bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of protein‐protein interactions using in vivo cross‐linking and mass spectrometry
Authors: Vasilescu Julian , Guo Xuecui , Kast Juergen 
Published: November 2004

AbstractThe purification of protein complexes can be accomplished by different types of affinity chromatography. In a typical immunoaffinity experiment, protein complexes are captured from a cell lysate by an immobilized antibody that recognizes an epitope on one of the known components of the complex. After extensive washing to remove unspecifically bound proteins, the complexes are eluted and analyzed by mass spectrometry (MS). Transient complexes, which are characterized by high dissociation constants, are typically lost by this approach. In the present study, we describe a novel method for identifying transient protein‐protein interactions using in vivo cross‐linking and MS‐based protein identification. Live cells are treated with formaldehyde, which rapidly permeates the cell membrane and generates protein‐protein cross‐links. Proteins cross‐linked to a Myc‐tagged protein of interest are copurified by immunoaffinity chromatography and subjected to a procedure which dissociates the cross‐linked complexes. After separation by SDS‐PAGE, proteins are identified by tandem mass spectrometry. Application of this method enabled the identification of numerous proteins that copurified with a constitutively active form of M‐Ras (M‐RasQ71L). Among these, we identified the RasGAP‐related protein IQGAP1 to be a novel interaction partner of M‐RasQ71L. This method is applicable to many proteins and will aid in the study of protein‐protein interactions.
Establishment of a near‐standard two‐dimensional human urine proteomic map
Authors: Oh Jisun , Pyo Jae‐Hoon , Jo Eun‐Hyun , Hwang Sun‐Il , Kang Sun‐Chul , Jung Jae‐Hwan , Park Eui‐Kyun , Kim Shin‐Yoon , Choi Je‐Yong , Lim Jinkyu 
Published: November 2004

AbstractA proteomic map for human urine on two‐dimensional (2‐D) gels has been developed. Initial studies demonstrated that the urine proteins prepared by conventional methods showed interference and poor reproducibility in 2‐D electrophoresis (2‐DE). To address this issue, urine samples were dialyzed to remove any interfering molecules. The dialysis of urine proteins and the concentration by lyophilization without fractionation significantly improved the reproducibility and resolution and likely represents the total urine proteins on a 2‐D gel. In addition, removing albumin from urine using Affi‐Gel Blue helped to identify the low‐abundant proteins. Using the developed method, we prepared proteins from urine collected from healthy females and males. The large inter‐ and intra‐subject variation in protein profiles on 2‐D gels made it difficult to establish a normal human urine proteomic 2‐D map. To resolve this problem, urinary proteins were prepared from the pooled urine collected from 20 healthy females and males, respectively. The established male and female urine proteomes separated on 2‐D gels were almost identical except for some potential sex‐dependent protein spots. We have annotated 113 different proteins on the 2‐D gel by peptide mass fingerprinting (PMF). We propose that the established total urine proteome can be used for 2‐DE analysis, liquid chromatography‐tandem mass spectrometry (LC‐MS/MS), and identification of novel disease‐specific biomarkers.
Psychrophilicity of Bacillus psychrosaccharolyticus: A proteomic study
Authors: Seo Jong Bok , Kim Hye Sook , Jung Gyoo Yeol , Nam Myung Hee , Chung Joo Hee , Kim Jin Young , Yoo Jong Shin , Kim Chan Wha , Kwon Ohoak 
Published: November 2004

AbstractPsychrophilicity of Gram‐positive bacterium, Bacillus psychrosaccharolyticus was investigated in a proteomic approach. One hundred and thirty‐one protein spots were analyzed by electrospray ionization‐quadrupole‐time of flight‐tandem mass spectrometry and identified using an unpublished translated contig database as well as a nonredundant Gram‐positive bacteria protein database from NCBI because of the lack of a genome sequence of this organism. Results focused on proteomic behavior of cold‐response show that global up‐regulation of metabolic functions and protective mechanism by stress responses might play a major role in psychrophilicity of B. psychrosaccharolyticus.
Theoretical study of the thermal isomerization of isoxazole and 5‐methylisoxazole
Authors: Davico Gustavo E. 
Published: November 2004

