bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and dynamics of dark‐state bovine rhodopsin revealed by chemical cross‐linking and high‐resolution mass spectrometry
Authors: Jacobsen Richard B. , Sale Kenneth L. , Ayson Marites J. , Novak Petr , Hong Joohee , Lane Pamela , Wood Nichole L. , Kruppa Gary H. , Young Malin M. , Schoeniger Joseph S. 
Published: May 2006

AbstractRecent work using chemical cross‐linking to define interresidue distance constraints in proteins has shown that these constraints are useful for testing tertiary structural models. We applied this approach to the G‐protein‐coupled receptor bovine rhodopsin in its native membrane using lysine‐ and cysteine‐targeted bifunctional cross‐linking reagents. Cross‐linked proteolytic peptides of rhodopsin were identified by combined liquid chromatography and FT‐ICR mass spectrometry with automated data‐reduction and assignment software. Tandem mass spectrometry was used to verify cross‐link assignments and locate the exact sites of cross‐link attachment. Cross‐links were observed to form between 10 pairs of residues in dark‐state rhodopsin. For each pair, cross‐linkers with a range of linker lengths were tested to determine an experimental distance‐of‐closest‐approach (DCA) between reactive side‐chain atoms. In all, 28 cross‐links were identified using seven different cross‐linking reagents. Molecular mechanics procedures were applied to published crystal structure data to calculate energetically achievable theoretical DCAs between reactive atoms without altering the position of the protein backbone. Experimentally measured DCAs are generally in good agreement with the theoretical DCAs. However, a cross‐link between C316 and K325 in the C‐terminal region cannot be rationalized by DCA simulations and suggests that backbone reorientation relative to the crystal coordinates occurs on the timescale of cross‐linking reactions. Biochemical and spectroscopic data from other studies have found that the C‐terminal region is highly mobile in solution and not fully represented by X‐ray crystallography data. Our results show that chemical cross‐linking can provide reliable three‐dimensional structural information and insight into local conformational dynamics in a membrane protein.
Structure and topology of the non‐amyloid‐β component fragment of human α‐synuclein bound to micelles: Implications for the aggregation process
Authors: Bisaglia Marco , Trolio Alessandra , Bellanda Massimo , Bergantino Elisabetta , Bubacco Luigi , Mammi Stefano 
Published: May 2006

AbstractHuman α‐synuclein is a small soluble protein abundantly expressed in neurons. It represents the principal constituent of Lewy bodies, the main neuropathological characteristic of Parkinson's disease. The fragment corresponding to the region 61–95 of the protein, originally termed NAC (non‐amyloid‐β component), has been found in amyloid plaques associated with Alzheimer's disease, and several reports suggest that this region represents the critical determinant of the fibrillation process of α‐synuclein. To better understand the aggregation process of α‐synuclein and the role exerted by the biological membranes, we studied the structure and the topology of the NAC region in the presence of SDS micelles, as membrane‐mimetic environment. To overcome the low solubility of this fragment, we analyzed a recombinant polypeptide corresponding to the sequence 57–102 of α‐synuclein, which includes some charged amino acids flanking the NAC region. Three distinct helices are present, separated by two flexible stretches. The first two helices are located closer to the micelle surface, whereas the last one seems to penetrate more deeply into the micelle. On the basis of the structural and topological results presented, a possible pathway for the aggregation process is suggested. The structural information described in this work may help to identify the appropriate target to reduce the formation of pathological α‐synuclein aggregation.
Structural basis for the enantiospecificities of R‐ and S‐specific phenoxypropionate/α‐ketoglutarate dioxygenases
Authors: Müller Tina A. , Zavodszky Maria I. , Feig Michael , Kuhn Leslie A. , Hausinger Robert P. 
Published: May 2006

