bluuebunny/crossref_metadata_2025_split huggingface dataset:
Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
Authors: Favrin Giorgio , Irbäck Anders , Wallin Stefan 
Published: August 2002

AbstractA reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three‐helix‐bundle protein, a 46‐amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Gō approximation, which ignores non‐native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root‐mean‐square deviation of 1.8 Å from the native structure. The sequence‐dependent part of our potential is pairwise additive. Our calculations suggest that fine‐tuning this potential by parameter optimization is of limited use. Proteins 2002;47:99–105. © 2002 Wiley‐Liss, Inc.
Simulations of ion current in realistic models of ion channels: The KcsA potassium channel
Authors: Burykin A. , Schutz C. N. , Villá J. , Warshel A. 
Published: August 2002

AbstractRealistic studies of ion current in biologic channels present a major challenge for computer simulation approaches. All‐atom molecular dynamics simulations involve serious time limitations that prevent their use in direct evaluation of ion current in channels with significant barriers. The alternative use of Brownian dynamics (BD) simulations can provide the current for simplified macroscopic models. However, the time needed for accurate calculations of electrostatic energies can make BD simulations of ion current expensive. The present work develops an approach that overcomes some of the above challenges and allows one to simulate ion currents in models of biologic channels. Our method provides a fast and reliable estimate of the energetics of the system by combining semimacroscopic calculations of the self‐energy of each ion and an implicit treatment of the interactions between the ions, as well as the interactions between the ions and the protein‐ionizable groups. This treatment involves the use of the semimacroscopic version of the protein dipole Langevin dipole (PDLD/S) model in its linear response approximation (LRA) implementation, which reduces the uncertainties about the value of the protein “dielectric constant.” The resulting free energy surface is used to generate the forces for on‐the‐fly BD simulations of the corresponding ion currents. Our model is examined in a preliminary simulation of the ion current in the KcsA potassium channel. The complete free energy profile for a single ion transport reflects reasonable energetics and captures the effect of the protein‐ionized groups. This calculated profile indicates that we are dealing with the channel in its closed state. Reducing the barrier at the gate region allows us to simulate the ion current in a reasonable computational time. Several limiting cases are examined, including those that reproduce the observed current, and the nature of the productive trajectories is considered. The ability to simulate the current in realistic models of ion channels should provide a powerful tool for studies of the biologic function of such systems, including the analysis of the effect of mutations, pH, and electric potentials. Proteins 2002;47:265–280. © 2002 Wiley‐Liss, Inc.
Expression in Pichia pastoris and characterization by circular dichroism and NMR of rhodostomin
Authors: Guo Rey‐Ting , Chou Li‐Jer , Chen Yen‐Chin , Chen Chiu‐Yueh , Pari Koteppa , Jen Chauying J. , Lo Szecheng J. , Huang Shou‐Ling , Lee Chun‐Yann , Chang Tsai‐Wang , Chaung Woei‐Jer 
Published: August 2002

AbstractRhodostomin (Rho) is a snake venom protein isolated from Calloselasma rhodostoma. Rho is a disintegrin that inhibits platelet aggregation by blocking the binding of fibrinogen to the integrin αIIbβ3 of platelets. Rho produced in Escherichia coli inhibited platelet aggregation with a KI value of 263 nM. Although functional, Rho produced in E. coli is misfolded based on our 2D and 3D NMR studies. In order to correct the folding problem, Rho was expressed in Pichia pastoris. The recombinant Rho expressed in P. pastoris inhibited platelet aggregation with a resulting KI value of 70 nM. This is the same potency as that of native Rho. CD analysis showed that the secondary structures of Rho are pH‐independent and contain 3.5–7.9% α‐helix, 48.2–50.5% β‐structures, and 42.3–47% coil. The sequential assignment and structure analysis of Rho were obtained using 2D and 3D 15N‐edited NMR spectra. These results provide the first direct evidence that highly disulfide‐bonded disintegrin can be expressed in P. pastoris with the correct fold. This evidence may serve as the basis for exploring the structure and function relationships as well as the dynamics of disintegrin and its variants. Proteins 2001;43:499–508. © 2001 Wiley‐Liss, Inc.
Crystal structure of an aldehyde reductase Y50F mutant‐NADP complex and its implications for substrate binding
Authors: Ye Qilu , Hyndman David , Green Nancy , Li Xuhong , Korithoski Bryan , Jia Zongchao , Flynn T. Geoffrey 
Published: August 2002

