bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breaking non‐native hydrophobic clusters is the rate‐limiting step in the folding of an alanine‐based peptide
Authors: Chowdhury Shibasish , Zhang Wei , Wu Chun , Xiong Guoming , Duan Yong 
Published: February 2003

AbstractThe formation mechanism of an alanine‐based peptide has been studied by all‐atom molecular dynamics simulations with a recently developed all‐atom point‐charge force field and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty‐two simulations were conducted. Each simulation was performed for 100 ns. A surprisingly complex folding process was observed. The development of the helical content can be divided into three phases with time constants of 0.06–0.08, 1.4–2.3, and 12–13 ns, respectively. Helices initiate extreme rapidly in the first phase similar to that estimated from explicit solvent simulations. Hydrophobic collapse also takes place in this phase. A folding intermediate state develops in the second phase and is unfolded to allow the peptide to reach the transition state in the third phase. The folding intermediate states are characterized by the two‐turn short helices and the transition states are helix–turn–helix motifs—both of which are stabilized by hydrophobic clusters. The equilibrium helical content, calculated by both the main‐chain Φ–Ψ torsion angles and the main‐chain hydrogen bonds, is 64–66%, which is in remarkable agreement with experiments. After corrected for the solvent viscosity effect, an extrapolated folding time of 16–20 ns is obtained that is in qualitative agreement with experiments. Contrary to the prevailing opinion, neither initiation nor growth of the helix is the rate‐limiting step. Instead, the rate‐limiting step for this peptide is breaking the non‐native hydrophobic clusters in order to reach the transition state. The implication to the folding mechanisms of proteins is also discussed. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 63–75, 2003
Modeling HIV‐1 integrase complexes based on their hydrodynamic properties
Authors: Podtelezhnikov Alexei A. , Gao Kui , Bushman Frederic D. , McCammon J. Andrew 
Published: February 2003

AbstractWe present a model structure of a candidate tetramer for HIV‐1 integrase. The model was built in three steps using data from fluorescence anisotropy, structures of the individual integrase domains, cross‐linking data, and other biochemical data. First, the structure of the full‐length integrase monomer was modeled using the individual domain structures and the hydrodynamic properties of the full‐length protein that were recently measured by fluorescence depolarization. We calculated the rotational correlation times for different arrangements of three integrase domains, revealing that only structures with close proximity among the domains satisfied the experimental data. The orientations of the domains were constrained by iterative tests against the data on cross‐linking and footprinting in integrase–DNA complexes. Second, the structure of an integrase dimer was obtained by joining the model monomers in accordance with the available dimeric crystal structures of the catalytic core. The hydrodynamic properties of the dimer were in agreement with the experimental values. Third, the active sites of the two model dimers were placed in agreement with the spacing between the sites of integration on target DNA as well as the integrase–DNA cross‐linking data, resulting in twofold symmetry of a tetrameric complex. The model is consistent with the experimental data indicating that the F185K substitution, which is found in the model at a tetramerization interface, selectively disrupts correct complex formation in vitro and HIV replication in vivo. Our model of the integrase tetramer bound to DNA may help to design anti‐integrase inhibitors. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 110–120, 2003
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM‐PBSA and thermodynamic integration methods
Authors: Gouda Hiroaki , Kuntz Irwin D. , Case David A. , Kollman Peter A. 
Published: February 2003

AbstractWe have applied the molecular mechanics Poisson–Boltzmann surface area (MM‐PBSA) method (J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, Journal of the American Chemical Society, 1998, Vol. 120, pp. 9401–9409) to study the interaction of an RNA aptamer with theophylline and its analogs. The MM‐PBSA free energy analysis provides a reasonable absolute binding free energy for the RNA aptamer–theophylline complex formation. Energetic analysis reveals that the van der Waals interaction and the nonpolar contribution to solvation provide the basis for the favorable absolute free energy of complex. This trend is similar to other protein–ligand interactions studied previously. The MM‐PBSA method also ranks the relative binding energies of five theophylline analogs approximately correctly, but not as well as the more conventional thermodynamic integration calculations, which were carried out to convert theophylline into its analogs. The comparison of MM‐PBSA with TI suggests that the MM‐PBSA method has some difficulties with the first‐solvation‐shell energetics. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 16–34, 2003
Simulation of the different biological activities of diethylstilbestrol (DES) on estrogen receptor α and estrogen‐related receptor γ
Authors: Nam Kiyean , Marshall Paul , M. Wolf Romain , Cornell Wendy 
Published: February 2003