Abstract(R)‐ and (S)‐dichlorprop/α‐ketoglutarate dioxygenases (RdpA and SdpA) catalyze the oxidative cleavage of 2‐(2,4‐dichlorophenoxy)propanoic acid (dichlorprop) and 2‐(4‐chloro‐2‐methyl‐phenoxy)propanoic acid (mecoprop) to form pyruvate plus the corresponding phenol concurrent with the conversion of α‐ketoglutarate (αKG) to succinate plus CO2. RdpA and SdpA are strictly enantiospecific, converting only the (R) or the (S) enantiomer, respectively. Homology models were generated for both enzymes on the basis of the structure of the related enzyme TauD (PDB code 1OS7). Docking was used to predict the orientation of the appropriate mecoprop enantiomer in each protein, and the predictions were tested by characterizing the activities of site‐directed variants of the enzymes. Mutant proteins that changed at residues predicted to interact with (R)‐ or (S)‐mecoprop exhibited significantly reduced activity, often accompanied by increased Km values, consistent with roles for these residues in substrate binding. Four of the designed SdpA variants were (slightly) active with (R)‐mecoprop. The results of the kinetic investigations are consistent with the identification of key interactions in the structural models and demonstrate that enantiospecificity is coordinated by the interactions of a number of residues in RdpA and SdpA. Most significantly, residues Phe171 in RdpA and Glu69 in SdpA apparently act by hindering the binding of the wrong enantiomer more than the correct one, as judged by the observed decreases in Km when these side chains are replaced by Ala.
Identification of novel quaternary domain interactions in the Hsp90 chaperone, GRP94
Authors: Chu Feixia , Maynard Jason C. , Chiosis Gabriela , Nicchitta Christopher V. , Burlingame Alma L. 
Published: May 2006

AbstractThe structural basis for the coupling of ATP binding and hydrolysis to chaperone activity remains a central question in Hsp90 biology. By analogy to MutL, ATP binding to Hsp90 is thought to promote intramolecular N‐terminal dimerization, yielding a molecular clamp functioning in substrate protein activation. Though observed in studies with recombinant domains, whether such quaternary states are present in native Hsp90s is unknown. In this study, native subunit interactions in GRP94, the endoplasmic reticulum Hsp90, were analyzed using chemical cross‐linking in conjunction with tandem mass spectrometry. We report the identification of two distinct intermolecular interaction sites. Consistent with previous studies, one site comprises the C‐terminal dimerization domain. The remaining site represents a novel intermolecular contact between the N‐terminal and middle (M) domains of opposing subunits. This N+M domain interaction was present in the nucleotide‐empty, ADP‐, ATP‐, or geldanamycin‐bound states and could be selectively disrupted upon addition of synthetic geldanamycin dimers. These results identify a compact, intertwined quaternary conformation of native GRP94 and suggest that intersubunit N+M interactions are integral to the structural biology of Hsp90.
Free energies of protein–protein association determined by electrospray ionization mass spectrometry correlate accurately with values obtained by solution methods
Authors: Krishnaswamy Sanjay R. , Williams Evan R. , Kirsch Jack F. 
Published: May 2006

AbstractThe advantages of electrospray ionization mass spectrometry (ESIMS) to measure relative solution‐phase affinities of tightly bound protein–protein complexes are demonstrated with selected variants of the Bacillus amyloliquefaciens protein barstar (b*) and the RNAase barnase (bn), which form protein–protein complexes with a range of picomolar to nanomolar dissociation constants. A novel chemical annealing procedure rapidly establishes equilibrium in solutions containing competing b* variants with limiting bn. The relative ion abundances of the complexes and those of the competing unbound monomers are shown to reflect the relative solution‐phase concentrations of those respective species. No measurable dissociation of the complexes occurs either during ESI or mass detection, nor is there any evidence for nonspecific binding at protein concentrations <25 μM. Differences in ΔΔG of dissociation between variants were determined with precisions <0.1 kcal/mol. The ΔΔG values obtained deviate on average by 0.26 kcal/mol from those measured with a solution‐phase enzyme assay. It is demonstrated that information about the protein conformation and covalent modifications can be obtained from differences in mass and charge state distributions. This method serves as a rapid and precise means to interrogate protein–protein‐binding surfaces for complexes that have affinities in the picomolar to nanomolar range.
Characterization of three areas of interactions stabilizing complexes between SecA and SecB, two proteins involved in protein export
Authors: Patel Chetan N. , Smith Virginia F. , Randall Linda L. 
Published: May 2006

