bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calculation of protein ionization equilibria with conformational sampling: pKa of a model leucine zipper, GCN4 and barnase
Authors: Gorfe Alemayehu A. , Ferrara Philippe , Caflisch Amedeo , Marti Daniel N. , Bosshard Hans Rudolf , Jelesarov Ilian 
Published: September 2002

AbstractThe use of conformational ensembles provided by nuclear magnetic resonance (NMR) experiments or generated by molecular dynamics (MD) simulations has been regarded as a useful approach to account for protein motions in the context of pKa calculations, yet the idea has been tested occasionally. This is the first report of systematic comparison of pKa estimates computed from long multiple MD simulations and NMR ensembles. As model systems, a synthetic leucine zipper, the naturally occurring coiled coil GCN4, and barnase were used. A variety of conformational averaging and titration curve‐averaging techniques, or combination thereof, was adopted and/or modified to investigate the effect of extensive global conformational sampling on the accuracy of pKa calculations. Clustering of coordinates is proposed as an approach to reduce the vast diversity of MD ensembles to a few structures representative of the average electrostatic properties of the system in solution. Remarkable improvement of the accuracy of pKa predictions was achieved by the use of multiple MD simulations. By using multiple trajectories the absolute error in pKa predictions for the model leucine zipper was reduced to as low as approximately 0.25 pKa units. The validity, advantages, and limitations of explicit conformational sampling by MD, compared with the use of an average structure and a high internal protein dielectric value as means to improve the accuracy of pKa calculations, are discussed. Proteins 2002;46:41–60. © 2001 Wiley‐Liss, Inc.
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
Authors: Österberg Fredrik , Morris Garrett M. , Sanner Michel F. , Olson Arthur J. , Goodsell David S. 
Published: September 2002

AbstractProtein motion and heterogeneity of structural waters are approximated in ligand‐docking simulations, using an ensemble of protein structures. Four methods of combining multiple target structures within a single grid‐based lookup table of interaction energies are tested. The method is evaluated using complexes of 21 peptidomimetic inhibitors with human immunodeficiency virus type 1 (HIV‐1) protease. Several of these structures show motion of an arginine residue, which is essential for binding of large inhibitors. A structural water is also present in 20 of the structures, but it must be absent in the remaining one for proper binding. Mean and minimum methods perform poorly, but two weighted average methods permit consistent and accurate ligand docking, using a single grid representation of the target protein structures. Proteins 2002;46:34–40. © 2001 Wiley‐Liss, Inc.
Reversible substrate‐induced domain motions in ribonuclease A
Authors: Vitagliano Luigi , Merlino Antonello , Zagari Adriana , Mazzarella Lelio 
Published: September 2002

AbstractDespite the increasing number of successful determinations of complex protein structures the understanding of their dynamics properties is still rather limited. Using X‐ray crystallography, we demonstrate that ribonuclease A (RNase A) undergoes significant domain motions upon ligand binding. In particular, when cytidine 2′‐monophosphate binds to RNase A, the structure of the enzyme becomes more compact. Interestingly, our data also show that these structural alterations are fully reversible in the crystal state. These findings provide structural bases for the dynamic behavior of RNase A in the binding of the substrate shown by Petsko and coworkers (Rasmussen et al. Nature 1992;357:423–424). These subtle domain motions may assume functional relevance for more complex system and may play a significant role in the cooperativity of oligomeric enzymes. Proteins 2002;46:97–104. © 2001 Wiley‐Liss, Inc.
Continuum electrostatic analysis of irregular ionization and proton allocation in proteins
Authors: Koumanov Assen , Rüterjans Heinz , Karshikoff Andrey 
Published: September 2002

AbstractIrregular (nonsigmoidal) ionization behavior of titratable groups in proteins is analyzed theoretically, using a computational algorithm designed to count explicitly for tautomers of titratable groups and different locations of polar hydrogens. On the basis of calculations for different model systems (acid–acid, base–base, acid–base pairs, and cluster of three strongly interacting groups), it is demonstrated that the pKvalues, extracted from nonsigmoidal titration curves by fitting to a sum of Henderson–Hasselbalch equations, do not describe the ionization equilibrium correctly. The conditions for observation of irregular titration curves are derived analytically for the case of arbitrary couple of interacting ionizable groups. A possible relation between irregularly shaped titration curves and tautomerization is also illustrated. The protonation–deprotonation equilibrium of Asp76 in ribonucleaseT1is shown to be coupled to dipole reorientation of a water molecule bound at the protein–solvent interface. This finding provides a new interpretation of the experimentally observed chemical shift of this residue. Proteins 2002;46:85–96. © 2001 Wiley‐Liss, Inc.
What are the dielectric “constants” of proteins and how to validate electrostatic models?
Authors: Schutz Claudia N. , Warshel Arieh 
Published: September 2002

