bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase
Authors: Rigden Daniel J. , Jedrzejas Mark J. 
Published: June 2003

AbstractHyaluronate lyase enzymes degrade hyaluronan, the main polysaccharide component of the connective tissues of higher animals, thereby destroying the normal connective tissue structure and exposing the host tissue cells to various endo‐ and exogenous factors, including bacterial toxins. The 3D crystal structures of functionally active but truncated Streptococcus pneumoniae and S. agalactiae hyaluronate lyases, along with their substrate and product complexes, have been determined. The enzymes are multidomain proteins with helical barrel‐like catalytic domains and two types of β‐sheet domains. Here, through genome‐based bioinformatics studies we identify an additional β‐sheet domain present in the most N‐terminal part of streptococcal hyaluronate lyases. Fold recognition and modeling studies show that the domain is structurally similar to carbohydrate binding modules and is therefore likely to be directly involved in hyaluronan binding. Likely carbohydrate binding residues were identified and electrostatic complementarity of the hyaluronate lyase domain with hyaluronan demonstrated. The newly identified presumed hyaluronan binding domain likely improves catalytic efficiency by colocalizing the enzyme and its substrate. Other possible functions are discussed. Two contacting aromatic residues are conserved in the hydrophobic core of the hyaluronate lyase domain and in many, perhaps all, families in the superfamily in which they may be placed. This observation may help the identification and classification of other carbohydrate binding modules. Proteins 2003;52:203–211. © 2003 Wiley‐Liss, Inc.
pH‐dependent stability of the human α‐lactalbumin molten globule state: Contrasting roles of the 6—120 disulfide and the β‐subdomain at low and neutral pH
Authors: Horng Jia‐Cherng , Demarest Stephen J. , Raleigh Daniel P. 
Published: June 2003

AbstractMany proteins are capable of populating partially folded states known as molten globule states. α‐Lactalbumin forms a molten globule under a range of conditions including low pH (the A‐state) and at neutral pH in the absence of Ca2+with modest amounts of denaturant. The A‐state is the most thoroughly characterized and thought to mimic a kinetic intermediate populated during refolding at neutral pH. We demonstrate that the properties and interactions that stabilize the A‐state and the pH 7 molten globule of human α‐lactalbumin differ. The unfolding of the wild‐type protein is compared to the unfolding of a variant that lacks the 6120 disulfide bond and to an autonomously folded peptide construct that we have previously shown represents the minimum core structure of the A‐state of human α‐lactalbumin. Studies conducted at pH 2 and 7 show that the disulfide makes little contribution to the stability of the molten globule at pH 7 but is important at pH 2. In contrast, the β‐subdomain of the protein is less important at pH 2 than at pH 7. The role of helix propensity in stabilizing the different forms of the molten globule state is examined and it is shown that it cannot account for the differences. The strikingly different behavior observed at pH 2 and 7 indicates that the A‐state may not be a rigorous mimic of the folding intermediate populated at pH 7. Proteins 2003;52:193–202. © 2003 Wiley‐Liss, Inc.
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative
Authors: Sica Filomena , Di Fiore Anna , Zagari Adriana , Mazzarella Lelio 
Published: June 2003

AbstractBovine seminal ribonuclease, a homodimeric enzyme joined covalently by two interchain disulphide bonds, is an equilibrium mixture of two conformational isomers, M×M and M=M. The major form, M×M, whose crystal structure has been previously determined at 1.9 Å resolution, presents the swapping of the N‐terminal segments (residues 1–15) and composite active sites formed by residues of different chains. The three‐dimensional domain swapping does not occur in the M=M form. The different fold of each N‐terminal tail is directed by the hinge loop (residue 16–22) connecting the swapping domain to the body of the protein. Reduction and alkylation of interchain disulphide bridges produce a monomeric derivative and a noncovalent swapped dimer, which are both active. The free and nucleotide‐bound forms of the monomer have been crystallized at an alkaline pH and refined at 1.45 and 1.65 Å resolution, respectively. In both cases, the N‐terminal fragment is folded on the main body of the protein to produce an intact active site and a chain architecture very similar to that of bovine pancreatic ribonuclease. In this new fold of the seminal chain, the hinge loop is disordered. Despite the difference between the tertiary structure of the monomer and that of the chains in the M×M form, the active sites of the two enzymes are virtually indistinguishable. Furthermore, the structure of the liganded enzyme represents the first example of a ribonuclease complex studied at an alkaline pH and provides new information on the binding of a nucleotide when the catalytic histidines are deprotonated. Proteins 2003;52:263–271. © 2003 Wiley‐Liss, Inc.
Possible locally driven folding pathways of TC5b, a 20‐residue protein
Authors: Nikiforovich Gregory V. , Andersen Niels H. , Fesinmeyer R. Matthew , Frieden Carl 
Published: June 2003

