bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum mechanics simulation of protein dynamics on long timescale
Authors: Liu Haiyan , Elstner Marcus , Kaxiras Efthimios , Frauenheim Thomas , Hermans Jan , Yang Weitao 
Published: September 2002

AbstractProtein structure and dynamics are the keys to a wide range of problems in biology. In principle, both can be fully understood by using quantum mechanics as the ultimate tool to unveil the molecular interactions involved. Indeed, quantum mechanics of atoms and molecules have come to play a central role in chemistry and physics. In practice, however, direct application of quantum mechanics to protein systems has been prohibited by the large molecular size of proteins. As a consequence, there is no general quantum mechanical treatment that not only exceeds the accuracy of state‐of‐the‐art empirical models for proteins but also maintains the efficiency needed for extensive sampling in the conformational space, a requirement mandated by the complexity of protein systems. Here we show that, given recent developments in methods, a general quantum mechanical‐based treatment can be constructed. We report a molecular dynamics simulation of a protein, crambin, in solution for 350 ps in which we combine a semiempirical quantum‐mechanical description of the entire protein with a description of the surrounding solvent, and solvent‐protein interactions based on a molecular mechanics force field. Comparison with a recent very high‐resolution crystal structure of crambin (Jelsch et al., Proc Natl Acad Sci USA 2000;102:2246–2251) shows that geometrical detail is better reproduced in this simulation than when several alternate molecular mechanics force fields are used to describe the entire system of protein and solvent, even though the structure is no less flexible. Individual atomic charges deviate in both directions from “canonical” values, and some charge transfer is found between the N and C‐termini. The capability of simulating protein dynamics on and beyond the few hundred ps timescale with a demonstrably accurate quantum mechanical model will bring new opportunities to extend our understanding of a range of basic processes in biology such as molecular recognition and enzyme catalysis. Proteins 2001;44:484–489. © 2001 Wiley‐Liss, Inc.
Folding and stability of the three‐stranded β‐sheet peptide Betanova: Insights from molecular dynamics simulations
Authors: Colombo Giorgio , Roccatano Danilo , Mark Alan E. 
Published: September 2002

AbstractThe dynamics of the three‐stranded β‐sheet peptide Betanova has been studied at four different temperatures (280, 300, 350, and 450 K by molecular dynamics simulation techniques, in explicit water. Two 20‐ns simulations at 280 K indicate that the peptide remains very flexible under “folding” conditions sampling a range of conformations that together satisfy the nuclear magnetic resonance (NMR)‐derived experimental constraints. Two simulations at 300 K (above the experimental folding temperature) of 20 ns each show partial formation of “native”‐like structure, which also satisfies most of the NOE constraints at 280 K. At higher temperature, the presence of compact states, in which a series of hydrophobic contacts remain present, are observed. This is consistent with experimental observations regarding the role of hydrophobic contacts in determining the peptide's stability and in initiating the formation of turns and loops. A set of different structures is shown to satisfy NMR‐derived distance restraints and a possible mechanism for the folding of the peptide into the NMR‐determined structure is proposed. Proteins 2002;46:380–392. © 2002 Wiley‐Liss, Inc.
Bound xenobiotic residues in food commodities of plant and animal origin
Authors: Skidmore M W , Paulson G D , Kuiper H A , Ohlin B , Reynolds S 
Published: September 2002

AbstractThe following are extended summaries of Technical Reports which are produced at intervals by the International Union of Pure and Applied Chemistry (IUPAC). They are entirely the responsibility of IUPAC/the authors and do not necessarily reflect the views of the Editorial Board of Pest Management Science.Copyright © 2002 Society of Chemical Industry
The effects of phytochemical pesticides on the growth of cultured invertebrate and vertebrate cells
Authors: Salehzadeh Areaf , Jabbar Abdul , Jennens Lynn , Ley Steven V , Annadurai Ramasamy S , Adams Roger , Strang Robin H C 
Published: September 2002