AbstractImplicit models for evaluation of electrostatic energies in proteins include dielectric constants that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielectric constant. Furthermore, the factors that determine the optimal value of these constants are far from being obvious. This review considers the meaning of the protein dielectric constants and the ways to determine their optimal values. It is pointed out that typical benchmarks for validation of electrostatic models cannot discriminate between consistent and inconsistent models. In particular, the observed pKa values of surface groups can be reproduced correctly by models with entirely incorrect physical features. Thus, we introduce a discriminative benchmark that only includes residues whose pKa values are shifted significantly from their values in water. We also use the semimacroscopic version of the protein dipole Langevin dipole (PDLD/S) formulation to generate a series of models that move gradually from microscopic to fully macroscopic models. These include the linear response version of the PDLD/S models, Poisson Boltzmann (PB)‐type models, and Tanford Kirkwwod (TK)‐type models. Using our different models and the discriminative benchmark, we show that the protein dielectric constant, εp, is not a universal constant but simply a parameter that depends on the model used. It is also shown in agreement with our previous works that εp represents the factors that are not considered explicitly. The use of a discriminative benchmark appears to help not only in identifying nonphysical models but also in analyzing effects that are not reproduced in an accurate way by consistent models. These include the effect of water penetration and the effect of the protein reorganization. Finally, we show that the optimal dielectric constant for self‐energies is not the optimal constant for charge‐charge interactions. Proteins 2001;44:400–417. © 2001 Wiley‐Liss, Inc.
Modeling of the metallo‐β‐lactamase from B. fragilis: Structural and dynamic effects of inhibitor binding
Authors: Salsbury Freddie R. , Crowley Michael F. , Brooks Charles L. 
Published: September 2002

AbstractThe structure and dynamics of an inhibitor‐bound complex of the metallo‐β‐lactamase from Bacteroides fragilis are studied by using molecular dynamics. A search of the conformational space was performed to obtain three distinct models of the complex, which were then subjected to solvated molecular dynamics. A solvated molecular dynamics study of the apo protein was performed to serve as a baseline for comparison with the bound simulations. We find loop conformation changes due to binding as well as a decrease in flexibility of the protein as a whole and especially in the major loop of the β‐lactamase. We report the structural and dynamical features of the inhibitor‐bound and apo models, as well as experimentally measurable quantities, which should be capable of distinguishing the two binding modes we have determined. Proteins 2001;44:448–459. © 2001 Wiley‐Liss, Inc.
Molecular dynamics simulations of the conformational changes of the glutamate receptor ligand‐binding core in the presence of glutamate and kainate
Authors: Mendieta Jesús , Ramírez Galo , Gago Federico 
Published: September 2002

AbstractExcitatory synaptic transmission is mediated by ionotropic glutamate receptors (iGluRs) through the induced transient opening of transmembrane ion channels. The three‐dimensional structure of the extracellular ligand‐binding core of iGluRs shares the overall features of bacterial periplasmic binding proteins (PBPs). In both families of proteins, the ligand‐binding site is arranged in two domains separated by a cleft and connected by two peptide stretches. PBPs undergo a typical hinge motion of the two domains associated with ligand binding that leads to a conformational change from an open to a closed form. The common architecture suggests a similar closing mechanism in the ligand‐binding core of iGluRs induced by the binding of specific agonists. Starting from the experimentally determined kainate‐bound closed form of the S1S2 GluR2 construct, we have studied by means of molecular dynamics simulations the opening motion of the ligand‐binding core in the presence and in the absence of both glutamate and kainate. Our results suggest that the opening/closing interdomain hinge motions are coupled to conformational changes in the insertion region of the transmembrane segments. These changes are triggered by the interaction of the agonists with the essential Glu 209 residue. A plausible mechanism for the coupling of agonist binding to channel gating is discussed. Proteins 2001;44:460–469. © 2001 Wiley‐Liss, Inc.
Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N‐acetylgalactosamine
Authors: Rabijns A. , Verboven C. , Rougé P. , Barre A. , Van Damme E.J.M. , Peumans W.J. , De Ranter C.J. 
Published: September 2002