AbstractWe describe the application of the molecular dynamics (MD) and molecular mechanics–generalized Born/surface area (MM‐GB/SA) approaches to the simulation of the different biological activity of diethylstilbestrol (DES) on two highly homologous nuclear receptors—estrogen receptor α (ER‐α) and estrogen‐related receptor γ (ERR‐γ). DES exerts an agonistic effect against ER‐α and an antagonistic effect against ERR‐γ. Using the x‐ray crystal structures of ER‐α in the canonical agonist bound form (PDB code: 3ERD) and antagonist bound form (PDB code: 3ERT), ERR‐γ homology models have been constructed for the receptor in two different conformations. MM‐GB/SA binding free energy calculations of DES in the ER‐α and ERR‐γ structures suggest that DES exhibits a greater free energy of binding in the agonist bound conformation of ER‐α, while the antagonist bound conformation is preferred for ERR‐γ. Further dissection of the free energy contributions coupled with calculation of the ligand binding pocket volume suggests that the van der Waals interactions for DES within the smaller binding pocket volume of ERR‐γ are less favorable and this is the main factor for DES antagonism in ERR‐γ. This approach has potential general applicability to the prediction of the biological activity of nuclear receptor ligands. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 130–138, 2003
Parvalbumin, calbindin, or calretinin in cortically projecting and GABAergic, cholinergic, or glutamatergic basal forebrain neurons of the rat
Authors: Gritti Ivana , Manns Ian D. , Mainville Lynda , Jones Barbara E. 
Published: February 2003

AbstractThe basal forebrain (BF) plays an important role in modulating cortical activity and facilitating processes of attention, learning, and memory. This role is subserved by cholinergic neurons but also requires the participation of other noncholinergic neurons. Noncholinergic neurons include γ‐amino butyric acidergic (GABAergic) neurons, some of which project in parallel with the cholinergic cells to the cerebral cortex, others of which project caudally or locally. With the original aim of distinguishing different subgroups of GABAergic neurons, we examined immunostaining for the calcium binding proteins (CBPs) parvalbumin (Parv), calbindin (Calb), and calretinin (Calret) in the rat. Although the CBP+ cell groups were distributed in a coextensive manner with the GABAergic cells, they were collectively more numerous. Of cells retrogradely labeled with cholera toxin (CT) from the prefrontal or parietal cortex, Parv+ and Calb+ cells, but not Calret+ cells, represented substantial proportions (∼35–45% each) that collectively were greater than that of GABAergic projection neurons. From dual immunostaining for the CBPs and glutamic acid decarboxylase (GAD), it appeared that the vast majority (>90%) of the Parv+ group was GAD+, whereas only a small minority (<10%) of the Calb+ or Calret+ group was GAD+. Significant proportions of Calb+ (>40%) and Calret+ (>80%) neurons were immunopositive for phosphate‐activated glutaminase, the synthetic enzyme for transmitter glutamate. The results suggested that, whereas Calret+ cells predominantly comprise caudally or locally projecting, possibly glutamatergic BF neurons, Parv+ cells likely comprise the cortically projecting GABAergic BF neurons and Calb+ cells the cortically projecting, possibly glutamatergic BF neurons that would collectively participate with the cholinergic cells in the modulation of cortical activity. J. Comp. Neurol. 458:11–31, 2003. © 2003 Wiley‐Liss, Inc.
Distribution of dopamine D2 receptor mRNAs in the brain and the pituitary of female rainbow trout: An in situ hybridization study
Authors: Vacher Coralie , Pellegrini Elisabeth , Anglade Isabelle , Ferriére François , Saligaut Christian , Kah Olivier 
Published: February 2003

