bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oviposition preference and larval performance of monarch butterflies (Danaus plexippus) on two invasive swallow‐wort species
Authors: DiTommaso Antonio , Losey John E. 
Published: August 2003

AbstractThe potential of two invasive herbaceous vinesVincetoxicum nigrum(L.) Moench andVincetoxicum rossicum(Kleopow) Barbar. (Asclepiadaceae) to reduce monarch butterfly (Danaus plexippusL.) (Lepidoptera: Nymphalidae, Danainae) populations was investigated by evaluating oviposition selection in adult monarch butterflies and larval feeding preference in choice tests comparing the native host plant of monarch butterflies,Asclepias syriacaL. (Asclepiadaceae) and the two non‐indigenousVincetoxicumspecies. In both choice and no‐choice tests, no eggs were oviposited on either of the twoVincetoxicumspecies whereas over 66 eggs per female were oviposited onA. syriacaplants. All first instar larvae allowed to feed onA. syriacafor 48 h survived while a significantly lower proportion survived onV. rossicum(44%) andV. nigrum(14%). Mean weight of larvae that did survive on theVincetoxicumspecies was significantly lower than the mean weight of larvae that fed onA. syriaca. The mean weight of surviving larvae, however, did not differ between the twoVincetoxicumspecies. The mean proportion of leaves consumed by larvae feeding onA. syriacawas significantly greater than the mean proportion of leaves consumed by larvae feeding on eitherVincetoxicumspecies. Findings from this research indicate thatV. rossicumandV. nigrumare not viable hosts of monarch butterflies and are likely to pose little direct threat to their populations as oviposition sinks. The ability of these highly aggressive plants, however, to out‐compete and displace the native host of monarchs,A. syriaca, may pose a more serious threat. The potential of monarch populations to adapt to the twoVincetoxicumspecies as host plants over the long‐term is discussed.
Induction of heat shock protein (HSP)‐70 in posterior cingulate and retrosplenial cortex of rat brain by dizocilpine and phencyclidine: lack of protective effects of s receptor ligands
Authors: HASHIMOTO KENJI , TOMITAKA SHIN‐ICHIRO , NARITA NATSUKO , MINABE YOSHIO , IYO MASAOMI , FUKUI SUSUMU 
Published: August 2003

AbstractThe role of σ receptors in the induction of heat shock protein (HSP)‐70 by non‐competitive N‐methyl‐Daspartate (NMDA) receptor antagonists (+)‐MK‐801 (dizocilpine) and phencyclidine (PCP) was studied. HSP‐70 is induced in the posterior cingulate and retrosplenial cortex of rat brain 24 hours after a single administration of dizocilpine (1 mg/kg) or PCP (50 mg/kg). The induction of heat shock protein HSP‐70 by dizocilpine or PCP was attenuated partially by pre‐treatment with the antipsychotic drug haloperidol (3 mg/kg, i.p., 15 minutes previously). However, pre‐treatment with high potent and selective σ receptor ligands, 4‐phenyl‐4‐(1‐phenylbutyl)piperidine (4‐PPBP, 3 mg/kg, i.p., 15 minutes previously) and N,N‐dipropyl‐2‐[4‐methoxy‐3‐(2‐phenylethoxy)phenyl]‐ethylamine monohydrochloride) (NE‐100, 3 mg/kg, i.p., 15 minutes previously) did not alter the induction of HSP‐70 by dizocilpine or PCP. These findings suggest that σ receptors may not play a significant role in the induction of HSP‐70 by non‐competitive NMDA receptor antagonists dizocilpine and PCP, and that protective effects of haloperidol on induction of HSP‐70 protein by dizocilpine or PCP may be due to other effect(s) except σ receptors.
The PUF Family of RNA‐binding Proteins: Does Evolutionarily Conserved Structure Equal Conserved Function?
Authors: Spassov Danislav , Jurecic Roland 
Published: August 2003

