bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogenesis of methanol‐induced craniofacial defects in C57BL/6J mice
Authors: Degitz Sigmund J. , Zucker Robert M. , Kawanishi Clinton Y. , Massenburg Gwen S. , Rogers John M. 
Published: April 2004

AbstractBACKGROUNDMethanol administered to C57BL/6J mice during gastrulation causes severe craniofacial dysmorphology. We describe dysmorphogenesis, cell death, cell cycle assessment, and effects on development of cranial ganglia and nerves observed following administration of methanol to pregnant C57BL/6J mice on gestation day (GD) 7.METHODSMice were injected (i.p.) on GD 7 with 0, 2.3, 3.4, or 4.9 gm/kg methanol, split into two doses. In embryos of mice treated with 0 or 4.9 gm/kg methanol, we used histology and LysoTracker red staining on GD 8 0 hr through GD 8 18 hr to examine cell death and dysmorphogenesis, and we also evaluated cell‐cycle distribution and proliferation using flow cytometry (FCM) and BrdU immunohistochemistry. On GD 10, we evaluated the effect of GD 7 exposure to 0, 2.3, 3.4, or 4.9 gm/kg methanol on cranial ganglia and nerve development using neurofilament immunohistochemistry.RESULTSMethanol treatment on GD 7 resulted in reduced mesenchyme surrounding the fore‐ and midbrain, and in the first branchial arches, by GD 8 12 hr. There were disruptions in the forebrain neuroepithelium and optic pit. Neural crest cell emigration from the mid‐ and hindbrain region was reduced in methanol‐exposed embryos. Methanol had no apparent effect on BrdU incorporation or cell‐cycle distribution on GD 8. Cell death was observed in the hindbrain region along the path of neural crest migration and in the trigeminal ganglion on GD 8 18 hr. Development of the cranial ganglia and nerves was adversely affected by methanol. Development of ganglia V, VIII, and IX was decreased at all dosage levels; ganglion VII was reduced at 3.4 and 4.9 gm/kg, and ganglion X was reduced at 4.9 gm/kg.CONCLUSIONSThese results suggest that gastrulation‐stage methanol exposure affects neural crest cells and the anterior mesoderm and neuroepithelium. Cell death was evident in areas of migrating neural crest cells, but only at time points after methanol was cleared from the embryo, suggesting an indirect effect on these cells. Birth Defects Research (Part A), 2004. Published 2004 Wiley‐Liss, Inc.
Hydrogen‐deuterium exchange in membrane proteins monitored by IR spectroscopy: A new tool to resolve protein structure and dynamics
Authors: Vigano C. , Smeyers M. , Raussens V. , Scheirlinckx F. , Ruysschaert J.M. , Goormaghtigh E. 
Published: April 2004

AbstractAs more and more high‐resolution structures of proteins become available, the new challenge is the understanding of these small conformational changes that are responsible for protein activity. Specialized difference Fourier transform infrared (FTIR) techniques allow the recording of side‐chain modifications or minute secondary structure changes. Yet, large domain movements remain usually unnoticed. FTIR spectroscopy provides a unique opportunity to record 1H/2H exchange kinetics at the level of the amide proton. This approach is extremely sensitive to tertiary structure changes and yields quantitative data on domain/domain interactions. An experimental setup designed for attenuated total reflection and a specific approach for the analysis of the results is described. The study of one membrane protein, the gastric H+,K+‐ATPase, demonstrates the usefulness of 1H/2H exchange kinetics for the understanding of the molecular movement related to the catalytic activity. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Lipid hydration: Headgroup CH moieties are involved in water binding
Authors: Pohle W. , Gauger D. R. , Bohl M. , Mrazkova E. , Hobza P. 
Published: April 2004