AbstractA novel computational procedure for modeling possible locally driven folding pathways by stepwise elongations of the peptide chain was successfully applied to TC5b, a 20‐residue miniprotein. Systematic exploration of the possible locally driven pathways showed that the Trp‐cage structure of TC5b could be obtained by stepwise elongation starting from the noncentral local nucleation centers preexisting in the unfolded state of TC5b. The probable locally driven folding pathway starts with folding of α‐helical fragment 4‐9, followed by formation of the proper three‐dimensional structure of fragment 4‐12, and then 4‐18. Accordingly, the Trp‐cage‐forming interactions emerge successively, first Trp6–Pro12, then Trp6–Pro18, and then Trp6–Tyr3. The Trp‐cage‐like structures of TC5b found in this study by independent energy calculations are in excellent agreement with the NMR experimental data. The same procedure rationalizes the incomplete Trp‐cage formation observed for two analogs of TC5b. Generally, the success of this novel approach is encouraging and provides some justification for the use of computational simulations of locally driven protein folding. Proteins 2003;52:292–302. © 2003 Wiley‐Liss, Inc.
Effective energy function for proteins in lipid membranes
Authors: Lazaridis Themis 
Published: June 2003

AbstractA simple extension of the EEF1 energy function to heterogeneous membrane‐aqueous media is proposed. The extension consists of (a) development of solvation parameters for a nonpolar phase using experimental data for the transfer of amino acid side‐chains from water to cyclohexane, (b) introduction of a heterogeneous membrane‐aqueous system by making the reference solvation free energy of each atom dependent on the vertical coordinate, (c) a modification of the distance‐dependent dielectric model to account for reduced screening of electrostatic interactions in the membrane, and (d) an adjustment of the EEF1 aqueous model in light of recent calculations of the potential of mean force between amino acid side‐chains in water. The electrostatic model is adjusted to match experimental observations for polyalanine, polyleucine, and the glycophorin A dimer. The resulting energy function (IMM1) reproduces the preference of Trp and Tyr for the membrane interface, gives reasonable energies of insertion into or adsorption onto a membrane, and allows stable 1‐ns MD simulations of the glycophorin A dimer. We find that the lowest‐energy orientation of melittin in bilayers varies, depending on the thickness of the hydrocarbon layer. Proteins 2003;52:176–192. © 2003 Wiley‐Liss, Inc.
Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu
Authors: Paul Bindu Diana , Kanhere Aditi , Chakraborty Atanu , Bansal Manju , Nagaraja Valakunja 
Published: June 2003

AbstractThe C protein, a middle gene product of bacteriophage Mu, is the determinant of the transition from middle to late gene expression. C activates transcription from four late gene promoters, Plys, PI, PP, and Pmom by binding to a site overlapping their −35 elements. Site‐specific, high‐affinity binding of C to its recognition sequence results in both axial and torsional distortion of DNA at Pmom, which appears to play a role in recruitment of RNA polymerase to the promoter for mom gene transactivation. To identify the regions of C protein important for its function, deletion and site‐directed mutagenesis were carried out. We demonstrate here that a helix‐turn‐helix (HTH) motif located toward the carboxy terminal end of the protein is the DNA‐binding domain and amino acid residues involved in transactivation overlap the HTH motif. Mutagenesis studies also aided in the identification of the region important for dimerization. Structure‐based sequence alignment and molecular modeling in conjunction with mutational analysis suggest that the HTH motif is part of a three‐helix bundle, with remarkable similarity to paired (prd), a developmental regulatory protein from Drosophila. Additional key residues identified in the model to be crucial for C protein structure and DNA binding were shown to be important by mutagenesis. These results provide a structural framework for C function and insight into the mechanism of transactivation at the mom promoter. Proteins 2003;52:272–282. © 2003 Wiley‐Liss, Inc.
Crystal structure of a putative CN hydrolase from yeast
Authors: Kumaran Desigan , Eswaramoorthy Subramaniam , Gerchman Sue Ellen , Kycia Helen , Studier F. William , Swaminathan Subramanyam 
Published: June 2003