AbstractDrosophila Pumilio ( Pum ) protein is a founder member of a novel family of RNA‐binding proteins, known as the PUF family. The PUF proteins constitute an evolutionarily highly conserved family of proteins present from yeast to humans and plants, and are characterized by a highly conserved C‐terminal RNA‐binding domain, composed of eight tandem repeats. The conserved biochemical features and genetic function of PUF family members have emerged from studies of model organisms. PUF proteins bind to related sequence motifs in the 3' untranslated region (3'UTR) of specific target mRNAs and repress their translation. Frequently, PUF proteins function asymmetrically to create protein gradients, thus causing asymmetric cell division and regulating cell fate specification. Thus, it was recently proposed that the primordial role of PUF proteins is to sustain mitotic proliferation of stem cells. Here we review the evolution, conserved genetic and biochemical properties of PUF family of proteins, and discuss protein interactions, upstream regulators and downstream targets of PUF proteins. We also suggest that a conserved mechanism of PUF function extends to the newly described mammalian members of the PUF family (human PUM1 and PUM2, and mouse Pum1 and Pum2 ), that show extensive homology to Drosophila Pum, and could have an important role in cell development, fate specification and differentiation. IUBMB Life, 55: 359‐366, 2003
Unintentional Drownings among New York State Residents, 1988–1994
Authors: Browne Marilyn L. , Lewis-Michl Elizabeth L. , Stark Alice D. 
Published: August 2003

Objective. This study examines situations in which drownings occur (environmental risk factors) and the victims' personal risk factors (age, gender, use of personal flotation device, medical condition, alcohol or drug use) to provide guidance for future drowning prevention efforts. Methods. The authors investigated 883 non-bathtub drownings among New York State residents for the years 1988 to 1994 using medical examiner, coroner, police, and/or hospital records in addition to death certificate data. Results. Males, children ages 0–4 years, and African American males ages 5–14 years residing in New York State outside New York City experienced the highest rates of drowning. The majority of drownings occurred in a natural body of water for all age groups, with the exception of children ages 0–4 years. Most drownings among children ages 0–4 years occurred in residential swimming pools. The child usually gained access to the pool via inadequate fencing, an open or ineffective gate, or a ladder (to an above-ground pool) left in the “down” position. Less than 10% of victims of watercraft-related drownings were wearing personal flotation devices. Blood alcohol concentration (BAC) tests were positive for 44% of 250 persons 15 years of age and older for whom valid toxicology results were provided; 30% had BACs of 100 mg/dl or more. Conclusions. Suggested prevention efforts include stricter enforcement of fencing requirements for residential swimming pools and drowning prevention education stressing personal flotation device use while boating and the danger of mixing alcohol and water-related activities.
Watercraft-Related Drownings among New York State Residents, 1988–1994
Authors: Browne Marilyn L. , Lewis-Michl Elizabeth L. , Stark Alice D. 
Published: August 2003

Objective. To describe environmental and personal risk factors associated with watercraft-related drownings. This information may be useful in developing boating safety programs, regulations, and enforcement priorities. Methods. A companion article in this issue (Unintentional Drownings Among New York State Residents, page 448) summarizes an investigation of 883 non-bathtub drownings among New York State residents for the years 1988 to 1994 using medical examiner, coroner, police, and hospital records in addition to death certificate data. This report details the environmental and personal risk factors associated with 216 watercraft-related drownings. Results. Ninety-three percent of watercraft-related drowning victims were male, with the highest rate of drowning observed among males ages 15–44 years. Most commonly, the victim entered the water when the watercraft capsized (36%), the victim fell overboard (24%), or the victim intended to swim (11%). Personal flotation devices (PFDs) were known to be worn by only 9% of drowning victims, and in these cases other risks overwhelmed the effectiveness of the PFD. Of 73 individuals 15 years of age or older for whom adequate blood alcohol concentration analyses were provided, 44% were positive for blood alcohol. Conclusions. Based on this study, increased use of PFDs, avoidance of dangerous currents, and less alcohol use by operators and passengers of all types of watercraft would result in a reduction in watercraft-related drownings. In addition to continued education efforts, boating safety measures that deserve consideration include enforcement of current PFD and boating while intoxicated (BWI) regulations and expansion of BWI laws to apply to all boaters.
Single‐stranded DNA binding of the cold‐shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization
Authors: Zeeb Markus , Balbach Jochen 
Published: August 2003