AbstractThe structure of the bark lectin RPbAI (isoform A4) from Robinia pseudoacacia has been determined by protein crystallography both in the free form and complexed with N‐acetylgalactosamine. The free form is refined at 1.80 Å resolution to an R‐factor of 18.9% whereas the complexed structure has an R‐factor of 19.7% at 2.05 Å resolution. Both structures are compared to each other and to other available legume lectin structures. The polypeptide chains of the two structures exhibit the characteristic legume lectin tertiary fold. The quaternary structure resembles that of the Phaseolus vulgaris lectin, the soybean agglutinin, and the Dolichos biflorus lectin, but displays some unique features leading to the extreme stability of this lectin. Proteins 2001;44:470–478. © 2001 Wiley‐Liss, Inc.
Studies on a new group of biodegradable surfactants for glyphosate
Authors: Haefs Roland , Schmitz‐Eiberger Michaela , Mainx Hans‐G , Mittelstaedt Werner , Noga Georg 
Published: September 2002

AbstractThe effectiveness of a homologous series of biodegradable rapeseed oil derivatives (triglyceride ethoxylates; Agnique RSO® series containing an average of 5, 10, 30 and 60 units of ethylene oxide (EO) as adjuvants for foliage‐applied, water‐soluble, systemic active ingredients was evaluated employing glyphosate as an example. Previous experiments had revealed that the surfactants used are not phytotoxic at concentrations ranging from 1 to 10 g litre−1. The experiments were performed usingPhaseolus vulgarisL and nine selected weed species, grown in a growth chamber at 25/20 (± 2) °C day/night temperature and 40/70 (±10)% relative humidity. The surfactants were evaluated for enhancement of spray retention, and foliar penetration biological efficacy of glyphosate. Glyphosate was applied at a concentration of 43 mM. The surfactants were added at concentrations of 1 g litre−1. The commercial glyphosate 360 g AE litre−1SL Roundup Ultra and unformulated glyphosate served as references. The surfactants used improved spray retention, foliar penetration and biological efficacy. Some of the formulations were comparable to the performance of Roundup Ultra in the aspects evaluated; some were even more effective in enhancing spray liquid retention and promoting glyphosate phytotoxicity in several plant species. In these studies Agnique RSO 60 generally was most effective.© 2002 Society of Chemical Industry
Quantitative screening and matrix effect studies of drug discovery compounds in monkey plasma using fast‐gradient liquid chromatography/tandem mass spectrometry
Authors: Hsieh Yunsheng , Chintala Madhu , Mei Hong , Agans Jacqueline , Brisson Jean‐Marc , Ng Kwokei , Korfmacher Walter A. 
Published: September 2002

AbstractA higher‐throughput bioanalytical method based on fast‐gradient (1 min run time) high‐performance liquid chromatography (HPLC) coupled with tandem mass spectrometry (MS/MS) was developed for screen‐type analyses of plasma samples from early drug discovery studies in support of exploratory pharmacodynamic studies. The HPLC system equipped with minibore column was interfaced with either atmospheric pressure chemical ionization (APCI) or electrospray (ESI) ionization techniques. The matrix ion suppression effect of both quantitative HPLC/MS/MS analyses was compared using the post‐column infusion system. The use of the described methods provided advantages such as a shorter chromatographic region of ion suppression, less solvent consumption and shorter run times in comparison with standard analytical column HPLC/MS/MS methods. The analytical results obtained by both HPLC/MS/MS methods were in good agreement (within 15% of error) and displayed a good correlation with the pharmacodynamic outcome. Copyright © 2001 John Wiley & Sons, Ltd.
Electrospray tandem mass spectrometry of aminochromes
Authors: Lemos‐Amado Francisco , Domingues Pedro , Ferrer‐Correia A. , Remião Fernando , Milhazes Nuno , Borges Fernanda , Carvalho Félix D. , Bastos Maria L. 
Published: September 2002