AbstractThe general secretory, Sec, system translocates precursor polypeptides from the cytosol across the cytoplasmic membrane in Escherichia coli. SecB, a small cytosolic chaperone, captures the precursor polypeptides before they fold and delivers them to the membrane translocon through interactions with SecA. Both SecB and SecA display twofold symmetry and yet the complex between the two is stabilized by contacts that are distributed asymmetrically. Two distinct regions of interaction have been defined previously and here we identify a third. Calorimetric studies of complexes stabilized by different subsets of these interactions were carried out to determine the binding affinities and the thermodynamic parameters that underlie them. We show here that there is no change in affinity when either one of two contact areas out of the three is lacking. This fact and the asymmetry of the binding contacts may be important to the function of the complex in protein export.
Crystal structure of the yeast His6 enzyme suggests a reaction mechanism
Authors: Quevillon‐Cheruel Sophie , Leulliot Nicolas , Graille Marc , Blondeau Karine , Janin Joel , Tilbeurgh Herman Van 
Published: May 2006

AbstractThe Saccharomyces cerevisiae His6 gene codes for the enzyme phosphoribosyl‐5‐amino‐1‐phosphoribosyl‐4‐imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X‐ray structure at a resolution of 1.30 Å using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 Å wavelength. His6 folds in an (α/β)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence.
Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein
Authors: Feng Yongjun , Jiao Wangwang , Fu Xinmiao , Chang Zengyi 
Published: May 2006

AbstractMany cellular proteins exist as homo‐oligomers. The mechanism of the assembly process of such proteins is still poorly understood. We have previously observed that Hsp16.3, a protein exhibiting chaperone‐like activity, undergoes stepwise disassembly and nonstepwise reassembly. Here, the disassembly and reassembly of a nonchaperone protein RbsD, from Escherichia coli, was studied in vitro. The protein was found to mainly exist as decamers with a small portion of apparently larger oligomeric forms, both of which are able to refold/reassemble effectively in a spontaneous way after being completely unfolded. Disassembly RbsD intermediates including pentamers, tetramers, trimers, dimers, and monomers were detected by using urea‐containing pore gradient polyacrylamide gel electrophoresis, while only pentamers were detected for its reassembly. The observation of stepwise disassembly and apparent nonstepwise reassembly for both a chaperone protein (Hsp16.3) and a nonchaperone protein (RbsD) strongly suggests that such a feature is most likely general for homo‐oligomeric proteins.
Structure‐based function inference using protein family‐specific fingerprints
Authors: Bandyopadhyay Deepak , Huan Jun , Liu Jinze , Prins Jan , Snoeyink Jack , Wang Wei , Tropsha Alexander 
Published: May 2006

AbstractWe describe a method to assign a protein structure to a functional family using family‐specific fingerprints. Fingerprints represent amino acid packing patterns that occur in most members of a family but are rare in the background, a nonredundant subset of PDB; their information is additional to sequence alignments, sequence patterns, structural superposition, and active‐site templates. Fingerprints were derived for 120 families in SCOP using Frequent Subgraph Mining. For a new structure, all occurrences of these family‐specific fingerprints may be found by a fast algorithm for subgraph isomorphism; the structure can then be assigned to a family with a confidence value derived from the number of fingerprints found and their distribution in background proteins. In validation experiments, we infer the function of new members added to SCOP families and we discriminate between structurally similar, but functionally divergent TIM barrel families. We then apply our method to predict function for several structural genomics proteins, including orphan structures. Some predictions have been corroborated by other computational methods and some validated by subsequent functional characterization.
NMR structure of the first Ig module of mouse FGFR1
Authors: Kiselyov Vladislav V. , Bock Elisabeth , Berezin Vladimir , Poulsen Flemming M. 
Published: May 2006