AbstractPig aldehyde reductase containing the active site mutation tyrosine(50) to phenylalanine has been crystallized in the presence of the cofactor NADP(H) to a resolution of 2.2 Å. This structure clearly shows loss of the tyrosine hydroxyl group and no other significant perturbations compared with previously determined structures. The mutant binds cofactor (both oxidized and reduced) more tightly than the wild‐type enzyme but shows a complete lack of binding of the aldehyde reductase inhibitor barbitone, as determined by fluorescence titrations. Numerous attempts at preparing a ternary complex with a range of small aldehyde substrates were unsuccessful. This result, in addition to the inability of the mutant protein to bind the inhibitor, provides strong evidence for the proposal that the tyrosine hydroxyl group is essential for substrate binding in addition to catalysis. Proteins 2001;44:12–19. © 2001 Wiley‐Liss, Inc.
Solution structure and dynamics of ribonuclease Sa
Authors: Laurents Douglas , Pérez‐Cañadillas José Manuel , Santoro Jorge , Rico Manuel , Schell David , Pace C. Nick , Bruix Marta 
Published: August 2002

AbstractWe have used NMR methods to characterize the structure and dynamics of ribonuclease Sa in solution. The solution structure of RNase Sa was obtained using the distance constraints provided by 2,276 NOEs and the C6C96 disulfide bond. The 40 resulting structures are well determined; their mean pairwise RMSD is 0.76 Å (backbone) and 1.26 Å (heavy atoms). The solution structures are similar to previously determined crystal structures, especially in the secondary structure, but exhibit new features: the loop composed of Pro 45 to Ser 48 adopts distinct conformations and the rings of tyrosines 51, 52, and 55 have reduced flipping rates. Amide protons with greatly reduced exchange rates are found predominantly in interior β‐strands and the α‐helix, but also in the external 3/10 helix and edge β‐strand linked by the disulfide bond. Analysis of 15N relaxation experiments (R1, R2, and NOE) at 600 MHz revealed five segments, consisting of residues 1–5, 28–31, 46–50, 60–65, 74–77, retaining flexibility in solution. The change in conformation entropy for RNase SA folding is smaller than previously believed, since the native protein is more flexible in solution than in a crystal. Proteins 2001;44:200–211. © 2001 Wiley‐Liss, Inc.
Focusing of the electrostatic potential at EF‐hands of calbindin D9k: Titration of acidic residues
Authors: Kesvatera Tõnu , Jönsson Bo , Thulin Eva , Linse Sara 
Published: August 2002

AbstractBiological functions for a large class of calmodulin‐related proteins, such as target protein activation and Ca2+ buffering, are based on fine‐tuned binding and release of Ca2+ ions by pairs of coupled EF‐hand metal binding sites. These are abundantly filled with acidic residues of so far unknown ionization characteristics, but assumed to be essential for protein function in their ionized forms. Here we describe the measurement and modeling of pKa values for all aspartic and glutamic acid residues in apo calbindin D9k, a representative of calmodulin‐related proteins. We point out that while all the acidic residues are ionized predominantly at neutral pH, the onset of proton uptake by Ca2+ ligands with high pKa under these conditions may have functional implications. We also show that the negative electrostatic potential is focused at the bidental Ca2+ ligand of each site, and that the potential is significantly more negative at the N‐terminal binding site. Proteins 2001;45:129–135. © 2001 Wiley‐Liss, Inc.
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins
Authors: Gelpí Josep Lluis , Kalko Susana G. , Barril Xavier , Cirera Jordi , de la Cruz Xavier , Luque F. Javier , Orozco Modesto 
Published: August 2002

AbstractThe latest version of the classical molecular interaction potential (CMIP) has the ability to predict the position of crystallographic waters in several proteins with great accuracy. This article analyzes the ability of the CMIP functional to improve the setup procedure of the molecular system in molecular dynamics (MD) simulations of proteins. To this end, the CMIP strategy is used to include both water molecules and counterions in different protein systems. The structural details of the configurations sampled from trajectories obtained using the CMIP setup procedure are compared with those obtained from trajectories derived from a standard equilibration process. The results show that standard MD simulations can lead to artifactual results, which are avoided using the CMIP setup procedure. Because the CMIP is easy to implement at a low computational cost, it can be very useful in obtaining reliable MD trajectories. Proteins 2001;45:428–437. © 2001 Wiley‐Liss, Inc.
Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics
Authors: Sanbonmatsu K.Y. , García A.E. 
Published: August 2002