AbstractHigh‐level ab initio and semi‐empirical computations were carried out to investigate the mechanisms of thermal isomerization of isoxazole (1a) and 5‐methylisoxazole (2a). The calculations were made over the whole isomerization potential energy surface at the MP2/cc‐pVDZ and QCISD(T)/aug‐cc‐pVDZ//MP2/cc‐pVDZ levels. The predicted rate‐limiting transition states were refined further at the QCISD(T)/aug‐cc‐pVDZ//QCISD/cc‐pVDZ level. Ab initio results are in excellent agreement with available experimental results. Furthermore, they allow us to propose a detailed reaction mechanism and to exclude reaction paths proposed earlier. We also report the results from semi‐empirical computations. The MNDO method predicts reasonable values for the heat of formation of the reactants but it fails for other isomers and overestimates the activation energies for most reaction steps. The AM1 method yields improved values for the activation energies, at the expense of less reliable heats of formation for the minima in the potential energy surface. In general, both methods produce results that are good when the simplicity of the model is considered; however, there is no simple way to determine in advance when the results are meaningful. Thermochemical and kinetic parameters obtained by the different theoretical methods are discussed and compared with experimental values. Copyright © 2004 John Wiley & Sons, Ltd.
Hydrogen‐bonding‐aided synthesis of novel ladderlike organobridged polysiloxane containing side‐chain naphthyl groups
Authors: Sun Jin , Tang Huadong , Jiang Jinqiang , Zhou Xiaoshu , Xie Ping , Zhang Rongben , Fu Peng‐Fei 
Published: November 2004

AbstractWith a hydrogen‐bonding template, a novel soluble aryl amide‐bridged ladderlike polysiloxane, containing naphthyl as the side‐chain group, has been successfully synthesized via a stepwise coupling polymerization. It is proposed that the monomer, N,N′‐di(3‐naphthyldiethoxylsilyl‐propyl)‐[4,4′‐oxybis(benzyl amide)], prepared by Grignard and hydrosilylation reactions, undergoes self‐assembly first via amido hydrogen bonding and then via hydrolysis, followed by condensation under controlled reaction conditions to yield a high molecular weight, soluble, dark yellow polymer. The analytical results (Fourier transform infrared, 1H NMR, 29Si NMR, X‐ray diffraction, differential scanning calorimetry, and vapor pressure osmometry) show that the polymer possesses an ordered ladderlike architecture. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 636–644, 2003
Thiol–ene coupling reaction of fatty acid monomers
Authors: Samuelsson Johan , Jonsson Mats , Brinck Tore , Johansson Mats 
Published: November 2004

AbstractThe reactivities and reaction rates of the thiol–ene coupling reaction of 2‐ethyl‐(hydroxymethyl)‐1,3‐propanediol trimercapto acetate and 2‐ethyl‐(hydroxymethyl)‐1,3‐propanediol trimercapto propionate with two common unsaturated fatty acid methyl esters (methyl oleate and methyl linoleate) were evaluated. The reactions were monitored with real‐time IR and 1H NMR, which both showed that the mercapto acetate was more reactive than the mercapto propionate. Both thiols were more prone to add to the monounsaturated methyl oleate than to methyl linoleate, which contained two unconjugated double bonds. According to bond energy calculations, the thiol hydrogen of mercapto acetate was somewhat more difficult to abstract than the hydrogen of mercapto propionate. Consequently, the formed SC bond in the acetate case was stronger than in the propionate case, and so the equilibrium was more shifted toward the addition products. The real‐time IR measurements also showed that the cis unsaturation in methyl oleate isomerized much more quickly than that in methyl linoleate, and this also had an impact on the overall addition rate of the thiols because a trans unsaturation was more reactive than a cis unsaturation. The higher isomerization rates in the oleate systems, compared with those of the linoleate systems, was suggested to be due to a more restricted rotation along the CC bond of the reacted unsaturation in linoleate. This study showed the importance of trans unsaturations in obtaining reasonable reaction rates in thiol–ene reactions with fatty acid derivatives. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 6346–6352, 2004
Preparation of calixarene‐containing polymer with proton transport ability
Authors: Wang Li , Shi Xianfa , Jia Pengjing , Yang Yong 
Published: November 2004

