge‐based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D‐LDH subunit shows, as for the formate dehydrogenase, an α/β structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His‐296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg‐235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe‐299, a candidate for stabilizing the methyl group of the substrate. © 1995 Wiley‐Liss, Inc.
Mass spectrometry in environmental analysis
Authors: Medved Miran 
Published: May 2005

AbstractThe coupling of gas chromatography/mass spectrometry provides the most useful technique for structure elucidation and quantitative analysis of organic compounds in environmental samples. The technique finds its application in all environmental media: air, water, wastes, soil, particularly in connection with reliable sampling and sample preparation. Alternative separation and ionization techniques are used in practice on special occassions, such as the assessment of the health hazard caused by an unknown compound, when structure elucidation cannot be performed by the standard gas chromatography/mass spectrometry equipment.
Phase‐system switching in liquid chromatography/continuous‐flow fast‐atom bombardment mass spectrometry
Authors: Kokkonen P. S. , Niessen W. M. A. , Tjaden U. R. , van der Greef J. 
Published: May 2005

AbstractA new, attractive application of the phase‐system switching (PSS) technique is demonstrated. The PSS system is used in combination with liquid chromatography coupled to continuous‐flow fast‐atom bombardment mass spectrometry (LC/CF‐FABMS) to achieve flow‐rate reduction from 1.0 mL/min in the high‐performace liquid chromatography (HPLC) system to 15μL/min going into the mass spectrometer. In PSS, a compound of interest, in this case erythromycin 2′‐ethylsuccinate, is enriched after the analytical separation, on a short trapping column, from which it is desorbed subsequently to the LC/MS interface. Optimal mobile phases and flow‐rates can be used for the HPLC separation as well as for the mass spectrometric detection. Desorption of the analyte is achieved either by using a flow‐rate of 15 μL/min without a splitter or a flow‐rate of 230 μL/min with a splitter. Compared to the LC/CF‐FAB MS methods using a conventional bore HPLC column and a splitter, improved detection limits for the model compound were achieved using the PSS method.
Transannular interaction in the gas phase
Authors: Vairamani M. , Rajeev M. S. , Kumar K. V. Siva 
Published: May 2005

AbstractAcetone chemical ionization mass spectra of cycloalkenes clearly show the operation of transannular interaction in medium sized rings in the form of water loss from [M + 43]+ adduct ions. Based on labelling studies a mechanism has been proposed.
Heats of formation of BF ions and the fluorine anion affinity of BF3 molecules
Authors: Veljković M. , Nešković O. , Zmbov K. F. , Borshchevsky A. Ya. , Vaisberg V. E. , Sidorov L. N. 
Published: May 2005

AbstractThe effusion method, together with mass spectral analysis, has been used to study ion/molecule equilibria involving the negative ion BF. The experimental data obtained have made it possible to calculate enthalples for the reactions:
equation image
and the enthalpy of formation ΔHf(BF, 298) as ( −1716±8) kj/mol. The fluorine anion affinity of BF3 has been determined as FA((BF3)g, 298)=(331±8)kj/mol−1 and compared with Literature data.
Time‐of‐flight mass spectrometry with a compact two‐stage electrostatic mirror: Metastable‐ion studies with high mass resolution and ion emission from thick insulators
Authors: Brunelle A. , Della‐Negra S. , Depauw J. , Joret H. , Le Beyec Y. 
Published: May 2005

AbstractA compact two‐grids mirror is described. Although analytical calculations and computer simulations are useful it is found that experimental adjustments of the mirror voltage and of the bias divider resistors are needed to achieve the optimum performance. The experimental procedure is given. It is shown that a second‐order time‐focusing mirror is appropriate for metastable‐ion studies with high mass resolution. Large variations of sample voltage can be compensated by the mirror. Thick insulators can be analysed.
High energy collision‐induced dissociation of alkali‐metal ion adducts of crown ehters and acyclic analogs
Authors: Maleknia Simin , Brodbelt Jenifer 
Published: May 2005

AbstractHigh energy collision‐induced dissociation (CID) techniques were applied for structural elucidiation of alkli‐metal ion adducts of crown ethers. The CID of alkali‐metal adducts of tetraglyme and hexaethylene glycol were also evaluated to contrast the fragmentation pathways of the cyclic ethers with those of acylic analogs. A common fragmentation channel for alkali‐metal ion adducts of all the ethers, which results in distonic radical cations, is the homolytic cleavage of carbon—carbon bonds. Additionally, dissociation by carbob—oxygen bond cleavage occurs, and these processes are analogous to the fragmentation pathways observed for simple protonated ethers. The proposed fragmentation pathways for alkali‐metal ion adducts of crown ethers result mostly in odd‐electron, acyclic product ions. Dissociation of the alkali‐metal ion adducts of the acyclic ethers is dominated by losses of various neutral species after an initial hydride or proton transfer. The CID processes for all ethers are independent of alkali‐metal ion sizes; however, the extent of dissociation of the complexes to bare alkali‐metal ion increases with the size of the metal.
Proton affinity of arginine measured by the kinetic approach
Authors: Wu Zhuchun , Fenselau Catherine 
Published: May 2005