AbstractFibroblast growth factor (FGF) receptors (FGFRs) regulate a multitude of cellular processes during embryogenesis and in the adult. The extracellular part of the prototypical FGFR consists of three Ig modules (Ig1 – Ig3), in which Ig2 and Ig3 determine affinity and specificity for FGF and heparin, while the Ig1 module is thought to have a regulatory function. The crystal structures of the Ig2 and Ig3 modules alone and in complex with FGF have previously been reported. The structure of the Ig1 module is unknown, and very little is known about the structural determinants for the regulatory function of this module. We describe here the NMR structure of the Ig1 module of mouse FGFR1. The three‐dimensional fold of the module belongs to the intermediate Ig subgroup and can be described as a β‐barrel consisting of two β‐sheets. One sheet is formed by A′, G, F, C, and C′, and the other by A, B, B′, E, and D β‐strands. The overall strand topology of the Ig1 module is similar to that of the Ig2 and Ig3 modules. However, the A/A′ loop of the Ig1 module is much longer than that of the Ig2 and Ig3 modules. It contains eight extra residues compared to the Ig3 module, and five extra residues compared to Ig2.
The assimilation efficiency of Asellus aquaticus L. (Crustacea, Isopoda)
Authors: PRUS TADEUSZ 
Published: May 2006

Summary(1) Comparative studies of the ash‐ratio and gravimetric methods of determining assimilation efficiency in Asellus aquaticus showed that the differential use of minerals by this species rendered the ash‐ratio method unreliable. Results obtained by the gravimetric method were therefore employed in the analysis of further experiments.(2) The assimilation efficiencies estimated for A. aquaticus ranged between 26 and 44%, and varied according to population density and reproductive condition.(3) Individual winter males had a significantly lower assimilation efficiency (26%) than grouped animals (35%), but the assimilation efficiency of summer males (33%) did not differ significantly from that of winter males at the same density. It is concluded that density affects assimilation efficiency in A. aquaticus.(4) The assimilation efficiency of summer males (33 %) is significantly different from that of summer females (non‐ovigerous, 41 %; ovigerous, 44%). A mean assimilation efficiency of 40% is proposed for the summer period whereas an overall annual mean of 30% is suggested.(5) Despite the various assimilation efficiencies reported within any one season consumption rate per unit weight is fairly constant (winter, 0·04–0·05 cal/24 h; summer, 0·36–0·38 cal/24 h) and it is suggested that the different assimilation rates are a mechanism whereby the additional energy and material requirements of females for breeding can be met without increasing food intake.
Growth, gas vacuolation and buoyancy in a natural population of a planktonic blue‐green alga
Authors: REYNOLDS C. S. 
Published: May 2006

Summary(1)The growth and development of a natural population of Anabaena circinalisis described in relation to physical and chemical conditions within a small, shallow eutrophic lake.(2)Germination of resting spores took place when the lake was destratified, in response to improving conditions of light and temperature.(3)The growth of the population was monitored for chlorophyll and nutrient content, and parallel determinations of heterocyst ratio, gas vacuole volume, turgor and buoyancy were made.(4)Growth of the population was probably limited by phosphorus deficiency.(5)Cessation of growth was marked by increases in gas vacuole volume and buoyancy.(6)Gas vacuole volume is determined primarily by the rate of increase of the alga. It is modified by turgor changes, associated with photosynthetic rates.(7)Surface blooms are the result of the redistribution of buoyant algae when turbulence currents are weak.(8)Buoyancy is increased in algae lodged at the surface.
Studies on the genus Stenostomum O. Schmidt (Turbellaria; Catenulida).
Authors: KOLASA J. , YOUNG J. O. 
Published: May 2006

SummaryTwo species of Stenostomum, viz. S. glanduloswn Kepner and Carter and S. anops Nuttycombe and Waters, are recorded for the first time from Poland. Descriptions of the Polish material are given, and these are compared with published information on the structure of the species. A new sub‐species, viz. S. Corderoi Marcus s. sp. poznanensis s. sp. nov. is recorded from Poland, and fully described. Fealures which separate the new sub‐species from S. corderoi corderoi Marcus are listed.
Studies on the genus Stenostomum O. Schmidt (Turbellaria; Catenulida).
Authors: YOUNG J. O. , KOLASA J. 
Published: May 2006