AbstractTo explore the interaction potential of phospholipids, we have studied the hydration of diacyl phosphatidylcholine (PC) and methylphosphocholine (MePC), a pertinent model compound, by ir spectroscopy. Related ab initio Hartree—Fock calculations were performed for MePC. Water is considered ideal as a relevant probe molecule. Spectroscopic data for MePC reveal a strong influence of bound hydration water not only on the phosphate groups but also onto the putatively apolar CHn groups. The same could be demonstrated for deuterated dimyristoyl PC taken as a “complete” lipid molecule: both headgroup methyl and methylene moieties are gradually, but remarkably affected by hydration, as evidenced by strong wavenumber upshifts of CH stretching vibration bands. These findings may originate in directed interactions of the CHn groups with bound water molecules, but hydration‐driven conformational changes of PC headgroups could also occur. The results of the ab initio calculations rationalize the first explanation by predicting a substantial contribution of specific CH · · · OH2 interactions, mainly characterized by a dramatic loss of electron density of the σ* antibonding molecular orbitals of CH bonds. Hence, the propensity of the lipid headgroup methyl and methylene groups to act as donor sites in hydrogen bonding must no longer be ignored when considering the interaction potential of PCs. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Dynamics of human serum albumin studied by acoustic relaxation spectroscopy
Authors: Hushcha T. , Kaatze U. , Peytcheva A. 
Published: April 2004

AbstractSonic absorption spectra of solutions of human serum albumin (SA) in water and in aqueous phosphate buffer systems have been measured between 0.2 and 2000 MHz at different temperatures (15–35°C), pH values (1.8–12.3), and protein concentrations (1–40 g/L). Several spectra, indicating relaxation processes in the whole frequency range, have been found. The spectra at neutral pH could be fitted well with an analytical function consisting of the asymptotic high frequency absorption and two relaxation contributions, a Debye‐type relaxation term with discrete relaxation time and a term with asymmetric continuous distribution of relaxation times. Both relaxation contributions were observed in water and in buffer solutions and increased with protein concentration. The contribution represented by a Debye‐type term is practically independent of temperature and was attributed to cooperative conformational changes of the polypeptide chain featuring a relaxation time of about 400 ns. The distribution of the relaxation times corresponding to the second relaxation contribution was characterized by a short time cutoff, between about 0.02 and 0.4 ns depending on temperature, and a long time tail extending to microseconds. Such relaxation behavior was interpreted in terms of solute–solvent interactions reflecting various hydration layers of HSA molecules. At acid and alkaline pH, an additional Debye‐type contribution with relaxation time in the range of 30–100 ns exists. It seems to be due to proton transfer reactions of protein side‐chain groups. The kinetic and thermodynamic parameters of these processes have been estimated from these first measurements to indicate the potential of acoustic spectra for the investigation of the elementary kinetics of albumin processes. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
The charge transfer band in horseradish peroxidase correlates with heme in‐plane distortions induced by calcium removal
Authors: Laberge Monique , Szigeti Krisztian , Fidy Judit 
Published: April 2004

AbstractHorseradish peroxidase C (HRPC) is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme. The spin state of the iron, a mixture of high spin (HS) and mixed quantum spin state (QS) consisting of intermediate spin (IS) 3/2 + (HS) 5/2, is also significantly affected by calcium removal, going from a predominant QS component to a predominant HS component upon removal of one calcium. Removal of both calcium ions, however, results in the appearance of a significant LS contribution, easily monitored in the charge transfer (CT) band region by low‐T absorption. Normal structural decomposition (NSD) calculations of the in‐plane (ip) modes of the heme extracted from HRPC native and Ca2+‐depleted models show that removal of the proximal calcium is associated with perturbed Eu and increased A1g ip distortions of the heme. The effect of complete or distal calcium removal on the heme also results in increased A1g ip distortions, but in significantly decreased Eu distortions. The overall effect is to decrease the nonplanarity of the heme: the total ip distortion of the native HRPC heme is 0.200 and 0.134 Å for the Ca2+‐depleted species. Our NSD results corroborate the role proposed for the protein matrix, namely to fine‐tune the active site by inducing subtle changes in heme planarity and spin state of the iron. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
pH dependence of heme electrochemistry in cytochromes investigated by multiconformation continuum electrostatic calculations
Authors: Hauser K. , Mao J. , Gunner M. R. 
Published: April 2004