AbstractThe distribution of D2R (dopamine D2 receptor) mRNAs was studied in the forebrain of maturing female rainbow trout by means of in situ hybridization using a 35S‐labeled riboprobe (810 bp) spanning the third intracytoplasmic loop. A hybridization signal was consistently obtained in the olfactory epithelium, the internal cell layer of the olfactory bulbs, the ventral and dorsal subdivisions of the ventral telencephalon, and most preoptic subdivisions, with the notable exception of the magnocellular preoptic nucleus, and the periventricular regions of the mediobasal hypothalamus, including the posterior tuberculum. In the pituitary, the signal was higher in the pars intermedia than in the proximal and the rostral pars distalis, but no obvious correspondence with a given cell type could be assigned. Labeled cells were also located in the thalamic region, some pretectal nuclei, the optic tectum, and the torus semicircularis. These results provide a morphologic basis for a better understanding on the functions and evolution of the dopaminergic systems in lower vertebrates. J. Comp. Neurol. 458:32–45, 2003. © 2003 Wiley‐Liss, Inc.
Morphologic and cytochemical criteria for the identification and delineation of individual subnuclei within the lateral habenular complex of the rat
Authors: Geisler Stefanie , Andres Karl Hermann , Veh Rüdiger W. 
Published: February 2003

AbstractThe lateral habenular complex is part of the habenular nuclei, a distinct structure in the dorsal diencephalon of all vertebrates. In contrast to the bewildering diversity of behaviors, in which the lateral habenular complex is thought to be involved, there is an astonishing lack of information concerning its cellular organization, its neuronal circuits, and the neurophysiological mechanisms, which may provide the physiological and molecular basis for its diverse biological functions. This problem may be due to an unexpected heterogeneity of the lateral habenular complex. Recently, a detailed subnuclear organization has been described (Andres et al. [1999] J Comp Neurol 407:130–150), which provides the base for a subsequent physiological and behavioral analysis of this area. Available criteria, however, can be applied to semithin sections only. To facilitate further investigations, the present work aimed to elaborate novel morphologic and immunocytochemical criteria that can be applied to conventional cryostat or Vibratome sections to allow identification and delineation of subnuclei of the lateral habenular complex. Consequently, the regional, cellular, and subcellular localization of approximately 30 different neuroactive molecules was investigated. Of these candidate molecules, γ‐aminobutyric acid‐B receptor protein, Kir3.2 potassium channel protein, tyrosine hydroxylase, and neurofilament heavy chain proved to be suitable markers. Our observation suggests that the habenular subnuclei express distinct immunocytochemical characteristics. These features may be used to identify and delineate the subnuclei on conventional cryostat or Vibratome sections. From our results, it is expected that the further functional analysis of the lateral habenular complex will be facilitated considerably. J. Comp. Neurol. 458:78–97, 2003. © 2003 Wiley‐Liss, Inc.
Nanoelectrospray‐based detection and sequencing of substoichiometric amounts of phosphopeptides in complex mixtures
Authors: Köcher Thomas , Allmaier Günter , Wilm Matthias 
Published: February 2003

AbstractA novel immobilized metal affinity chromatography (IMAC)‐based protocol was successfully used for sample preparation prior to nanoelectrospray‐based sequencing of phosphopeptides. In a first step, phosphorylated peptides are detected in an unseparated peptide mixture using precursor ion scanning in the negative ion mode on a triple‐quadrupole mass spectrometer. Then the phosphorylated peptides are enriched by passing the sample over an IMAC column and sequenced in the positive ion mode. The IMAC‐based enrichment allows the sequencing of phosphorylated peptides even if other, much more abundant, peptides are present at the same m/z value in the original mixture. Using this two‐step approach, we are able to combine the simplicity, sensitivity and specificity of precursor ion scanning‐based detection of phosphopeptides using the nanoelectrospray ion source with the ability to sequence phosphorylated peptides even if they are present in substoichiometric amounts. Copyright © 2003 John Wiley & Sons, Ltd.
Electrospray mass spectra of group 6 (Fischer) carbenes in the presence of electron‐donor compounds
Authors: Sierra M. A. , Gómez‐Gallego M. , Mancheño M. J. , Martínez‐Alvarez R. , Ramírez‐López P. , Kayali N. , González A. 
Published: February 2003

AbstractFischer carbene complexes 1–7 are not ionized under standard electrospray ionization (ESI) conditions. We report here that unsaturated chromium and tungsten (Fischer) carbene complexes can be ionized in an electrospray ion source in the presence of electron‐donor compounds such as hydroquinone (HQ) or tetrathiafulvalene (TTF). The addition of these compounds, which seem to act as electron transfer agents, permits the recording and study of their ESI mass spectra in the negative mode of detection. Both chromium and tungsten(0) carbene complexes undergo in the first fragmentation stage a double simultaneous decarbonylation process. Copyright © 2003 John Wiley & Sons, Ltd.
Fragmentation reactions of protonated peptides containing glutamine or glutamic acid
Authors: Harrison Alex. G. 
Published: February 2003