AbstractThe proton affinity of arginine is obtained from the kinetic method of dissociation of proton‐bound dimers, as 245.2kcal/mol with an uncertainty of ±0.5 kcal/mol higher than that of histidine, the next most basic of the commonly occuring mammalian amino acids, in contrast to the average difference of 1 kcal/mol between the other 19 amino acids. The order of proton affinity of these 20 amino acids is also determined and discussed.
Artefact interpretation in the tandem mass spectrum of the fragment ion at m/z 299 of N,N‐bissalicylidene 1,2‐phenylenediamine
Authors: Mouget Yves , Bertrand Michel J. 
Published: May 2005

AbstractThe advantages offered by the scanning facility of a multisector hybrid mass spectrometer of E1BE2qQ geometry, with software featuring an ‘experimental design’ function, are used to elucidate the origin of an artefact observed at m/z 290.8 in the linked scan spectrum at constant B/E of the m/z 299 ion of N,N‐bissalicylidene 1,2‐phenylenediamine, when performed using a forward geometry (EB) instrument. A previously proposed explanation, whereby the artefact peak was thought to originate from a fragmentation in the first field‐free region, could not be verified by repeating the scan using an instrument of E1BE2qQ geometry, where E1 and E2 were linked during the scan at constant B/E. Several different scans were performed using an ‘experimental design’ scanning function, which allows analyzers to be scanned and linked by means of user‐defined relationships. Thus, a mass‐analysed ion kinetic energy (MIKE) (E2) scan, with E1 set to a value of 0.9725E0, revealed a peak at a value of 0.9462E0 which was subsequently determined to be due to an ion with a mass‐to‐charge ratio of 299, by using the quadrupole mass filter. A recently proposed graphical method, that allows the field values at which the artefact ion is transmitted to be plotted three dimensionally on a cube, illustrates that while the peak will appear in the spectrum obtained using a linked scan at constant B/E using an EB instrument, this will not be the case with an EBE geometry instrument. The EBE arrangement shows that the interference peak at m/z 290.8 appears to be the result of the transition of a higher‐mass ion within the first electrostatic sector.
Diels–Alder reactions of mass‐selected ions in an ion trap mass spectrometer
Authors: Soni Manish , Amy Jon , Frankevich Vladimir , Cooks R. Graham , Taylor Dennis , McKewan Andrew , Schwartz Jae C. 
Published: May 2005

AbstractThis Communication describes the use of a bench‐top ion trap mass spectrometer for the study of structurally diagnostic ion/molecule reactions. The power of the experiment is increased by the broad‐band ion‐isolation and tandem mass spectrometry capabilities of the ion trap which are used to isolate the reactant ion and study its reactions under controlled conditions. The availability of multiple‐stage mass spectrometry (MSn where n = number of stages) provides additional information on the nature of the productions. The compound to be ionized is conveniently introduced into the ion trap from aqueous solution using membrane introduction techniques while the neutral reagent is leaked into the trap through the calibration gas inlet. Polar Diels–Alder reactions of the [4 + 2+] type are investigated and comparisons are made between the reactions occurring in the ion trap and those in a pentaquadrupole mass spectrometer. Three‐stage tandem mass spectra (MS3) are used to characterize the ion/molecule reaction products in the quadrupole ion trap.
Tautomerism of some amino diol and amino alcohol derivatives in the gas, phase1
Authors: Pykäläinen Mika , Vainiotalo Pirjo , Lázár László , Fülöp Ferenc , Bernáth Gábor 
Published: May 2005

AbstractThe mass spectrometric behaviour of condensation products of nine substituted benzaldehydes with 3‐amino‐1,2‐propanediol and 3‐amino‐1‐phenoxy‐2‐propanol was studied under electron impact and chemical ionization. The 70 eV electron impact mass spectra showed that, as in solution, the amino diol derivatives existed as three different structural isomers in the gas phase: viz. open‐chain Schiff base, oxazolidine and tetrahydro‐1,3‐oxazine. The fragmentations revealed a large amount of the decomposed molecular ions to have the open‐chain structure, but also that the amount of both ring forms was considerable. In the same way, with the amino alcohol derivatives both the open‐chain and the oxazolidine ring forms were present in the gas phase. In all cases, the ring formation was much more favourable in the gas phase than in solution. Substituents at the phenyl ring caused changes in the relative amounts of the different forms: electron‐withdrawing substituents shifted the equilibria in favour of the ring forms while electron‐donating substituents favoured the open‐chain form. Under chemical ionization, methane, isobutane and acetone were used as reagent gas. Methane was the only reagent gas that led to some fragmentation of the protonated molecules.
Quantitative surface analysis by XPS: A comparison among different quantitative approaches
Authors: Battistoni C. , Mattogno G. , Paparazzo E. 
Published: May 2005