AbstractTo prepare calixarene‐based polymers with proton transport ability, the calix[4]arene derivatives with one polymerizable group at the upper rim were first prepared via selective nitration, amination, and acrylamidation of calix[4]arene. Two methods, solution polymerization and emulsion polymerization, were then employed to carry out the copolymerization of these derivatives with other monomers such as styrene, vinyl acetate, or methyl methacrylate. Transport experiments show that the resulting calixarene‐based polymers have a very good ability to transport protons. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 6259–6266, 2004
Design and synthesis of optically transparent calcium‐incorporated polymer complexes
Authors: Sindhu S. , Valiyaveettil S. 
Published: November 2004

AbstractTransparent thin films of calcium‐ion‐incorporated polymer composites were synthesized with calcium carbonate (CaCO3) and polymers such as poly(acrylic acid) (PAA), poly(ethylene glycol) (PEG), and methylcellulose. The homogeneous distribution of Ca2+ in the composite films was observed because of the high concentration of COO− groups along the PAA backbone for the complexation of Ca2+ ions. The optical transparency of the composites depends on the weight percentages of the three polymers and the molar concentration of CaCO3 in the composites. Maximum transparency was obtained for a composite film with a PAA/CaCO3 ratio of 9:1. The results indicated that methylcellulose improved the film‐forming capabilities and that PEG improved the transparency of the composites. All polymer complexes were characterized with X‐ray diffraction, fourier transfer infrared spectroscopy, scanning electron microscopy, energy‐dispersive X‐ray spectroscopy, dynamic mechanical analysis, and optical transparency measurements. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4459–4465, 2004
ATCUN‐like metal‐binding motifs in proteins: Identification and characterization by crystal structure and sequence analysis
Authors: Sankararamakrishnan Ramasubbu , Verma Sandeep , Kumar Sandeep 
Published: November 2004

AbstractThe amino terminal Cu(II)‐ and Ni(II)‐binding (ATCUN) motif is a small metal‐binding site found in the N‐terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N‐terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal‐binding geometry helps in the design of metal‐binding peptides and in understanding of the mechanisms of metal‐mediated functions. Since the N‐terminus region of ATCUN‐containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal‐bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN‐like motifs in any position along the polypeptide chain. Only ≈1.9% and ≈0.3% of histidines are involved in partial and full ATCUN‐like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN‐like motifs occur in the middle of an α‐helix or a β‐strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar‐Mammary Syndrome. Our analysis suggests that the ATCUN‐like motif in TBX3 is a potential metal‐binding site, although a structural role was not completely ruled out. Metal‐binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN‐like motifs in other proteins. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Distant replay: What can reinvestigation of a 40‐year‐old incident tell you? A look at Eastman Chemical's 1960 aniline plant explosion
Authors: Lodal Peter N. 
Published: November 2004

AbstractOn October 4, 1960, Eastman Chemical Company suffered the worst accident in its 83‐year history, when an aniline manufacturing facility exploded. Sixteen people were killed, and more than 300 injured, as a result of the blast. This paper analyzes the incident and its aftermath using both historical records and modern analytical techniques. The results provide useful insight into both the technical and cultural safety issues raised, as well as valuable information that can be applied to current processes. Careful analysis, even years after the fact, can reveal new information, as well as reinforce that which is already known. For example, the used of residue curve mapping techniques, combined with the ternary liquid–liquid phase diagram revealed a combination of circumstances that was not anticipated in 1960. As a result of this accident, Eastman instituted a Process Safety Review Committee structure that has continued to this day. One of the results of this structured approach has been an order‐of‐magnitude reduction in serious incidents, sustained over a four‐decade period. © 2004 American Institute of Chemical Engineers Process Saf Prog 23:221–228, 2004
An inherent safety–based incident investigation methodology
Authors: Goraya Attiq , Amyotte Paul R. , Khan Faisal I. 
Published: November 2004