AbstractA range of cultured cells of invertebrate and vertebrate origin was grown in the presence of a number of phytochemical pesticides to test the effect of the latter on cell proliferation. The main observation was that azadirachtin was a potent inhibitor of insect cell replication, with an EC50 of 1.5 × 10−10 M against Spodoptera cells and of 6.3 × 10−9 M against Aedes albopictus cells, whilst affecting mammalian cells only at high concentrations (>10−4 M). As expected, the other phytochemical pesticides, except for rotenone, had little effect on the growth of the cultured cells. Rotenone was highly effective in inhibiting the growth of insect cells (EC50:10−8 M) but slightly less toxic towards mammalian cells (EC50:2 × 10−7 M). Neem terpenoids other than azadirachtin and those very similar in structure significantly inhibited growth of the cell cultures, but to a lesser degree. The major neem seed terpenoids, nimbin and salannin, for example, inhibited insect cell growth by 23% and 15%, respectively.© 2002 Society of Chemical Industry
Aerosolized essential oils and individual natural product compounds as brown treesnake repellents
Authors: Clark Larry , Shivik John 
Published: September 2002

AbstractChemical irritants useful as repellents for brown treesnakes (Boiga irregularis) were identified. Exposure to various compounds produced a range of intensities for locomotory behavior in snakes. Essential oils comprised of 10 g liter−1 solutions of cedarwood, cinnamon, sage, juniper berry, lavender and rosemary each were potent snake irritants. Brown treesnakes exposed to a 2‐s burst of aerosol of these oils exhibited prolonged, violent undirected locomotory behavior. In contrast, exposure to a 10 g liter−1 concentration of ginger oil aerosol caused snakes to locomote, but in a deliberate, directed manner. We also tested specific compounds, all derivative of food and flavor ingredients. 10 g liter−1 solutions delivered as aerosols of m‐anisaldehyde, trans‐anethole, cineole, cinnamaldehyde, citral, ethyl phenylacetate, eugenol, geranyl acetate or methyl salicylate all acted as potent irritants for brown treesnakes. The individual ingredients were classified using cluster analysis into groups that promoted different levels of response by snakes. This study is the first to systematically investigate the irritant potential of natural products for snakes. These data will be useful in the development of practical pest management tools for snakes.Published in 2002 for SCI by John Wiley & Sons, Ltd.
Group effects on insecticide toxicity in workers of the Formosan subterranean termite, Coptotermes formosanus Shiraki
Authors: Valles Steven M , Woodson W David 
Published: September 2002

AbstractCoptotermes formosanus workers were treated topically with insecticide and subsequently held individually or in groups to examine possible effects on insecticide toxicity. Chlorpyrifos, cypermethrin and chlordane toxicities were 1.4‐, 1.5‐, and 1.3‐fold greater, respectively, among workers held in groups compared with those held individually after insecticide treatment. Experiments were conducted to examine how enhanced toxicity occurred among termites held in groups after topical insecticide treatment. When workers were treated topically with chlordane and immediately placed with untreated workers, significantly greater numbers of untreated workers were killed compared with controls at all ratios examined (insecticide‐treated:untreated). These data indicated that workers treated topically with insecticide were capable of somehow transferring a lethal dose of insecticide to untreated workers confined in the vial. Chlordane was recovered from untreated workers which had been confined with chlordane‐treated workers; significantly higher quantities of chlordane were recovered from dead workers exposed to chlordane‐treated workers compared with surviving workers exposed to chlordane‐treated workers. Possible mechanisms of insecticide transfer from insecticide‐treated to untreated termites are discussed.Published in 2002 for SCI by John Wiley & Sons, Ltd.
Location of Disulfide bonds in mature α‐L;‐fucosidase from pea
Authors: Codina Anna , Vilaseca Marta , Tarragó Teresa , Fernández Irene , Ludevid Dolors , Giralt Ernest 
Published: September 2002

AbstractFuc‐9 is the mature form of a vacuolar α‐L;‐fucosidase enzyme which seems to play an important role in plant growth regulation. Fuc‐9 is a 202‐residue protein containing five Cys residues located at positions 64, 109, 127, 162 and 169. In this study, the disulfide structure of Fuc‐9 was determined by MALDI‐TOF mass spectrometry (MS), with minimal clean‐up of the samples and at a nanomolar scale. Two strategies, based on a specific chemical cleavage (with 2‐nitro‐5‐thiocyanobenzoic acid and alkaline conditions) at the Cys residues and modification of Cys residues by acrylamide/deuterium labeled acrylamide alkylation, were used. Using these methods, the disulfide pairings Cys64‐Cys109 and Cys162‐Cys169 could be established. The advantages and limitations of our experimental approach are discussed. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.
Conformation of the tripeptide Cbz‐Pro‐Leu‐Trp‐OBzl(CF3)2 deduced from two‐dimensional 1H‐NMR and conformational energy calculations is related to its affinity for NK1‐receptor
Authors: Millet Régis , Goossens Laurence , Goossens Jean‐François , Chavatte Philippe , Bertrand‐Caumont Karine , Houssin Raymond , Hénichart Jean‐Pierre 
Published: September 2002