AbstractReplica exchange molecular dynamics (MD) simulations of Met‐enkephalin in explicit solvent reveal helical and nonhelical structures. Four predominant structures of Met‐enkephalin are sampled with comparable probabilities (two helical and two nonhelical). The energy barriers between these configurations are low, suggesting that Met‐enkephalin switches easily between configurations. This is consistent with the requirement that Met‐enkephalin be sufficiently flexible to bind to several different receptors. Replica exchange simulations of 32 ns are shown to sample approximately five times more configurational space than constant temperature MD simulations of the same duration. The energy landscape for the replica exchange simulation is presented. A detailed study of replica trajectories demonstrates that the significant increases in temperature provided by the replica exchange technique enable transitions from nonhelical to helical structures that would otherwise be prevented by kinetic trapping. Met‐enkephalin (Type Entrez Proteins; Value A61445; Service Entrez Proteins) Proteins 2002;46:225–234. Published 2001 Wiley‐Liss, Inc.
Mode of action of new diethylamines in lycopene cyclase inhibition and in photosystem II turnover
Authors: Fedtke Carl , Depka Brigitte , Schallner Otto , Tietjen Klaus , Trebst Achim , Wollweber Detlef , Wroblowsky Heinz‐Jürgen 
Published: August 2002

AbstractThe new bleaching herbicidal compound N,N‐diethyl‐N‐(2‐undecynyl)amine (NDUA) is identified here as an inhibitor of lycopene cyclase and is compared with the known cyclase inhibitors N,N‐diethyl‐N‐[2‐(4‐chlorophenylthio)ethyl]amine (CPTA) and N,N‐diethyl‐N‐[2‐(4‐methylphenoxy)ethyl]amine (MTPA). HPLC separation of chloroplast pigments shows lycopene accumulation in NDUA treated tissue. Variation in chain length of the undecynylamine moeity of NDUA from 7 to 21 C atoms reveals an optimum of 11 to 14 C atoms for herbicidal activity. A series of seven further analogues of NDUA and CPTA reveals the structural elements necessary for inhibition of lycopene cyclase. The effect of NDUA derivatives on photosynthesis has been studied in Chlamydomonas reinhardtii. Photosynthesis is highly sensitive, particularly towards the C14 and longer chain length analogues at nanomolar concentrations. It is shown that the breakdown of photosynthesis by NDUA is due to interference with the turnover of the D1 protein of the photosystem II reaction centre that requires the continous biosynthesis of the two reaction‐centre β‐carotene moieties in the reassembly phase. The D1 protein disappearance is most marked under strong light conditions. The depletion of photosystem II occurs before total pigment bleaching. This newly recognized mechanism in herbicidal activity is also the basis for the mode of action of other lycopene cyclase inhibitors as well as phytoene desaturase inhibitors.© 2001 Society of Chemical Industry
Monitoring insecticide resistance in house flies (Diptera: Muscidae) from New York dairies
Authors: Kaufman Phillip E , Scott Jeffrey G , Rutz Donald A 
Published: August 2002

AbstractHouse flies were collected from dairies across New York state and the levels of resistance to seven insecticides were measured using standard laboratory assays with three to five diagnostic concentrations. The highest levels of resistance were found for tetrachlorvinphos, permethrin and cyfluthrin. Although levels of resistance to methomyl were somewhat lower, they were among the highest ever reported for field‐collected house flies. Resistance to pyrethrins was limited primarily to the lowest diagnostic concentration. House flies were susceptible to fipronil at all dairies, suggesting that this material would be highly effective for fly control. The levels of resistance were similar at all the dairies, irrespective of their insecticide use, suggesting substantial movement of flies between facilities. Relative to resistance levels found at New York dairies in 1987, resistance levels had increased for permethrin, were unchanged for tetrachlorvinphos and had decreased for dimethoate. To identify a single diagnostic concentration that could be used in the laboratory assays to assess accurately resistance levels in future studies, we carried out a ‘simulated’ field bioassay using formulated materials. A diagnostic concentration for each insecticide is proposed on the basis of a comparison of our bioassays.© 2001 Society of Chemical Industry
Sensitivity of mitochondrial respiration to different inhibitors in Venturia inaequalis
Authors: Steinfeld Ute , Sierotzki Helge , Parisi Sandro , Poirey Sylvie , Gisi Ulrich 
Published: August 2002