AbstractThe crystal structure of a yeast hypothetical protein with sequence similarity to CN hydrolases has been determined to 2.4 Å resolution by the multiwavelength anomalous dispersion (MAD) method. The protein folds as a four‐layer αββα sandwich and exists as a dimer in the crystal and in solution. It was selected in a structural genomics project as representative of CN hydrolases at a time when no structures had been determined for members of this family. Structures for two other members of the family have since been reported and the three proteins have similar topology and dimerization modes, which are distinct from those of other αββα proteins whose structures are known. The dimers form an unusual eight‐layer αββα:αββα structure. Although the precise enzymatic reactions catalyzed by the yeast protein are not known, considerable information about the active site may be deduced from conserved sequence motifs, comparative biochemical information, and comparison with known structures of hydrolase active sites. As with serine hydrolases, the active‐site nucleophile (cysteine in this case) is positioned on a nucleophile elbow. Proteins 2003;52:283–291. © 2003 Wiley‐Liss, Inc.
Side‐chain dynamics and protein folding
Authors: Kussell Edo , Shimada Jun , Shakhnovich Eugene I. 
Published: June 2003

AbstractThe processes by which protein side chains reach equilibrium during a folding reaction are investigated using both lattice and all‐atom simulations. We find that rates of side‐chain relaxation exhibit a distribution over the protein structure, with the fastest relaxing side chains located in positions kinetically important for folding. Traversal of the major folding transition state corresponds to the freezing of a small number of side chains, belonging to the folding nucleus, whereas the rest of the protein proceeds toward equilibrium via backbone fluctuations around the native fold. The postnucleation processes by which side chains relax are characterized by very slow dynamics and many barrier crossings, and thus resemble the behavior of a glass. Proteins 2003;52:303–321. © 2003 Wiley‐Liss, Inc.
Fish assemblage response to recent mitigation of a channelized warmwater stream
Authors: Raborn Scott. W. , Schramm Harold L. 
Published: June 2003

AbstractVarious designs of low‐head dams are used to rehabilitate streams or forestall upstream channel incision after channelization. We report on the efficacy of using notched sills and grade control structures (GCS) to restore the fish assemblage in Luxapallila Creek, Mississippi. We tested the null hypotheses that habitat variables and species richness, evenness, and assemblage structure would not differ among: (1) a channelized segment with no modifications; (2) a channelized segment mitigated by the installation of sills and GCS; (3) a segment upstream of the installations and undergoing channel incision; and (4) an unaltered segment. Although habitat variables changed, neither species richness, evenness, nor fish assemblage structure differed between mitigated and channelized segments with both exhibiting less richness and different assemblage structures than the unaltered segment. Lack of differences in species richness between the incised and unaltered segments suggest that the GCS may have halted the negative effects of upstream channel incision before species were extirpated. Conspicuous habitat differences between the altered (channelized and mitigated) and unaltered segments were lack of backwaters and canopy coverage and finer substrates in the altered segments. Our results suggest a more comprehensive rehabilitation strategy is required in Luxapallila Creek. Published in 2003 by John Wiley & Sons, Ltd.
Survival of salmonid eggs in a degraded gravel‐bed stream: effects of groundwater–surface water interactions
Authors: Malcolm Iain A. , Youngson Alan F. , Soulsby Chris 
Published: June 2003