AbstractCytochromes belong to a diverse family of heme‐containing redox proteins that function as intermediaries in electron transfer chains. They can be soluble, extrinsic, or intrinsic membrane proteins, and are found in different structural motifs (globin, 4‐helix bundles, αβ roll, β sandwich). Measured electrochemical midpoint potentials vary over a wide range even though the basic redox reaction at the heme is the same for all cytochromes. The perturbation of the heme electrochemistry is induced by the protein structure. Also, the pH dependence varies since it depends on the strength of interaction between the heme and surrounding residues as well as the ionization states of these groups. Multiconformation continuum electrostatics (MCCE) has been used to investigate the pH dependence of heme electrochemistry in cytochromes with different folds. Often propionates are the primary contributors for pH dependence especially if they are partially protonated in the reduced heme as it is shown for globin cytochrome c551 P. aeruginosa and cytochrome b5 R. norvegicus (αβ roll). However, if the propionates are already fully ionized at a certain pH they do not contribute to the pH dependence even if they have big interaction with the heme. At pH 7 there is no propionate contribution for cytochrome f C. reinhardtii (β sandwich) and the 4‐helix bundle c′ R. palustris. Other residues can also change their ionization significantly during heme oxidation and therefore be involved in proton release and pH dependence. These residues have been identified for different cytochrome types. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Changes of near‐UV CD spectrum of human hemoglobin upon oxygen binding: A study of mutants at α42, α140, β145 tyrosine or β37 tryptophan
Authors: Jin Yayoi , Sakurai Hiroshi , Nagai Yukifumi , Nagai Masako 
Published: April 2004

AbstractThe deoxy‐form of human adult hemoglobin (Hb A) exhibits a distinct negative CD band at 287 nm that disappears in the oxy‐form. It has been suggested that the negative CD band is due to the environmental alteration of Tyr‐α42 or Trp‐β37 at the α1β2 contact upon deoxygenation. To evaluate the contributions of the aromatic residues at the α1β2 contact and the penultimate tyrosine residues of the α and β subunits (α140 and β145) to the negative CD band, three recombinant (r) Hbs (rHb Ser‐α42, rHb His‐β37, and rHb Thr‐β145) were produced in Escherichia coli, and we compared the near‐uv CD spectra of these three rHbs and Hb Rouen (Tyr‐α140→His) with the spectra of Hb A under the condition in which all mutant Hbs were able to undergo the T→R transition (Hill's n > 2.0). The contributions of Tyr‐α42, Trp‐β37, Tyr‐α140, and Tyr‐β145 to the negative CD band were estimated from changes in the ellipticity of the negative CD band at 287 nm to be 4, 18, 32, and 27%, respectively. These results indicate that environmental alteration of the penultimate tyrosine residues caused by the formation of salt bridges upon the R→T transition is primarily responsible for the negative CD band. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Fourier transform infrared spectroscopic study on the binding of Mg2+ to a mutant Akazara scallop troponin C (E142Q)
Authors: Nara Masayuki , Yumoto Fumiaki , Nagata Koji , Tanokura Masaru , Kagi Hiroyuki , Ojima Takao , Nishita Kiyoyoshi 
Published: April 2004

AbstractTroponin C (TnC) is the Ca2+‐binding regulatory protein of the troponin complex in muscle tissue. Vertebrate fast skeletal muscle TnCs bind four Ca2+, while Akazara scallop (Chlamys nipponensis akazara) striated adductor muscle TnC binds only one Ca2+ at site IV, because all the other EF‐hand motifs are short of critical residues for the coordination of Ca2+. Fourier transform infrared (FTIR) spectroscopy was applied to study coordination structure of Mg2+ bound in a mutant Akazara scallop TnC (E142Q) in D2O solution. The result showed that the side‐chain COO− groups of Asp 131 and Asp 133 in the Ca2+‐binding site of E142Q bind to Mg2+ in the pseudo‐bridging mode. Mg2+ titration experiments for E142Q and the wild‐type of Akazara scallop TnC were performed by monitoring the band at about 1600 cm−1, which is due to the pseudo‐bridging Asp COO− groups. As a result, the binding constants of them for Mg2+ were the same value (about 6 mM). Therefore, it was concluded that the side‐chain COO− group of Glu 142 of the wild type has no relation to the Mg2+ ligation. The effect of Mg2+ binding in E142Q was also investigated by CD and fluorescence spectroscopy. The on–off mechanism of the activation of Akazara scallop TnC is discussed on the basis of the coordination structures of Mg2+ as well as Ca2+. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Anomalous acceleration of the photocycle in photosynthetic reaction centers inhibited on the acceptor side
Authors: Gerencsér L. , Maróti P. 
Published: April 2004