AbstractA methodology has been developed to enable the explicit use of the principles of inherent safety in an incident investigation protocol. The usefulness of this approach is demonstrated by application to the Westray coal mine explosion that occurred in Nova Scotia in 1992. This process‐related disaster resulted in the deaths of 26 workers, destruction of the underground workings, and bankruptcy of the parent company. The purpose in presenting this case study is twofold: to validate the methodology and to identify the inherent safety considerations that could have prevented the incident. These findings have application beyond the realm of coal mining, extending well into the world of the chemical process industries. © 2004 American Institute of Chemical Engineers Process Saf Prog 23:197–205, 2004
Fault tree and layer of protection hybrid risk analysis
Authors: Rothschild Marc 
Published: November 2004

AbstractLayer of protection analysis (LOPA) is a relatively quick and straightforward method for quantifying risk. However, LOPA may be inadequate if used for compound failures when the required failure rate data are not available or when the failures are not independent. Fault tree analysis (FTA) can be used in these situations. FTA is designed to thoroughly and accurately evaluate compound failures and account for any dependencies between failures. FTA can augment LOPA, combining the best qualities of both methods into one powerful hybrid tool for risk analysis. © 2004 American Institute of Chemical Engineers (AIChE) Process Saf Prog 23:185‐190, 2004
An Improved R (Range) Control Chart for Monitoring the Process Variance
Authors: Khoo Michael B. C. , Lim E. G. 
Published: November 2004

AbstractAn R chart is often used to monitor shifts in the process variability. However, the range, $R_i, i = 1, 2, \dots$, statistics from a sampling distribution are highly skewed. Hence, the classical R chart based on the $\pm3\sigma$ control limits will not give an in‐control average run length of approximately 370, or equivalently a type I error, $\alpha = 0.0027$. In this paper, an approach is shown to obtain the control limits of an improved R chart based on a desired type I error from the density function of the Ri statistics. Copyright © 2004 John Wiley & Sons, Ltd.
Modeling of Activity of Efavirenz with the Mutant of HIV Reverse Transcriptase using Variable Connectivity Indices
Authors: Zhong Chongli , He Jingtao , Xia Zhiqiang , Li Yajun 
Published: November 2004

AbstractA model for estimation of activity for efavirenz analogues with the K 103N mutant of HIV‐1 RT was proposed in this work. The new model is predictive that requires only variable connectivity indices in the calculations. Compared with the existing models based on Monte Carlo simulation, the new model is easier to apply with better predictive accuracy, giving an r2of 0.85, cross‐validated Q2 of 0.82 and average error of only 0.23 kcal/mol for the 47 efavirenz analogues concerned. This work also demonstrates that variable connectivity indices, a class of not widely recognized structural descriptors, are quite useful in the QSAR studies in the fields of pharmaceutics and biochemistry. These topological indices may play a more important role in these fields in future.
Superconducting first‐order pairing: Finite‐temperature simulations
Authors: Böhm Michael C. , Schulte Joachim 
Published: November 2004