AbstractThe effect of hyporheic water quality on developing salmonids was assessed between spawning and hatch. Results from a low‐lying degraded agricultural catchment (Newmills Burn) were compared with those from a near‐pristine upland spawning stream (Girnock Burn), providing a set of comparisons beyond the range of hyporheic conditions present in the Newmills Burn. It was demonstrated that hyporheic water quality in the Newmills Burn varied temporally and spatially as a consequence of variable fluxes of chemically reduced groundwater through heterogeneous drift deposits. Mortality rates from samplers located within artificial redds ranged from 0 to 100% and showed a clear negative relationship with mean dissolved oxygen (DO) concentrations (r2 = 0.85, P < 0.01). Where embryo mortality was less than 100%, low DO appeared to affect rates of embryo development. Embryos exposed to lower DO concentrations were observed to have a higher percentage mass of yolk sac than those developing in more favourable conditions. The chemical characteristics of hyporheic water in the stream were indicative of the mixing of longer residence regional groundwater with local surface water at shallow depths. The hyporheic water of the Girnock Burn approximated closely to that of surface water suggesting a local origin. Hyporheic water quality affects egg survival and may limit recruitment when egg deposition is marginal or inadequate. A consideration of hyporheic dynamics and groundwater–stream interactions should form part of channel modification or restoration works in salmonid spawning streams. Copyright © 2003 John Wiley & Sons, Ltd.
Suitable habitats for 0‐group fish in rehabilitated floodplains along the lower River Rhine
Authors: Grift R. E. , Buijse A. D. , Van Densen W. L. T. , Machiels M. A. M. , Kranenbarg J. , Klein Breteler J. G. P. , Backx J. J. G. M. 
Published: June 2003

AbstractThe suitability of rehabilitated floodplains along the lower River Rhine for rheophilic cyprinids was assessed by investigating the spatial distribution of 0‐group fish among, and within, three newly created secondary channels, an oxbow lake reconnected at its downstream end and several existing groyne fields. Fish were sampled during April through September 1997–1999 with seine nets and trawls and, for each sample, the habitat (physical environment) was characterized (flow, depth, substrate and inundated terrestrial vegetation). The new water bodies provide more suitable habitats for 0‐group fish than the groyne fields. Their beneficial value differs, however, between reproductive guilds and depends on the morphological and hydrological conditions. Total fish density increased along a gradient of decreasing water flow whereas the proportion of rheophilic species (Barbus barbus, Gobio gobio, Leuciscus idus and Aspius aspius) decreased. Flow velocity and water depth were the most important factors determining habitat utilization. Rheophilic fish were spatially separated from eurytopic fish (e.g. Abramis brama, Rutilus rutilus and Stizostedion lucioperca). During flood events, inundated terrestrial vegetation was an important habitat for the larvae of all species. To enhance the riverine fish community, floodplain water bodies should have complex shorelines, and a high variability of flow velocities. Their slopes should be moderate to maximize the probability of terrestrial vegetation getting inundated during spring and summer. Future management of similar floodplains should focus on more diverse and accessible aquatic habitats to increase overall fish species diversity, since different types of water body clearly have complementary values. Copyright © 2003 John Wiley & Sons, Ltd.
Asymmetric modulation of a catecholamine‐regulated protein in the rat brain, following quinpirole administration
Authors: Gabriele Joseph , Culver Kirsten , Sharma Sunjay , Zhang Bingjun , Szechtman Henry , Mishra Ram 
Published: June 2003