AbstractCold‐shock proteins (CSPs) bind to single‐stranded nucleic acids, thereby acting as a “RNA chaperone.” To gain deeper insights into the rather unspecific nature of ssDNA/RNA binding, we characterized the binding interface of CspB from Bacillus subtilis to a 25‐mer of ssDNA (Y‐Box25) using heteronuclear 2D NMR spectroscopy. Seventeen residues, including eight out of nine aromatic amino acids, are directly involved in the Y‐Box25 interaction and were identified by extreme line broadening of their cross‐peaks. Eight residues belong to the earlier proposed RNP binding motifs. A second set of seven backbone amides becomes evident by major chemical shift perturbations reporting remote conformational rearrangements upon binding. These residues are located in loop β3–β4 and loopβ4–β5, and include Ile18. The individual contributions of the so‐identified residues were examined by fluorescence titration experiments of 15 CspB variants. Phenylalanine substitutions in‐ and outside the RNP motifs significantly reduce the binding affinity. Unrestricted possible backbone conformations of loop β3–β4 also markedly contribute to binding. Stopped‐flow fluorescence kinetics revealed that the different binding affinities of CspB variants are determined by the dissociation rate, whereas the association rate remains unchanged. This might be of importance for the “RNA chaperone” activity of CspB.
Comparison of β‐lactamases of classes A and D: 1.5‐Å crystallographic structure of the class D OXA‐1 oxacillinase
Authors: Sun Tao , Nukaga Michiyoshi , Mayama Kayoko , Braswell Emory H. , Knox James R. 
Published: August 2003

AbstractThe crystallographic structure of the Escherichia coli OXA‐1 β‐lactamase has been established at 1.5‐Å resolution and refined to R = 0.18. The 28.2‐kD oxacillinase is a class D serine β‐lactamase that is especially active against the penicillin‐type β‐lactams oxacillin and cloxacillin. In contrast to the structures of OXA‐2, OXA‐10, and OXA‐13 belonging to other subclasses, the OXA‐1 molecule is monomeric rather than dimeric and represents the subclass characterized by an enlarged Ω loop near the β‐lactam binding site. The 6‐residue hydrophilic insertion in this loop cannot interact directly with substrates and, instead, projects into solvent. In this structure at pH 7.5, carboxylation of the conserved Lys 70 in the catalytic site is observed. One oxygen atom of the carboxylate group is hydrogen bonded to Ser 120 and Trp 160. The other oxygen atom is more exposed and hydrogen bonded to the Oγ of the reactive Ser 67. In the overlay of the class D and class A binding sites, the carboxylate group is displaced ca. 2.6 Å from the carboxylate group of Glu 166 of class A enzymes. However, each group is equidistant from the site of the water molecule expected to function in hydrolysis, and which could be activated by the carboxylate group of Lys 70. In this ligand‐free OXA‐1 structure, no water molecule is seen in this site, so the water molecule must enter after formation of the acyl‐Ser 67 intermediate.
Protein hydrogen exchange mechanism: Local fluctuations
Authors: Maity Haripada , Lim Woon Ki , Rumbley Jon N. , Englander S. Walter 
Published: August 2003

AbstractExperiments were done to study the dynamic structural motions that determine protein hydrogen exchange (HX) behavior. The replacement of a solvent‐exposed lysine residue with glycine (Lys8Gly) in a helix of recombinant cytochrome c does not perturb the native structure, but it entropically potentiates main‐chain flexibility and thus can promote local distortional motions and large‐scale unfolding. The mutation accelerates amide hydrogen exchange of the mutated residue by about 50‐fold, neighboring residues in the same helix by less, and residues elsewhere in the protein not at all, except for Leu98, which registers the change in global stability. The pattern of HX changes shows that the coupled structural distortions that dominate exchange can be several residues in extent, but they expose to exchange only one amide NH at a time. This ‘local fluctuation’ mode of hydrogen exchange may be generally recognized by disparate near‐neighbor rates and a low dependence on destabilants (denaturant, temperature, pressure). In contrast, concerted unfolding reactions expose multiple neighboring amide NHs with very similar computed protection factors, and they show marked destabilant sensitivity. In both modes, ionic hydrogen exchange catalysts attack from the bulk solvent without diffusing through the protein matrix.
Induced fit in guanidino kinases—comparison of substrate‐free and transition state analog structures of arginine kinase
Authors: Yousef Mohammad S. , Clark Shawn A. , Pruett Pamela K. , Somasundaram Thayumanasamy , Ellington W. Ross , Chapman Michael S. 
Published: August 2003