AbstractThe rate of the photocycle (quinone reduction cycle) was measured under continuous light excitation in an isolated reaction center protein of the photosynthetic bacterium Rhodobacter sphaeroides. The rate is determined by the slowest step of the photocycle, which could be the photochemistry (charge separation), the quinone/quinol and cytochrome c2+/c3+ exchanges, or proton delivery to the secondary quinone. The photocycle was driven by high light intensity of a laser diode (5 W/cm2 at 808 nm) to avoid light limitation of the observed rate. The fast turnover of the reaction center (up to 103 s–1) was slowed down by inhibition of the proton delivery to the secondary quinone by transition metal ions (Cd2+ and Ni2+), by mutation of a key protonatable group (L213Asp → Asn), or by use of low‐affinity ubiquinone (UQ0) to the secondary quinone binding site. Although in all of these cases the rate of turnover was 2–3 orders of magnitude less than that of the primary photochemistry, marked light intensity dependence was observed. The rate of the photocycle increased from 7 s–1 (Ni2+, low light intensity) to 27 s–1 (high light intensity) at pH 8.4. The anomalous reacceleration is due to alternative events on the acceptor side induced by continuous excitation. We argue that the continuous excitation of the protein trapped in the reduced acceptor (QA−QB−) state produces short‐lived reduced bacteriopheophytin (I−) that delivers activation energy to anomalous changes on the acceptor side as second interquinone electron transfer before proton uptake or increase of the quinone dissociation constant. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004
Identification of stable helical bundles from a combinatorial library of amphipathic peptides
Authors: Boon Chandra L. , Frost David , Chakrabartty Avijit 
Published: April 2004

AbstractA set of combinatorial amphipathic helical peptides referred to as the KIA series has been screened to identify native‐like helical bundles. The series contains the following consensus sequence: AKAxAAxxKAxAAxxKAGGY, where “x” positions are occupied by either Ala or Ile. The peptide sequences in the series comprise all possible combinations of four Ile residues occupying the six x positions. In each case, Ala occupied the two x positions not occupied by Ile. There are a total of 15 peptides in the KIA series; all of the peptides differ in the number of ridges and grooves formed by the Ile side chains, and two of the KIA peptides possess a canonical knobs‐into‐holes heptad repeat. The structure and stability of these 15 peptides and their pairwise mixtures were evaluated. One peptide in the series formed a stable four‐helix bundle that folded with cooperativity similar to native proteins. Ten peptides assembled into molten globular helical assemblies, two peptides were unstructured, and two peptides assembled into helical filaments that were several micrometers long. One of the helical filament forming peptides could be diverted from forming filaments by the addition of another KIA peptide, and resulted in the formation of a heteromeric six‐helix bundle. This study demonstrates that combinatorial peptides composed of only three types of amino acids can form a diverse array of structures, some of which are native‐like. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2004
Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks
Authors: Çakir Tunahan , Kirdar Betül , Ülgen Kutlu Ö. 
Published: April 2004

AbstractCentral carbon metabolism of the yeast Saccharomyces cerevisiae was analyzed using metabolic pathway analysis tools. Elementary flux modes for three substrates (glucose, galactose, and ethanol) were determined using the catabolic reactions occurring in yeast. Resultant elementary modes were used for gene deletion phenotype analysis and for the analysis of robustness of the central metabolism and network functionality. Control‐effective fluxes, determined by calculating the efficiency of each mode, were used for the prediction of transcript ratios of metabolic genes in different growth media (glucose–ethanol and galactose–ethanol). A high correlation was obtained between the theoretical and experimental expression levels of 38 genes when ethanol and glucose media were considered. Such analysis was shown to be a bridge between transcriptomics and fluxomics. Control‐effective flux distribution was found to be promising in in silico predictions by incorporating functionality and regulation into the metabolic network structure. © 2004 Wiley Periodicals, Inc.
A new, mild cross‐linking methodology to prepare cross‐linked enzyme aggregates
Authors: Mateo Cesar , Palomo José M. , van Langen Luuk M. , van Rantwijk Fred , Sheldon Roger A. 
Published: April 2004

AbstractCross‐linked enzyme aggregates (CLEAs) were prepared from several enzymes (penicillin G acylase, hydroxynitrile lyase, alcohol dehydrogenase, and two different nitrilases) by precipitation and subsequent cross‐linking using dextran polyaldehyde. In most cases, higher immobilization yields were obtained using the latter cross‐linker as compared with the commonly used glutaraldehyde. Active site titration of penicillin acylase CLEAs showed that the higher activity originated from a significantly lower loss in active sites using dextran polyaldehyde as a cross‐linking agent. It is proposed that macromolecular cross‐linkers are too large to penetrate the protein active site and react with catalytically essential amino acid residues. © 2004 Wiley Periodicals, Inc.
Comparison of two‐stage thermophilic (68°C/55°C) anaerobic digestion with one‐stage thermophilic (55°C) digestion of cattle manure
Authors: Nielsen H. B. , Mladenovska Z. , Westermann P. , Ahring B. K. 
Published: April 2004