AbstractAtomic ratio determinations in a series of pure inorganic compounds have been derived from XPS peak intensity measurements taken by area via the so‐called ‘first principles model’ (FPM) and the ‘elemental sensitivity factors’ (ESF) methods. The two methods show similar degrees of accuracy, with a typical error of about ±10% when a set of experimental ESF is developed.A lower accuracy, as expected, has been obtained when the literature ESF have been applied, Some discrepancy between the two approaches are evident when the kinetic energy separations of the XPS elemental peaks involved in the atomic ratio calculations is large. This aspect is discussed in the light of the instrumental responses which are of primary concern for the transferability of ESF results from one instrument to another.
Ion induced surface compositional changes of α brass; a comparative study by AES and sputtered thermal ion mass spectrometry. Application to quantitative AES
Authors: Darque‐Ceretti E. , Delamare F. , Blaise G. 
Published: May 2005

AbstractSurface concentrations and sputtered‐off atom concentrations of α brass are measured during ion bombardment, respectively by Auger spectroscopy and by a new quantitative sputtered thermal ion mass spectrometry method. A new formulation of the problem of surface composition change is proposed which leads to a definition of matrix effect coefficients, sputter elemental yields and a sputter correction factor μ, connecting surface concentrations to sputtered‐off atom concentrations. Implications in quantitative analysis by Auger spectroscopy or any mass spectrometry technique are discussed.
Surface analytical study of the initial stages of growth and composition of protecting oxide‐ and oxycarbide layers on FeAlTi alloys
Authors: Viefhaus H. , Peters J. , Grabke H. J. 
Published: May 2005

AbstractProtecting layers against carburizing atmospheres are of great importance for high temperature alloys. Very good results have been obtained with a model alloy FeAl0.5Ti. For a single crystal sample of this alloy, the composition and growth of the protecting layers were studied by AES and LEED. Excellent epitaxial fit was observed for a titanium oxycarbide layer growing on (100) and (110) oriented samples at high temperatures by surface segregation of C and Ti in oxygen containing atmosphers. At the same time Al segregated to the surface and diffused through this carbide layer. Reaction with oxygen led to the formation of an epitaxial Al2O3 layer on top of the carbide. Both layers were very dense and well adherent even for high quenching rates. Only very small amounts of carbon impurity were able to penetrate through the dense Al2O3 layer and were captured by the oxycarbide layer.
Charge compensation in SIMS analysis of polymer foils using negative secondary ions
Authors: Wittmaack K. 
Published: May 2005

AbstractThe experimental conditions required for charge compensation in depth profiling of polymer foils have been investigated with reference to the analysis of negative secondary ions. Low energy (≤500 eV) electron beams were employed in combination with 8 keV Xe+ ion beams. The minimum electron current required for the appearance of a stable SIMS signal was found to be equal to the ion current. Optimum SIMS signals were achieved by sufficiently overcompensating the primary ion current. Signals due to electron stimulated desorption could be suppressed by appropriate adjustment of the target bias. Reproducible depth profiles were obtained without major difficulties.
Molecular beam epitaxy of semiconductor interfaces and quantum wells for advanced optoelectronic devices
Authors: Ploog Klaus 
Published: May 2005

AbstractWe present selected examples for the control of interface formation with monolayer precision during molecular beam epitaxial growth and its application to modify the bulk properties of semiconductors arbitrarily through bandgap (or wavefunction) engineering. These examples concentrate on the materials system GaAs/AlAs which is important for high‐speed photonic and electron devices. In addition, as an example for strained‐layer superlattice, we briefly discuss Si/Six Ge1‐x superlattices, where the ordering of the electronic bands is strongly affected by the built‐in strain.
The interaction of group IB metals with van der waals faces of semiconducting metal dichalcogenides
Authors: Jaegermann W. , Ohuchi F. S. , Parkinson B. A. 
Published: May 2005

AbstractThe interaction of UHV cleaved van der Waals surfaces of the layered semiconductors SnS2, SnSe2, ZrS2, MoS2 and WS2 with deposited Cu, Ag and Au has been studied with XPS and LEED. It was observed for Cu on SnS2 and for Cu and Ag on SnSe2 that a bulk reaction ocurs leading to the formation of a new phase containing reduced Sn and oxidized Cu or Ag. Even at high coverages a metallic overlayer was not formed. An interfacial reaction at low coverages and subsequently a metallic layer was obtained for Cu on ZrS2 and Ag on SnS2 and Au on SnSe2. Cu, Ag and Au on MoS2 or WS2 form a metallic overlayer with an atomically abrupt semiconductor/metal interface. Epitaxial growth of a Au(111) layer was observed on WS2(0001). The differences in reactivity are related to differences in electrochemical standard potentials of the involved redox processes, structural features and to kinetic factors, e.g. ion transport.