AbstractThe catecholamines adrenaline, noradrenaline, dopamine, dopa and isoprenaline were oxidized into their respective aminochromes: adrenochrome, noradrenochrome, dopaminochrome, dopachrome and isoprenochrome. Tandem mass spectrometry (MS/MS) fragmentation patterns were examined for the five aminochromes in order to establish a general structural assignment of these oxidation products by electrospray mass spectrometry. Although protonated aminochromes undergo similar fragmentation patterns with a characteristic consecutive loss of two carbonyl groups, the presence of different substituents in the parent compounds led to significant changes in the CID spectra. This feature is more evident for isoprenochrome and dopachrome, especially for the latter where the MS/MS spectrum is dominated by the loss of formic acid. A general pattern of fragmentation for aminochromes is proposed, which should provide a suitable basis to aid their characterization in studies in vivo or in vitro. Copyright © 2001 John Wiley & Sons, Ltd.
Direct characterization of iodine covalently bound to fulvic acids by electrospray mass spectrometry
Authors: Moulin Valérie , Reiller Pascal , Amekraz Badia , Moulin Christophe 
Published: September 2002

AbstractNumerous studies have demonstrated that humic substances (HS) react with iodine to form iodo derivatives and thereby can control the bioavailability of radioisotopes. Unfortunately, none of these studies have provided detailed insights into product compounds and so far, to our knowledge, the direct analysis of these species by electrospray ionization (ESI) mass spectrometry has not been explored. The reactivity of iodine with fulvic acids (FA) present in HS was investigated by means of ESI coupled with a quadrupole time‐of‐flight (Q‐TOF) mass spectrometer. ESI spectra of solutions, that were indicated by MS/MS analysis to have formed iodinated species, apparently displayed singly charged ions corresponding in m/z to hypothesized species, viz., [RI − H]−, R = (substituted FA compound). MS/MS analysis based on the diagnostic fragment ions for FA compounds and their iodo derivatives suggests that FA undergo aromatic substitutions. Furthermore, significant differences in mass profiles are observed that presumably result from extended redox reactions. The ESI‐MS technique opens up new opportunities to understand the scavenging properties of HS towards radionuclides and heavy metals for environmental studies. Copyright © 2001 John Wiley & Sons, Ltd.
Determination of anabolic steroids with gas chromatography–ion trap mass spectrometry using hydrogen as carrier gas
Authors: Impens Sandra , Wasch Katia De , Brabander Hubert De 
Published: September 2002

AbstractHelium is considered to be the ideal carrier gas for gas chromatography/mass spectrometry (GC/MS) in general, and for use with an ion trap in particular. Helium is an inert gas, can be used without special precautions for security and, moreover, it is needed as a damping gas in the trap. A disadvantage of helium is the high viscosity resulting in long GC run times. In this work hydrogen was tested as an alternative carrier gas for GC in performing GC/MS analyses. A hydrogen generator was used as a safe source of hydrogen gas. It is demonstrated that hydrogen can be used as a carrier gas for the gas chromatograph in combination with helium as make‐up gas for the trap. The analysis time was thus shortened and the chromatographic performance was optimized. Although hydrogen has proven useful as a carrier gas in gas chromatography coupled to standard detectors such as ECD or FID, its use is not mentioned extensively in the literature concerning gas chromatography–ion trap mass spectrometry. However, it is worth considering as a possibility because of its chromatographic advantages and its advantageous price when using a hydrogen generator. Copyright © 2001 John Wiley & Sons, Ltd.
Determination of benzene at trace levels in air by a novel method based on solid‐phase microextraction gas chromatography/mass spectrometry
Authors: Saba Alessandro , Cuzzola Angela , Raffaelli Andrea , Pucci Sergio , Salvadori Piero 
Published: September 2002