AbstractArginine kinase (AK) is a member of the guanidino kinase family that plays an important role in buffering ATP concentration in cells with high and fluctuating energy demands. The AK specifically catalyzes the reversible phosphoryl transfer between ATP and arginine. We have determined the crystal structure of AK from the horseshoe crab (Limulus polyphemus) in its open (substrate‐free) form. The final model has been refined at 2.35 Å with a final R of 22.3% (Rfree = 23.7%). The structure of the open form is compared to the previously determined structure of the transition state analog complex in the closed form. Classically, the protein would be considered two domain, but dynamic domain (DynDom) analysis shows that most of the differences between the two structures can be considered as the motion between four rigid groups of nonsequential residues. ATP binds near a cluster of positively charged residues of a fixed dynamic domain. The other three dynamic domains close the active site with separate hinge rotations relative to the fixed domain. Several residues of key importance for the induced motion are conserved within the phosphagen kinase family, including creatine kinase. Substantial conformational changes are induced in different parts of the enzyme as intimate interactions are formed with both substrates. Thus, although induced fit occurs in a number of phosphoryl transfer enzymes, the conformational changes in phosphagen kinases appear to be more complicated than in prior examples.
Electrostatic interactions in the reconstitution of an SH2 domain from constituent peptide fragments
Authors: Ojennus Deanna Dahlke , Lehto Sarah E. , Wuttke Deborah S. 
Published: August 2003

AbstractFragment complementation has been used to delineate the essential recognition elements for stable folding in Src homology 2 (SH2) domains by using NMR spectroscopy, alanine scanning, and surface plasmon resonance. The unfolded 9‐kD and 5‐kD peptide fragments formed by limited proteolytic digestion of the N‐terminal SH2 domain from the p85α subunit of phosphatidylinositol 3′‐kinase fold into an active native‐like structure on interaction with one another. The corresponding 5‐kD fragment of the homologous Src protein, however, was not capable of structurally complementing the p85 9‐kD fragment, indicating that fragment complementation among these SH2 domains is sensitive to the sequence differences between the Src and p85 domains. Partial complementation and folding activity could be recovered with hybrid sequences of these SH2 domains. Complete alanine scanning of the 5‐kD p85 fragment was used to identify the sequence recognition elements required for complex formation. The alanine substitutions in the p85 5‐kD fragment that abolished binding affinity with the cognate 9‐kD fragment correlate well with highly conserved residues among SH2 domains that are either integrally involved in core packing or found at the interface between fragments. Surprisingly, however, mutation of a nonconserved surface‐exposed aspartic acid to alanine was found to have a significant effect on complementation. A single additional mutation of arginine to aspartic acid allowed for recovery of native structure and increased the thermal stability of the designed Src‐p85 chimera by 18°C. This modification appears to relieve an unfavorable surface electrostatic interaction, demonstrating the importance of surface charge interactions in protein stability.
Stably folded de novo proteins from a designed combinatorial library
Authors: Wei Yinan , Liu Tun , Sazinsky Stephen L. , Moffet David A. , Pelczer István , Hecht Michael H. 
Published: August 2003

AbstractBinary patterning of polar and nonpolar amino acids has been used as the key design feature for constructing large combinatorial libraries of de novo proteins. Each position in a binary patterned sequence is designed explicitly to be either polar or nonpolar; however, the precise identities of these amino acids are varied extensively. The combinatorial underpinnings of the “binary code” strategy preclude explicit design of particular side chains at specified positions. Therefore, packing interactions cannot be specified a priori. To assess whether the binary code strategy can nonetheless produce well‐folded de novo proteins, we constructed a second‐generation library based upon a new structural scaffold designed to fold into 102‐residue four‐helix bundles. Characterization of five proteins chosen arbitrarily from this new library revealed that (1) all are α‐helical and quite stable; (2) four of the five contain an abundance of tertiary interactions indicative of well‐ordered structures; and (3) one protein forms a well‐folded structure with native‐like features. The proteins from this new 102‐residue library are substantially more stable and dramatically more native‐like than those from an earlier binary patterned library of 74‐residue sequences. These findings demonstrate that chain length is a crucial determinant of structural order in libraries of de novo four‐helix bundles. Moreover, these results show that the binary code strategy—if applied to an appropriately designed structural scaffold—can generate large collections of stably folded and/or native‐like proteins.
A structural basis for the mechanism of aspartate‐β‐semialdehyde dehydrogenase from Vibrio cholerae
Authors: Blanco Julio , Moore Roger A. , Kabaleeswaran Venkataraman , Viola Ronald E. 
Published: August 2003