AbstractChemical modifications of dual NK1/NK2 ligand Cbz‐Gly‐Leu‐Trp‐OBzl(CF3)2 (1) enabled us to create a high NK1 selective ligand Cbz‐Pro‐Leu‐Trp‐OBzl(CF3)2 (2). A determination of the conformational behavior of tripeptide 2 in solution is described. The 1D and 2D 1H‐NMR techniques (COSY and ROESY) were used to assign resonances. Observed interproton distance restraints were considered to characterize conformational behavior. Spectral data indicate that tripeptide 2 presents a rigidified structure in DMSO stabilized by H‐bond in two γ‐turns. Agreement with experimental data was obtained by averaging the 1H‐NMR parameters over several combinations of low‐energy conformations. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.
Conformational solution studies of [Sar7]desamino‐ and [MeAla7]desamino‐ vasopressin analogues using NMR spectroscopy
Authors: Rodziewicz‐Motowidło Sylwia , Zhukov Igor , Kasprzykowski Franciszek , Grzonka Zbigniew , Ciarkowski Jerzy , Wójcik Jacek 
Published: September 2002

AbstractSolution structures of two analogues of vasopressin with an amino acid sequence of c[Mpa1‐Tyr2‐Phe3‐Gln4‐Asn5‐Cys6]‐Xaa7‐Arg8‐Gly9‐NH2 (Xaa = Sar [I] or MeAla [II]) were established using ROE and the 3JHNHα couplings. Each of the peptides was found to exist in two stable isomers, pertaining to the cis or trans status of the Cys6‐Xaa7 peptide bond, thus giving rise to four study objects.Two methods for studies of the conformational properties of the structures were compared. In the first, the algorithm consisted of three steps: (i) An Electrostatically Driven Monte‐Carlo (EDMC) search for low‐energy conformations. (ii) Simulations of the NOESY spectra and the vicinal couplings for these conformations. (iii) Determination of the statistical weights of the conformations with the ANALYZE package, so as to meet the best fit of the averaged NOE intensities and couplings to the experimental data. In the second method, the distance constraints and the torsion angles were used as the usual constraints in the Distance Geometry and Simulated Annealing algorithms. The flexibility of the pressin ring and the C‐terminus was characterized by a large number of families of conformations. The presence of the β‐turn at position 4,5 was confirmed for all low energy structures found. The use of the EDMC method for the elaboration of the NMR data for small flexible peptides yielded an adequate description of their conformational diversity and is the method of choice for the analysis of their solution structures. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.
The terminology of guanidine formation
Authors: Jones John H 
Published: September 2002

AbstractThe terminology in recent use for the conversion NH2 to NHC(NH)NH2 is surveyed and shown to be in a state of extreme confusion: a pragmatic recommendation is made that the word guanidinylation should be generally adopted for this conversion. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.
New potent hGH‐RH analogues with increased resistance to enzymatic degradation
Authors: Izdebski Jan , Witkowska Ewa , Kunce Danuta , Orłowska Alicja , Baranowska Bogusława , Radzikowska Małgorzata , Smoluch Marek 
Published: September 2002

AbstractFour hGH‐RH analogues containing homoarginine (Har) and/or D‐Arg were obtained by solid‐phase methodology using Boc‐chemistry. To introduce Har residues, a Lys(Fmoc) protected Lys derivative was incorporated in the appropriate positions (11, 12, 20, 21 or 29); after assembly of the peptide chain the Fmoc group was removed and the peptide‐resin was guanidinylated by treatment with N, N′‐bis(tert‐butoxycarbonyl)‐S‐methylisothiourea. The peptides were cleaved from the resin by treatment with liquid HF, and the products were purified by RP‐HPLC. The peptides were subjected to digestion by trypsin, and the course of the reaction was followed by HPLC and ESI‐MS. It was found that peptide bonds formed by the carboxyl group of Har are completely stable to trypsin. The course of cleavage at Lys or Arg residues depends on the position of Har in the sequence. All the analogues investigated stimulate the release of GH in rats after subcutaneous administration, and were about 50–100 times as potent as rGH‐RH itself. The analogues had no effect on PRL, LH and FSH levels. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.
Reliability demonstration test for a finite population
Authors: Lu Ming‐Wei , Rudy Richard J. 
Published: September 2002