SummaryA new species of Stenostomum, viz. S. beryii sp. nov. is described from Kenya. It was recorded from a pool near Nairobi, in April and May. The new species resembles S. hemisphericum Nasonov.
Studies on the genus Stenostomum O. Schmidt (Turbellaria; Catenulida).
Authors: YOUNG J. O. , KOLASA J. 
Published: May 2006

SummaryStenostomum arevaloi Gieysztor, S. glandulosum Kepner and Carter, S. leucops (Duges), S. pseudoacetabtihtm Nuttycombe and Waters, and S. unicolor Schmidt are reported from E. Africa. The various localities in which each of the species were found are listed. All the species are new records for this region except S. Leucops which was recorded by Bohmig (1897) from Lake Victoria at Bukoba, Uganda. Descriptions of the species, based on the E. African material, are given.
Population dynamics of perch, Perca fluviatilis L. in Slapton Ley, Devon
Authors: CRAIG J. F. 
Published: May 2006

SummaryPerch, Percafluviatilis L. were studied in Slapton Ley which is a eutrophic freshwater lagoon in south Devon, England. The perch were caught in traps from February 1970 to June 1971. The traps selected males during the spawning season. The water temperature did not affect the numbers of trapped fish directly, but the sight of perch in the traps appeared to attract others. Sex ratios were found to be equal in the first 2 years of life but older year classes were predominantly female. The population consisted of young individuals. Males were found to mature in their first year and most females matured in their second. The fecundity varied from an average of 1000 eggs in perch n i the 9.75 cm length group to 30,500 eggs in fish in the 27.75 cm group. A few shoals of perch moved throughout the Ley although the majority of fish stayed in the same area. Population estimates showed a range from 10,000 to 95,000 for fish 9.75 cm and above. The large variations in population estimates and survival rates were attributed to the necessity of using traps which had variable catches and to the harmful effects of handling the perch. Chironomids were important in the diet of perch of all sizes. Plankton and Asellus were other important foods, the latter especially during the winter months. Perch 11.5 cm to 13.9 cm selected the widest range of food organisms. Only perch 14.0 cm and above ate fish.
Population dynamics and production of Daphnia hyalina in a eutrophic reservoir
Authors: GEORGE D. G. , EDWARDS R. W. 
Published: May 2006

SummaryThe population dynamics and production of Daphnia hyaiina^ the dominant cladoceran i n Eglwys Nynydd, a shallow eutrophic reservoir in South Wales, were studied for 2 years against a background of limnological measurements. The appearance and development of successive generations from egg to adult could be followed from changing numbers in arbitrarily defined size classes. Seasonal variations in mean length, mean brood‐size and proportion of gravid adults were recorded and mean brood‐size was related to changing food and temperature conditions. Egg‐development times for D. hyaiina were determined in culture and the population parameters finite birth (S), instantaneous birth (b′), instantaneous population change (r′), instantaneous death (d′) and finite death rates (D) were estimated from field data. Turnover and production estimates were calculated from finite death rates and biomass. The calculated potential rate of increase (b′) was nearly always greater than the observed rate of increase (r′): seasonal changes in death rate (d′) generally parallel changes in birth rate (b′) but remain somewhat out of phase. Population oscillations are probably due t o a delay in the expression of the effects of population density upon birth and death rates.The mean biomass of Daphnia in 1970 was 0‐57 mg dry wt/l (0‐88 g C/m2) and in 1971 0‐32 mg dry wt/l (0.49 g C/m2). Annual production for Daphnia was 11‐8 mg dry wt/l (18‐2 g C/m2) in 1970 and 8‐30 mg dry wt/l (12 8 g C/m2) in 1971. Information available on primary production in the reservoir suggests that the production of Daphnia accounts for less than 2% of gross primary production. However, the pattern of population growth of Daphnia in Eglwys Nynydd almost certainly reflects a food limited system. In summer, blue‐green algae may be abundant but serve as a poor food source: throughout the blue‐green bloom egg production remains low, at times remaining below 0‐5 eggs/adult.