AbstractA two‐stage 68°C/55°C anaerobic degradation process for treatment of cattle manure was studied. In batch experiments, an increase of the specific methane yield, ranging from 24% to 56%, was obtained when cattle manure and its fractions (fibers and liquid) were pretreated at 68°C for periods of 36, 108, and 168 h, and subsequently digested at 55°C. In a lab‐scale experiment, the performance of a two‐stage reactor system, consisting of a digester operating at 68°C with a hydraulic retention time (HRT) of 3 days, connected to a 55°C reactor with 12‐day HRT, was compared with a conventional single‐stage reactor running at 55°C with 15‐days HRT. When an organic loading of 3 g volatile solids (VS) per liter per day was applied, the two‐stage setup had a 6% to 8% higher specific methane yield and a 9% more effective VS‐removal than the conventional single‐stage reactor. The 68°C reactor generated 7% to 9% of the total amount of methane of the two‐stage system and maintained a volatile fatty acids (VFA) concentration of 4.0 to 4.4 g acetate per liter. Population size and activity of aceticlastic methanogens, syntrophic bacteria, and hydrolytic/fermentative bacteria were significantly lower in the 68°C reactor than in the 55°C reactors. The density levels of methanogens utilizing H2/CO2 or formate were, however, in the same range for all reactors, although the degradation of these substrates was significantly lower in the 68°C reactor than in the 55°C reactors. Temporal temperature gradient electrophoresis profiles (TTGE) of the 68°C reactor demonstrated a stable bacterial community along with a less divergent community of archaeal species. © 2004 Wiley Periodicals, Inc.
Gene expression in Bacillus subtilis surface biofilms with and without sporulation and the importance of yver for biofilm maintenance
Authors: Ren Dacheng , Bedzyk Laura A. , Setlow Peter , Thomas Stuart M. , Ye Rick W. , Wood Thomas K. 
Published: April 2004

AbstractFive independent DNA microarray experiments were used to study the gene expression profile of a 5‐day Bacillus subtilis air–liquid interface biofilm relative to planktonic cells. Both wild‐type B. subtilis and its sporulation mutant (ΔspoIIGB::erm) were investigated to discern the important biofilm genes (in the presence and absence of sporulation). The microarray results indicated that suspension cells were encountering anaerobic conditions, and the air–liquid interface biofilm was metabolically active. For the statistically significant differential expression (P < 0.05), there were 342 genes induced and 248 genes repressed in the wild‐type biofilm, whereas 371 genes were induced and 128 genes were repressed in the sporulation mutant biofilm. The microarray results were confirmed with RNA dot blotting. A small portion of cells (1.5%) in the wild‐type biofilm formed spores and sporulation genes were highly expressed. In the biofilm formed by the sporulation mutant, competence genes (comGA, srfAA, srfAB, srfAD, and comS) were induced which indicate a role for quorum sensing (bacterial gene expression controlled by sensing their population) in biofilms. There were 53 genes consistently induced in the biofilms of both the wild‐type strain and its spoIIGB mutant—those genes have functions for transport, metabolism, antibiotic production—and 26 genes with unknown functions. Besides the large number of genes with known functions induced in the biofilm (121 genes in the wild‐type biofilm and 185 genes in the sporulation mutant biofilm), some genes with unknown functions were also induced (221 genes in the wild‐type biofilm and 186 genes in the sporulation mutant biofilm), such as the yve operon which appears to be involved in polysaccharide synthesis and the ybc operon which inhibits the growth of competitors for nutrients. A knockout mutant of yveR was constructed, and the mutant showed major defects in biofilm maintenance. Both the wild‐type strain and its sporulation mutant formed normal biofilms, suggesting complete sporulation is not necessary for biofilm formation. The expression profiles of these two strains share more repressed genes than induced genes, suggesting that the biofilm cells repress similar pathways in response to starvation and high cell density. © 2004 Wiley Periodicals, Inc.