AbstractIn many situations, we want to accept or reject a population with small or finite population size. In this paper, we will describe Bayesian and non‐Bayesian approaches for the reliability demonstration test based on the samples from a finite population. The Bayesian method is an approach that combines prior experience with newer test data in the application of statistical tools for reliability quantification. When test time and/or sample quantity is limited, the Bayesian approach should be considered. In this paper, a non‐Bayesian reliability demonstration test is considered for both finite and large population cases. The Bayesian approach with ‘uniform’ prior distributions, Polya prior distributions, and sequential sampling is also presented. Copyright © 2001 John Wiley & Sons, Ltd.
Statistically constrained economic design of the multivariate exponentially weighted moving average control chart
Authors: Molnau Wade E. , Montgomery Douglas C. , Runger George C. 
Published: September 2002

AbstractThis paper shows that economic statistical design can provide for better statistical properties without significantly increasing optimal total costs. Cost comparisons between optimal economic statistical designs and optimal economic designs show no significant cost increases. The average run length (ARL) constraints added by economic statistical design significantly improve the statistical properties of the control chart scheme. False alarm frequency is limited while keeping good shift detection characteristics. In addition, the Multivariate Exponentially Weighted Moving Average (MEWMA) control schemes performed better from the cost standpoint than the benchmark pure statistical design—the Hotelling T2 control chart. This improvement held for unconstrained and constrained designs. Finally, cost comparisons at small values of n showed significant advantage for the MEWMA schemes. Copyright © 2001 John Wiley & Sons, Ltd.
Estimation of the expected ROCOF of a repairable system with bootstrap confidence region
Authors: Phillips M. J. 
Published: September 2002

AbstractBootstrap methods are presented for constructing confidence regions for the expected ROCOF of a repairable system. This is based on the work of Cowlinget al.(Journal of the American Statistical Association1996;91: 1516–1524) for the intensity function of a NHPP. The method is applied to the failure times of a photocopier given by Baker (Technometrics1996;38: 256–265). Copyright © 2001 John Wiley & Sons, Ltd.
Assessing the maintenance in a process using a semi‐parametric approach
Authors: Ansell Jake , Archibald Tom , Dagpunar John , Thomas Lyn , Abell Peter , Duncalf David 
Published: September 2002

AbstractIn developing any successful maintenance strategy it is important to be able to estimate the rate of occurrence of maintenance events. In a previous paper the authors have argued that there are advantages to using a non‐parametric or semi‐parametric approach to such analysis. In this paper the authors explore the use of the approach to data from the water industry using a case study. The approach provides insight into the context revealing the impact of maintenance on the process. The effect of the maintenance strategy can be evaluated. The paper explores the practical issues of missing values and implementation of an appropriate maintenance strategy. Copyright © 2001 John Wiley & Sons, Ltd.
Bayesian belief nets for managing expert judgement and modelling reliability
Authors: Sigurdsson J. H. , Walls L. A. , Quigley J. L. 
Published: September 2002

AbstractBayesian belief nets (BBNs) provide an effective way of reasoning under uncertainty. They have a firm mathematical background in probability theory and have been used in a variety of application areas, including reliability. BBNs can provide alternative representations of fault trees and reliability block diagrams. BBNs can be used to incorporate expert judgement formally into the modelling process. It has been claimed BBNs may overcome some of the limitations of standard reliability techniques. This paper presents an overview of BBNs and illustrates their use through a simple tutorial on system reliability modelling. The use of BBNs in reliability to date is reviewed. The challenge of using BBNs in reliability practice is explored and areas of research are identified. Copyright © 2001 John Wiley & Sons, Ltd.
Characterisation and determination of indole alkaloids in frog‐skin secretions by electrospray ionisation ion trap mass spectrometry
Authors: McClean Stephen , Robinson Robert C. , Shaw Chris , Smyth W. Franklin 
Published: September 2002