AbstractA new method for the determination of benzene at trace levels in air is presented. The method consists of the collection of air samples on adsorbent cartridges with simultaneous adsorption of pre‐established amounts of D6‐labeled internal standard. Desorption from the cartridge is performed by solid‐phase microextraction (SPME) with analysis by gas chromatography/mass spectrometry (GC/MS) using an ion trap mass spectrometer. The influence of several parameters (type of SPME fiber, temperature, time, for example) was investigated, and good linearity in the range 10–400 ng of C6D6, with a coefficient of variance (CV) around 3–5%, was obtained. The method was tested by sampling air in a town center in Italy, and a benzene concentration of approximately 50 µg/m3 was determined. The maximum limit recommended by the European Community is 10 µg/m3. Copyright © 2001 John Wiley & Sons, Ltd.
Automated molecular weight assignment of electrospray ionization mass spectra
Authors: Williams Jon D. , Weiner Brian E. , Ormand James R. , Brunner Jimmy , Thornquest Alan D. , Burinsky David J. 
Published: September 2002

AbstractProcess improvements in the synthesis of therapeutic agents and their intermediates are often facilitated by identification of reaction by‐products. Analysis by liquid chromatography/mass spectrometry (LC/MS) with electrospray ionization is a powerful approach for obtaining molecular weight information for these compounds. Such analyses are well suited for ‘open‐access’ mass spectrometry using generic chromatographic conditions, provided spectral interpretation for unknown compounds is facile. We have developed a software application (MassAssign) that facilitates automated data processing and molecular weight assignment for chromatographic peaks detected by any standard ultraviolet‐visible wavelength detector. The program assigns [M + H]+ ions (and thus molecular weight) in the mass spectra using predetermined criteria. This evaluation process differentiates [M + H]+ ions from other signals in a complex mass spectrum such as those resulting from chromatographic coelution or the presence of multiple species (i.e., fragment ions, singly charged ions, doubly charged ions, adduct ions, proton‐bound dimers, etc.). Once the program has evaluated all ions in a mass spectrum that exceed a preset abundance threshold, MassAssign reports either a numeric value—indicating the chromatographic peak consists of a single component having the displayed molecular weight, ‘MC’—indicating the peak consisted of multiple components, or ‘ND’—that a molecular weight could not be determined unequivocally. The performance of the program was evaluated by comparing mass assignments made by MassAssign against manual interpretation for 55 samples analyzed by positive electrospray ionization using a generic HPLC method. Correct molecular weight assignments were obtained in 90% of the cases. Copyright © 2001 John Wiley & Sons, Ltd.
Collision‐induced dissociation of glycero phospholipids using electrospray ion‐trap mass spectrometry
Authors: Larsen Åsmund , Uran Steinar , Jacobsen Petter Balke , Skotland Tore 
Published: September 2002

AbstractCharacterisation of phospholipids was achieved using collision‐induced dissociation (CID) with an ion‐trap mass spectrometer. The product ions were compared with those obtained with a triple quadrupole mass spectrometer. In the negative ion mode the product ions were mainly sn‐1 and sn‐2 lyso‐phospholipids with neutral loss of ketene in combination with neutral loss of the polar head group. Less abundant product ions were sn‐1 and sn‐2 carboxylate anions. CID using a triple quadrupole mass spectrometer, however, gave primarily the sn‐1 and sn‐2 carboxylate anions together with lyso‐phosphatidic acid with neutral loss of water. For the ion trap a charge‐remote‐type mechanism is proposed for formation of the lyso‐phospholipid product ions by loss of α‐hydrogen on the fatty acid moiety, electron rearrangement and neutral loss of ketene. A second mechanism involves nucleophilic attack of the phosphate oxygen on the sn‐1 and sn‐2 glycerol backbone to form carboxylate anions with neutral loss of cyclo lyso‐phospholipids. CID (MS3 and MS4) of the lyso‐phospholipids using the ion‐trap gave the same carboxylate anions as those obtained with a triple quadrupole instrument where multiple collisions in the collision cell are expected to occur. The data demonstrate that phospholipid species determination can be performed by using LC/MSn with an ion‐trap mass spectrometer with detection of the lyso‐phospholipid anions. The ion‐trap showed no loss in sensitivity in full scan MSn compared to multiple reaction monitoring data acquisition. In combination with on‐line liquid chromatography this feature makes the ion‐trap useful in the scanning modes for rapid screening of low concentrations of phospholipid species in biological samples as recently described (Uran S, Larsen Å, Jacobsen PB, Skotland T. J. Chromatogr. B 2001; 758: 265). Copyright © 2001 John Wiley & Sons, Ltd.