AbstractA recently developed first‐order mechanism for superconducting pairing has been extended from T = 0 K to finite temperatures. On the basis of quantum statistical considerations, we have suggested a direct pairing interaction that does not necessarily involve second‐order elements, such as the electron–phonon coupling or specific magnetic interactions submitted by spin fluctuations. The driving force for the (energy‐driven) first‐order pairing is an attenuation of the destabilizing influence of the Pauli antisymmetry principle (PAP). Only the moves of unpaired fermions are controlled by the PAP, while the moves of superconducting Cooper pairs are not. The quantum statistics of Cooper pairs is of a mixed type, as it combines fermionic on‐site and bosonic intersite properties. The strong correlation between the strength of PAP constraints and system topology in combination with the electron number has been discussed for some larger clusters. Detailed finite‐temperature simulations on first‐order pairing have been performed for four‐center–four‐electron clusters with different topologies. A canonical ensemble statistics has been employed to derive the electronic energy, the electronic configuration entropy, and the free energy of paired and unpaired states in thermal equilibrium. The simulations show that pairing can be caused by either the electronic energy or the electronic configuration entropy. The coexistence of two different sets of quantum particles in paired states (i.e., the Cooper pairs and the unpaired electrons) can lead to an enhanced configuration entropy. In this context, we discuss the possibility of an entropy‐driven high‐temperature superconductor emerging from a low‐temperature unpaired state. The charge and spin degrees of freedom of the four‐center–four‐electron systems have been studied with the help of the charge and spin fluctuations. The spin fluctuations are helpful in judging the validity of pairing theories based on magnetic interactions. The charge fluctuations are a measure for the carrier delocalization in unpaired and paired states. The well‐known proximity between Jahn–Teller activity and superconductivity is analyzed in the zero‐temperature limit. It is demonstrated that both processes compete in their ability to reduce PAP constraints. All theoretical results have been derived within the framework of the simple Hubbard Hamiltonian. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
Theoretical study of the unimolecular decomposition mechanisms of energetic TNAD and TNAZ explosives
Authors: Liu Min‐Hsien , Chen Cheng , Hong Yaw‐Shun 
Published: November 2004

AbstractCalculation methods based on hybrid Density Functional Theory (DFT) with the basis sets of the B3LYP/6‐31+G(d)//B3LYP/4‐31G(d) method and the differential overlap (INDO) program were used to derive reasonable decomposition mechanisms of 1,4,5,8‐tetranitro‐1,4,5,8‐tetraazadecalin (TNAD) and 1,3,3‐trinitroazetidine (TNAZ) explosives. All possible decomposition species and transition states, including intermediates and products, were identified and their corresponding enthalpy of formation and Gibbs free energy of formation were obtained using polyparametric modification equations. INDO bond energy calculation results reveal the weakest bonding site for reference and determine where cleavage can occur easily. This work is concerned mainly with eliminating HONO (cis or trans form). The activation energy for trans‐form HONO elimination is lower than that of cis‐form HONO elimination in the initial steps of both TNAD and TNAZ decomposition, being 18.5 kJ/mol and 33.3 kJ/mol, respectively. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005
A sensitive, rapid and specific determination of midazolam in human plasma and saliva by liquid chromatography/electrospray mass spectrometry
Authors: Quintela Oscar , Cruz Angelines , Concheiro Marta , Castro Ana de , López‐Rivadulla Manuel 
Published: November 2004

AbstractA rapid, sensitive and selective liquid chromatography/electrospray mass spectrometry (LC/ES‐MS) method was developed for the quantitative determination of the anaesthetic benzodiazepine midazolam (MID) in human saliva and plasma from patients undergoing anesthesia procedures. Biological samples spiked with diazepam‐d5, the internal standard, were extracted into diethyl ether. Compounds were separated on a Xterra® RP18 column using a mobile phase of acetonitrile/formic acid 0.1% at a flow rate of 0.25 mL/min under a linear gradient. Column effluents were analyzed using MS with an ES source in the positive ionization mode. Calibration curves were linear in the concentration ranges of 1–250 and 0.2–25 ng/mL in plasma and saliva, respectively. The limits of detection were 0.5 ng/mL in plasma and 0.1 ng/mL in saliva, using a 0.5‐mL sample volume. The recoveries of the spiked samples were above 65%. The method was applied to ten real samples from patients undergoing midazolam treatment. Copyright © 2004 John Wiley & Sons, Ltd.