AbstractThe characterisation of selected indole alkaloids in a quadrupole ion trap mass spectrometer is presented. Fragmentation profiles for tryptamine, 5‐hydroxytryptamine (5‐HT), N′‐methyl 5‐hydroxytryptamine (N′‐methyl 5‐HT), N′,N′‐dimethyl 5‐hydroxytryptamine (bufotenine), N′,N′,N′‐trimethyl 5‐hydroxytryptamine (5‐HTQ), and N′,N′‐dimethyl 5‐methoxytryptamine (5‐MeODMT) are presented with proposed structures given for each product ion observed. Such MSn experiments can be used to differentiate the isobaric molecular ions of the compounds 5‐HTQ (M+) and 5‐MeODMT (MH+). The quantitative determination of certain indole alkaloids in the skin secretions of the Australian Golden Bell frog, Litoria aurea, by LC/ESI‐ion trap MS is also presented. The concentrations of 5‐HT, N′‐methyl 5‐HT and 5‐HTQ were found to be 2.68, 0.26 and 0.54 µg per mg of skin secretion, respectively. Copyright © 2002 John Wiley & Sons, Ltd.
Determination of naphthodianthrones and phloroglucinols from Hypericum perforatum extracts by liquid chromatography/tandem mass spectrometry
Authors: Tolonen Ari , Uusitalo Jouko , Hohtola Anja , Jalonen Jorma 
Published: September 2002

AbstractHypericum perforatum L. (St. John's Wort) has long been known as a medicinal plant, and has been used for the treatment of depression and neuralgic disorders. Its main active constituents are believed to be a naphthodianthrone, hypericin, and a phloroglucinol, hyperforin. A sensitive high performance liquid chromatography (HPLC)/electrospray tandem mass spectrometric method for fast simultaneous determination of six major naphthodianthrones and phloroglucinols of Hypericum perforatum extract has been developed. The method, based on multiple dissociation reaction monitoring (MRM), allows the analysis of hypericin, protohypericin, pseudohypericin, protopseudo‐hypericin, hyperforin and adhyperforin from the extract in less than 5 min. Good linearity over the range 0.1–1000 ng/mL for hyperforin and 2–500 ng/mL for hypericin was observed. Intra‐assay accuracy and precision varied from 2 to 19% within these ranges. Lower levels of quantitation for hyperforin were 0.5 ng/mL and 2 ng/mL for hypericin. Copyright © 2002 John Wiley & Sons, Ltd.
Fragmentation studies on monensin A and B by accurate‐mass electrospray tandem mass spectrometry
Authors: Lopes Norberto P. , Stark Christian B. W. , Hong Hui , Gates Paul J. , Staunton James 
Published: September 2002

AbstractMonensin A and B were studied by electrospray ionisation tandem mass spectrometry (ESI‐MS/MS) and the fragment ions were confirmed by accurate‐mass measurements. Analyses were performed on both a quadrupole time‐of‐flight (QTOF) and a Fourier‐transform ion cyclotron resonance (FTICR) mass spectrometer. The analysis revealed that fragment ions were produced by Grob‐Wharton fragmentations and pericyclic rearrangements in addition to various simple neutral losses. A study of the protonated and sodiated sodium salt revealed different fragmentation pathways for these species, thus complementary structural information could be gained. A complete fragmentation pathway of monensin A and B protonated sodium salt [(M − H + Na) + H]+ and sodiated sodium salt [(M − H + Na) + Na]+ is proposed. MS3 analysis confirmed the separate fragmentation pathways. Copyright © 2002 John Wiley & Sons, Ltd.
Generic method for on‐line extraction of drug substances in the presence of biological matrices using turbulent flow chromatography
Authors: Herman J. L. 
Published: September 2002

AbstractThe use of liquid chromatography/mass spectrometry (LC/MS) to quantify drugs in biological matrices has been well established over the last decade. Extremely fast LC/MS methods are commonplace in the pharmaceutical industry for high‐throughput Absorption, Distribution, Metabolism and Excretion (ADME) screening. However, to truly take full advantage of high‐throughput ADME screening, a generic method is needed that eliminates the need to develop a new method for each new compound being screened. New developments in the stationary phase of turbulent flow columns has allowed us to develop an on‐line biological sample cleanup method that is suitable for over 99% of the compounds in the Cephalon database. Copyright © 2002 John Wiley & Sons, Ltd.