AbstractA variety of protonated dipeptides and tripeptides containing glutamic acid or glutamine were prepared by electrospray ionization or by fast atom bombardment ionization and their fragmentation pathways elucidated using metastable ion studies, energy‐resolved mass spectrometry and triple‐stage mass spectrometry (MS3) experiments. Additional mechanistic information was obtained by exchanging the labile hydrogens for deuterium. Protonated H—Gln—Gly—OH fragments by loss of NH3 and loss of H2O in metastable ion fragmentation; under collision‐induced dissociation (CID) conditions loss of H—Gly—OH + CO from the [MH − NH3]+ ion forms the base peak C4H6NO+ (m/z 84). Protonated dipeptides with an α‐linkage, H—Glu—Xxx—OH, are characterized by elimination of H2O and by elimination of H—Xxx—OH plus CO to form the glutamic acid immonium ion of m/z 102. By contrast, protonated dipeptides with a γ‐linkage, H—Glu(Xxx—OH)—OH, do not show elimination of H2O or formation of m/z 102 but rather show elimination of NH3, particularly in metastable ion fragmentation, and elimination of H—Xxx—OH to form m/z 130. Both the α‐ and γ‐dipeptides show formation of [H—Xxx—OH]H+, with this reaction channel increasing in importance as the proton affinity (PA) of H—Xxx—OH increases. The characteristic loss of H2O and formation of m/z 102 are observed for the protonated α‐tripeptide H—Glu—Gly—Phe—OH whereas the protonated γ‐tripeptide H—Glu(Gly—Gly—OH)—OH shows loss of NH3 and formation of m/z 130 as observed for dipeptides with the γ‐linkage. Both tripeptides show abundant formation of the y2″ ion under CID conditions, presumably because a stable anhydride neutral structure can be formed. Under metastable ion conditions protonated dipeptides of structure H—Xxx—Glu—OH show abundant elimination of H2O whereas those of structure H—Xxx—Gln—OH show abundant elimination of NH3. The importance of these reaction channels is much reduced under CID conditions, the major fragmentation mode being cleavage of the amide bond to form either the a1 ion or the y1″ ion. Particularly when Xxx = Gly, under CID conditions the initial loss of NH3 from the glutamine containing dipeptide is followed by elimination of a second NH3 while the initial loss of H2O from the glutamic acid dipeptide is followed by elimination of NH3. Isotopic labelling shows that predominantly labile hydrogens are lost in both steps. Although both [H—Gly—Glu—Gly—OH]H+ and [H—Gly—Gln—Gly—OH]H+ fragment mainly to form b2 and a2 ions, the latter also shows elimination of NH3 plus a glycine residue and formation of protonated glycinamide. Isotopic labelling shows extensive mixing of labile and carbon‐bonded hydrogens in the formation of protonated glycinamide. Copyright © 2003 John Wiley & Sons, Ltd.
Accurate mass measurements by Fourier transform mass spectrometry in the study of advanced glycation end products/peptides
Authors: Marotta Ester , Lapolla Annunziata , Fedele Domenico , Senesi Antonella , Reitano Rachele , Witt Matthias , Seraglia Roberta , Traldi Pietro 
Published: February 2003

AbstractThe Maillard reaction occurring between sugars and amino groups is important in living systems. When amino groups belonging to protein chains are involved, the Maillard reaction has been invoked as responsible for protein cross‐linking and the production of ‘toxic’ compounds. The reaction leads to the production of a heterogeneous group of substances, usually called advanced glycation end products (AGEs). Classical analytical approaches, such as spectroscopic (ultraviolet, fluorescence) and mass spectrometric (matrix‐assisted laser desorption/ionization, liquid chromatography/electrospray ionization mass spectrometry) methods, have shown that the digestion mixture is highly complex. However, there are clear differences between the digestion mixtures of glycated and unglycated human serum albumin (HSA). In the former case, possible glycated peptides belonging to the AGE peptide class may be identified. Tandem mass spectrometric experiments on selected species seemed to be promising as regards structural information, but it was thought of interest to undertake the present investigation, based on liquid chromatography/electrospray ionization Fourier transform mass spectrometry, in order to obtain definitive results on their elemental composition. Using this approach, about 20 glycated peptides were detected and their possible structures were postulated by examining the known sequence of HSA. Copyright © 2003 John Wiley & Sons, Ltd.
Saturation transfer in human red blood cells with normal and unstable hemoglobin
Authors: Sogami Masaru , Uyesaka Nobuhiro , Era Seiichi , Kato Kazuo 
Published: February 2003