AbstractL‐Aspartate‐β‐semialdehyde dehydrogenase (ASADH) catalyzes the reductive dephosphorylation of β‐aspartyl phosphate to L‐aspartate‐β‐semialdehyde in the aspartate biosynthetic pathway of plants and micro‐organisms. The aspartate pathway produces fully one‐quarter of the naturally occurring amino acids, but is not found in humans or other eukaryotic organisms, making ASADH an attractive target for the development of new antibacterial, fungicidal, or herbicidal compounds. We have determined the structure of ASADH from Vibrio cholerae in two states; the apoenzyme and a complex with NADP, and a covalently bound active site inhibitor, S‐methyl‐L‐cysteine sulfoxide. Upon binding the inhibitor undergoes an enzyme‐catalyzed reductive demethylation leading to a covalently bound cysteine that is observed in the complex structure. The enzyme is a functional homodimer, with extensive intersubunit contacts and a symmetrical 4‐amino acid bridge linking the active site residues in adjacent subunits that could serve as a communication channel. The active site is essentially preformed, with minimal differences in active site conformation in the apoenzyme relative to the ternary inhibitor complex. The conformational changes that do occur result primarily from NADP binding, and are localized to the repositioning of two surface loops located on the rim at opposite sides of the NADP cleft.
Weak alignment offers new NMR opportunities to study protein structure and dynamics
Authors: Bax Ad 
Published: August 2003

AbstractProtein solution nuclear magnetic resonance (NMR) can be conducted in a slightly anisotropic environment, where the orientational distribution of the proteins is no longer random. In such an environment, the large one‐bond internuclear dipolar interactions no longer average to zero and report on the average orientation of the corresponding vectors relative to the magnetic field. The desired very weak ordering, on the order of 10−3, can be induced conveniently by the use of aqueous nematic liquid crystalline suspensions or by anisotropically compressed hydrogels. The resulting residual dipolar interactions are scaled down by three orders of magnitude relative to their static values, but nevertheless can be measured at high accuracy. They are very precise reporters on the average orientation of bonds relative to the molecular alignment frame, and they can be used in a variety of ways to enrich our understanding of protein structure and function. Applications to date have focused primarily on validation of structures, determined by NMR, X‐ray crystallography, or homology modeling, and on refinement of structures determined by conventional NMR approaches. Although de novo structure determination on the basis of dipolar couplings suffers from a severe multiple minimum problem, related to the degeneracy of dipolar coupling relative to inversion of the internuclear vector, a number of approaches can address this problem and potentially can accelerate the NMR structure determination process considerably. In favorable cases, where large numbers of dipolar couplings can be measured, inconsistency between measured values can report on internal motions.
The solution structure of bovine pancreatic trypsin inhibitor at high pressure
Authors: Williamson Michael P. , Akasaka Kazuyuki , Refaee Mohamed 
Published: August 2003

AbstractThe solution structure of bovine pancreatic trypsin inhibitor (BPTI) at a pressure of 2 kbar is presented. The structure was calculated as a change from an energy‐minimized low‐pressure structure, using 1H chemical shifts as restraints. The structure has changed by 0.24 Å RMS, and has almost unchanged volume. The largest changes as a result of pressure are in the loop 10–16, which contains the active site of BPTI, and residues 38–42, which are adjacent to buried water molecules. Hydrogen bonds are compressed by 0.029 ± 0.117 Å, with the longer hydrogen bonds, including those to internal buried water molecules, being compressed more. The hydrophobic core is also compressed, largely from reduction of packing defects. The parts of the structure that have the greatest change are close to buried water molecules, thus highlighting the importance of water molecules as the nucleation sites for volume fluctuation of proteins in native conditions.