AbstractThe sensitivity of Venturia inaequalis field isolates to inhibitors of the cytochrome bc1 complex at the Qo site (QoIs) was characterised at the molecular, biochemical and physiological level, and compared to other respiration inhibitors. Comparison of a sensitive and a QoI‐resistant isolate revealed very high resistance factors both in mycelium growth and spore germination assays. Cross‐resistance was observed among QoIs such as trifloxystrobin, azoxystrobin, famoxadone, strobilurin B and myxothiazol. In the mycelium growth assay, antimycin A, an inhibitor of the cytochrome bc1 complex at the Qi site, was less active against the QoI‐resistant than against the sensitive isolate. The mixture of QoIs with salicylhydroxamic acid (SHAM), an inhibitor of the alternative oxidase, exerted synergistic effects in the spore germination but not in the mycelium growth assay. Thus, the cytochrome and the alternative respiration pathways are assumed to play different roles, depending on the developmental stage of the fungus. Induction of alternative oxidase (AOX) by trifloxystrobin was observed in mycelium cells at the molecular level for the sensitive but not the resistant isolate. Following QoI treatment, respiration parameters such as oxygen consumption, ATP level, membrane potential and succinate dehydrogenase activity were only slightly reduced in Qo‐resistant mycelium cells, and remained at much higher levels than in sensitive cells. In contrast, no difference was observed between sensitive and resistant isolates when NADH consumption was measured. Comparison of the cytochrome b (cyt b) gene of the sensitive and resistant isolates did not reveal any point mutations as is known to occur in resistant isolates of other plant pathogens. It is assumed that QoI resistance in V inaequalis may be based on a compensation of the energy deficiency following QoI application upstream of the NADH dehydrogenase of the respiratory chain.© 2001 Society of Chemical Industry
Photodegradation of diafenthiuron in water
Authors: Keum Young‐Soo , Kim Jeong‐Han , Kim Yong‐Whan , Kim Kyun , Li Qing X 
Published: August 2002

AbstractDiafenthiuron, 1‐tert‐butyl‐3‐(2,6‐di‐isopropyl‐4‐phenoxyphenyl)thiourea, is an effective insecticide and acaricide. Sunlight degradation of diafenthiuron in various aqueous solutions and pure hexane yielded two major identified products: 1‐tert‐butyl‐3‐(2,6‐di‐isopropyl‐4‐phenoxyphenyl)carbodiimide (CGA‐140 408) and 1‐tert‐butyl‐3‐(2,6‐di‐isopropyl‐4‐phenoxy‐phenyl)urea (CGA‐177 960). CGA‐140 408 was further photo‐transformed into CGA‐177 960 by sunlight. Direct photolysis appeared to be a major photolysis pathway of diafenthiuron in the environment. Photodegradation of CGA‐140 408 and CGA‐177 960 was enhanced in humic acid water, paddy water and aqueous acetone solutions, and followed first‐order kinetics. Isopropanol (a radical quencher) and de‐aeration strongly inhibited the photolysis of these chemicals, which suggested oxygen radical‐mediated reactions.© 2002 Society of Chemical Industry
Chemical synthesis and biological activity of rat INSL3
Authors: Smith Kathryn J. , Wade John D. , Claasz Antonia A. , Otvos Laszlo , Temelcos Catherine , Kubota Yoshihiro , Hutson John M. , Tregear Geoffrey W. , Bathgate Ross A. 
Published: August 2002