AbstractWe previously reported a brain‐specific 40 kDa catecholamine‐regulated protein (CRP40) that binds dopamine (DA) and related catecholamines. CPR40 shares significant sequence homology with human heat shock protein (Hsp70), GRP78/BIP, and human #BQ24193 protein. Recent studies with the DA D2 receptor antagonist, haloperidol, demonstrated a significant increase in expression of CRP40 in the striatum (STR). The objective of the present study was to investigate CRP40 expression in various brain regions following treatments with the DA D2/D3 receptor agonist quinpirole (QNP) in rats and examine possible relationships between neurochemical parameters and locomotor activity. Rats received injections of either QNP (0.5 mg/kg, for 27 days every third day) or saline (SAL) and their locomotor activities were measured for 90 min after each injection. At injection 9, QNP‐treated rats showed locomotor activity that was significantly greater than SAL controls (F(2,28) = 3.88, P < 0.05, Duncan's multiple range test, P < 0.05). Neurochemically, acute QNP‐treated rats demonstrated significant differential expression of CRP40 in the left/right prefrontal cortex (PFC) relative to SAL‐treated rats (–17.76 ± 2.10%, −10.35 ± 1.23%, P < 0.001). Chronic QNP significantly decreased CRP40 expression in the STR, ventral tegmental area (VTA), and left/right PFC (–24.85± 2.10%, −18.15 ± 5.64%, −49.13 ± 7.05%, −25 ± 3.63%, P < 0.001). Finally, chronic QNP treatment resulted in a significant increase in CRP40 levels in the nucleus accumbens (NA) (+39.32 ± 7.00%, P < 0.001). Heat shock protein (i.e., Hsp70 or Hsc70) expression remained unaltered following QNP treatment. Since QNP is a DA D2/D3 agonist, alterations in CRP40 expression following QNP treatment suggest the protein's function in dopaminergic neurotransmission. Synapse 49:261–269, 2003. © 2003 Wiley‐Liss, Inc.
Dopamine displaces [3H]domperidone from high‐affinity sites of the dopamine D2 receptor, but not [3H]raclopride or [3H]spiperone in isotonic medium: Implications for human positron emission tomography
Authors: Seeman Philip , Tallerico Teresa , Ko Françoise 
Published: June 2003

AbstractBecause the high‐affinity state of the dopamine D2 receptor, D2High, is the functional state of the receptor, has a role in demarcating typical from atypical antipsychotics, and is markedly elevated in amphetamine‐sensitized rats, it is important to have a method for the convenient detection of this state by a ligand. The present data show that, in contrast to [3H]spiperone or [3H]raclopride, [3H]domperidone labels D2High sites in the presence of isotonic NaCl in either striatum or cloned D2Long receptors, yielding a dopamine dissociation constant (1.75 nM) in agreement with that found with [3H]dopamine. Increased labeling of D2High sites occurred with [3H]domperidone after severe disruption of the cells, suggesting that [3H]domperidone has better access to the D2 receptor from the cytoplasmic aspect of the cell membrane. The density of the [3H]domperidone‐labeled D2 receptors was the same as that of the [3H]raclopride‐labeled D2 receptors, but twice the density of [3H]spiperone sites for human cloned D2Long receptors, compatible with the monomer‐dimer concept of the D2 receptor. [3H]domperidone readily labels the D2High sites in postmortem human brain homogenates. Although [3H]spiperone or [3H]raclopride can occupy D2High sites, the inability of 1–10 nM dopamine to displace these ligands under isotonic conditions suggests that these ligands may not be suitable for monitoring the physiological high‐affinity state of the dopamine D2 receptor by means of [11C]methylspiperone or [11C]raclopride in humans. Synapse 49:209–215, 2003. © 2003 Wiley‐Liss, Inc.
How is firing activity of substantia nigra cells regulated? Relevance of pattern‐code in the basal ganglia
Authors: Rodríguez Manuel , Pereda Ernesto , González Julián , Abdala Patricio , Obeso Jose A. 
Published: June 2003

AbstractThe current model of the basal ganglia (BG) assumes that neurons use a firing rate renewal code for movement computing under normal and pathological conditions. Here, we report nonrenewal firing (neuronal firing is influenced by its own previous activity) in cells of the anesthetized rat's substantia nigra (SN). Both compensatory (short interspike intervals (ISIs) are followed by long ISIs and vice versa) and persistent (short and long ISIs cluster for long time periods) nonrenewal activity was found in 52.6% and 33.8% of SN cells, respectively. A compensatory pattern was found in 77.7% of DA cells, but in only 9.8% of GABA‐cells. Conversely, a persistent pattern was observed in 74.6% of GABAergic cells and in only 9.9% of DA cells. These findings indicate two types of nonrenewal firing pattern codes specifically present in SN dopaminergic and GABAergic neurons. Disruption of these patterns may play a role in the pathophysiology of basal ganglia disorders such as Parkinson's disease and dyskinesias. Synapse 49:216–225, 2003. © 2003 Wiley‐Liss, Inc.