AbstractSaturation transfer phenomena from irradiated protein protons to observed water protons in packed human red blood cells (RBCs) with normal or unstable hemoglobin (Hb), i.e. Hb Yokohama and Hb Koeln, were studied using intermolecular cross‐relaxation rates [CR; 1/TIS(H2O)], action spectra {[1 −(I∞/I0)] vs f2 (ppm), where I0 and I∞ are the longitudinal magnetization of observed water protons before and after long‐time f2‐irradiation, respectively}, CR spectra [CR vs f2 (ppm)] and CR ratio vs f2 (ppm) with f2‐irradiation from −100 to 100 ppm at γH2/2π of 69 or 250 Hz. RBCs (Hb Yokohama) exhibited many large Heinz bodies and strongly impaired filterability, while RBCs (Hb Koeln) showed few microscopically typical Heinz bodies and virtually normal filterability. However, increases in CR values for RBCs (Hb Koeln) and RBCs (Hb Yokohama), monitored by f2‐irradiation below ∼−6 and above ∼14 ppm, clearly indicated marked increases in association or aggregation of unstable Hb in RBCs compared with those in normal RBCs. CR values, monitored between ∼0 and ∼10 ppm, were related to not only association or aggregation of unstable Hb but also amounts of water in RBCs. Aggregation or association of unstable Hb exhibited greater effects on CR values compared with those of methemoglobin formation. Copyright © 2003 John Wiley & Sons, Ltd.
In vivo monitoring of rat brain metabolites during vigabatrin treatment using localized 2D‐COSY
Authors: Welch John W. R. , Bhakoo Kishore , Dixon Ruth M. , Styles Peter , Sibson Nicola R. , Blamire Andrew M. 
Published: February 2003

AbstractA two‐dimensional COSY‐based localization sequence was designed to allow the in vivo monitoring of proton metabolites in rat brain [particularly γ‐aminobutyric acid (GABA), glutamine, taurine and myo‐inositol]. The sequence incorporated OSIRIS signal localization, B1‐insensitive water suppression and phase‐sensitive COSY acquisition. The method was used to study the effects of the GABA‐transaminase inhibitor vigabatrin on rat brain metabolite concentrations. Wistar rats were treated daily for 3 days with an oral dose of vigabatrin (200 mg/kg, n = 4). Localized COSY spectra were obtained during a 120 min acquisition from a 270 µl central brain voxel and compared with nine untreated control animals. Significant elevations were observed in GABA (267% of control, p < 0.005, Mann–Witney test), glutamine (130% of control, p < 0.005) and taurine (113% of control, p < 0.05). Changes in GABA and taurine were consistent with previous data on the action of Vigabatrin, and support a previously hypothesized link between these compounds. The increase in glutamine was more surprising and may reflect the balance between the level and/or site of GABA‐transaminase inhibition and downregulation of GABA synthesis. Copyright © 2003 John Wiley & Sons, Ltd.
Helix propensities of short peptides: Molecular dynamics versus bioinformatics
Authors: Bystroff Christopher , Garde Shekhar 
Published: February 2003

AbstractKnowledge‐based potential functions for protein structure prediction assume that the frequency of occurrence of a given structure or a contact in the protein database is a measure of its free energy. Here, we put this assumption to test by comparing the results obtained from sequence‐structure cluster analysis with those obtained from long all‐atom molecular dynamics simulations. Sixty‐four eight‐residue peptide sequences with varying degrees of similarity to the canonical sequence pattern for amphipathic helix were drawn from known protein structures, regardless of whether they were helical in the protein. Each was simulated using AMBER6.0 for at least 10 ns using explicit waters. The total simulation time was 1176 ns. The resulting trajectories were tested for reproducibility, and the helical content was measured. Natural peptides whose sequences matched the amphipathic helix motif with greater than 50% confidence were significantly more likely to form helix during the course of the simulation than peptides with lower confidence scores. The sequence pattern derived from the simulation data closely resembles the motif pattern derived from the database cluster analysis. The difficulties encountered in sampling conformational space and sequence space simultaneously are discussed. Key words: Proteins 2003;50:552–562. © 2003 Wiley‐Liss, Inc.