AbstractThe recently identified protein, insulin 3 (INSL3), has structural features that make it a bona fide member of the insulin superfamily. Its predicted amino acid sequence contains the classic two‐peptide chain (A‐ and B‐) structure with conserved cysteine residues that results in a disulphide bond disposition identical to that of insulin. Recently, the generation of insl3 knockout mice has demonstrated that testicular descent is blocked due to the failure of a specific ligament, the gubernaculum, to develop. The mechanism by which INSL3 exerts its action on the gubernaculum is currently unknown. The purpose of this study was to, for the first time, synthesize rat INSL3 and test its action on organ cultures of foetal rat gubernaculum. INSL3 also contains a cassette of residues Arg‐X‐X‐X‐Arg within the B‐chain, a motif that is essential for characteristic activity of another related member of the superfamily, relaxin. Hence, the relaxin activity of rat INSL3 was also tested in two different relaxin bioassays. The primary structure of rat INSL3 was determined by deduction from its cDNA sequence and successfully prepared by solid phase peptide synthesis of the two constituent chains followed by their combination in solution. Following confirmation of its chemical integrity by a variety of analytical techniques, circular dichroism spectroscopy confirmed the presence of high β‐turn and α‐helical content, with a remarkable spectral similarity to the synthetic ovine INSL3 peptide and to synthetic rat relaxin. The synthetic rat INSL3 bound with very low affinity to rat relaxin receptors and had no activity in a relaxin bioassay. Furthermore, it did not augment or antagonize relaxin activity. The rat INSL3 did however induce growth of foetal rat gubernaculum in whole organ cultures demonstrating that INSL3 has a direct action on this structure. Copyright © 2001 European Peptide Society and John Wiley & Sons, Ltd.
Effect of methanol extract from flower petals of Tagetes patula L. on acute and chronic inflammation model
Authors: Kasahara Yoshimasa , Yasukawa Ken , Kitanaka Susumu , Khan M. Taufiq , Evans Fred J. 
Published: August 2002

AbstractThe methanol extract of the florets of Tagetes patula (MEFTP) inhibited acute and chronic inflammation in mice and rats. MEFTP significantly suppressed hind‐paw oedema induced by γ‐carrageenin in mice. Furthermore, MEFTP not only inhibited the hind‐paw oedema induced by various acute phlogogens, such as histamine, serotonin, bradykinin and prostaglandin E1, but also suppressed the increase of vascular permeability by acetic acid, indicating that it primarily acts at the exudative stage of inflammation. In the chronic inflammation, MEFTP did not inhibit the proliferation of granulation tissue when tested by the cotton pellet method, however, it was effective on the development of adjuvant arthritis in rats. Oral MEFTP inhibited acute and chronic inflammation in mice and rats. Copyright © 2002 John Wiley & Sons, Ltd.
Inhibitory effects of sanguinarine on monoamine oxidase activity in mouse brain
Authors: Lee Sang Sun , Kai Masaaki , Lee Myung Koo 
Published: August 2002

AbstractThe effects of benzophenanthridine alkaloids, such as sanguinarine and chelidonine, on monoamine ­oxidase (MAO) activity in mouse brain were investigated. Sanguinarine showed an inhibitory effect on MAO activity in a concentration dependent manner (53.4% inhibition at 25 µM). However, chelidonine did not inhibit MAO activity. The IC50 value of sanguinarine was 24.5 µM. Sanguinarine inhibited non‐competitively MAO activity using kynuramine as a substrate. The Ki value for sanguinarine was 22.1 µM. These results suggest that sanguinarine partially contributes to the regulation of catecholamine content. Copyright © 2001 John Wiley & Sons, Ltd.
Studies on psychopharmacological activity ofAndrographis paniculata extract
Authors: Mandal Subhash C. , Dhara A. K. , Maiti B. C. 
Published: August 2002

AbstractPsychopharmacological studies were conducted on an extract of Andrographis paniculata herbs. The extract exhibited a significant alteration in behaviour pattern and a reduction in spontaneous motility. The extract also produced a prolongation of the pentobarbitone‐induced sleeping time and lowered the body temperature in different experimental animal models. Copyright © 2001 John Wiley & Sons, Ltd.
Studies on the antidiarrhoeal effect of dragon's blood from Croton urucurana
Authors: Gurgel Luilma A. , Silva Regilane M. , Santos Flavia A. , Martins Domingos T. O. , Mattos Paulo O. , Rao Vietla S. N. 
Published: August 2002

AbstractThe red sap obtained by slashing the bark of Croton urucurana Baill. (Euphorbiaceae), also known as dragon's blood, was screened for a possible antidiarrhoeal activity on castor oil‐induced diarrhoea in rats, cholera toxin‐induced intestinal secretion in mice and on small intestinal transit in mice. Dragon's blood at an oral dose of 600 mg/kg caused in marked inhibition of the diarrhoeal response following castor oil administration as well as the intestinal fluid accumulation promoted by cholera toxin. At a similar dose the red sap significantly inhibited the small intestinal transit which was, however, found to be independent of the opioid mechanism. These results suggest a potential usefulness of the red sap from Croton urucurana Baill. in the control of secretory diarrhoea associated pathologies. Copyright © 2001 John Wiley & Sons, Ltd.