bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the modeling of snake venom serine proteinase interactions with benzamidine‐based thrombin inhibitors
Authors: Henriques Elsa S. , Fonseca Nelson , Ramos Maria João 
Published: August 2004

AbstractPit viper venoms contain a number of serine proteinases that exhibit one or more thrombin‐like activities on fibrinogen and platelets, this being the case for the kinin‐releasing and fibrinogen‐clotting KN‐BJ from the venom of Bothrops jararaca. A three‐dimensional structural model of the KN‐BJ2 serine proteinase was built by homology modeling using the snake venom plasminogen activator TSV‐PA as a major template and porcine kallikrein as additional structural support. A set of intrinsic buried waters was included in the model and its behavior under dynamic conditions was molecular dynamics simulated, revealing a most interesting similarity pattern to kallikrein. The benzamidine‐based thrombin inhibitors α‐NAPAP, 3‐TAPAP, and 4‐TAPAP were docked into the refined model, allowing for a more insightful functional characterization of the enzyme and a better understanding of the reported comparatively low affinity of KN‐BJ2 toward those inhibitors.
Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl‐prolyl cis/trans isomerases
Authors: Kühlewein Angelika , Voll Georg , Hernandez Alvarez Birte , Kessler Horst , Fischer Gunter , Rahfeld Jens‐Ulrich , Gemmecker Gerd 
Published: August 2004

AbstractE. coli Par10 is a peptidyl‐prolyl cis/trans isomerase (PPIase) from Escherichia coli catalyzing the isomerization of Xaa‐Pro bonds in oligopeptides with a broad substrate specificity. The structure of E. coli Par10 has been determined by multidimensional solution‐state NMR spectroscopy based on 1207 conformational constraints (1067 NOE‐derived distances, 42 vicinal coupling‐constant restraints, 30 hydrogen‐bond restraints, and 68 ϕ/ψ restraints derived from the Chemical Shift Index). Simulated‐annealing calculations with the program ARIA and subsequent refinement with XPLOR yielded a set of 18 convergent structures with an average backbone RMSD from mean atomic coordinates of 0.50 Å within the well‐defined secondary structure elements. E. coli Par10 is the smallest known PPIase so far, with a high catalytic efficiency comparable to that of FKBPs and cyclophilins. The secondary structure of E. coli Par10 consists of four helical regions and a four‐stranded antiparallel β‐sheet. The N terminus forms a β‐strand, followed by a large stretch comprising three α‐helices. A loop region containing a short β‐strand separates these helices from a fourth α‐helix. The C terminus consists of two more β‐strands completing the four‐stranded anti‐parallel β‐sheet with strand order 2143. Interestingly, the third β‐strand includes a Gly‐Pro cis peptide bond. The curved β‐strand forms a hydrophobic binding pocket together with α‐helix 4, which also contains a number of highly conserved residues. The three‐dimensional structure of Par10 closely resembles that of the human proteins hPin1 and hPar14 and the plant protein Pin1At, belonging to the same family of highly homologous proteins.
Analysis of the stability of multimeric proteins by effective ΔG and effective m‐values
Authors: Park Chiwook , Marqusee Susan 
Published: August 2004

AbstractAnalyzing the stability of a multimeric protein is challenging because of the intrinsic difficulty in handling the mathematical model for the folded multimer‐unfolded monomer equilibrium. To circumvent this problem, we introduce the concept of effective stability, ΔGeff (= −RTlnKeff), where Keff is the equilibrium constant expressed in monomer units. Analysis of the denaturant effect on ΔGeff gives new insight into the stability of multimeric proteins. When a multimeric protein is mostly folded, the dependence of effective stability on denaturant concentration (effective m‐value) is simply the m‐value of its monomeric unit. However, when the protein is mostly unfolded, its stability depends on denaturant concentration with the m‐value of its multimeric form. We also find that the effective m‐value at the Cm is a good approximation of the apparent m‐value determined by fitting the equilibrium unfolding data from multimeric proteins with a two‐state monomer model. Moreover, when the m‐value of a monomeric unit is estimated from its size, the effective stability of a multimeric protein can be determined simply from Cm and this estimated m‐value. These simple and intuitive approaches will allow a facile analysis of the stability of multimeric proteins. These analyses are also applicable for high‐throughput analysis of protein stability on a proteomic scale.
Energetics of galactose– and glucose–aromatic amino acid interactions: Implications for binding in galactose‐specific proteins
Authors: Sujatha Mannargudi S. , Sasidhar Yellamraju U. , Balaji Petety V. 
Published: August 2004

AbstractAn aromatic amino acid is present in the binding site of a number of sugar binding proteins. The interaction of the saccharide with the aromatic residue is determined by their relative position as well as orientation. The position‐orientation of the saccharide relative to the aromatic residue was found to vary in different sugar‐binding proteins. In the present study, interaction energies of the complexes of galactose (Gal) and of glucose (Glc) with aromatic residue analogs have been calculated by ab initio density functional (U‐B3LYP/ 6‐31G**) theory. The position‐orientations of the saccharide with respect to the aromatic residue observed in various Gal‐, Glc‐, and mannose–protein complexes were chosen for the interaction energy calculations. The results of these calculations show that galactose can interact with the aromatic residue with similar interaction energies in a number of position‐orientations. The interaction energy of Gal–aromatic residue analog complex in position‐orientations observed for the bound saccharide in Glc/Man–protein complexes is comparable to the Glc–aromatic residue analog complex in the same position‐orientation. In contrast, there is a large variation in interaction energies of complexes of Glc‐ and of Gal‐ with the aromatic residue analog in position‐orientations observed in Gal–protein complexes. Furthermore, the conformation wherein the O6 atom is away from the aromatic residue is preferred for the exocyclic —CH2OH group in Gal–aromatic residue analog complexes. The implications of these results for saccharide binding in Gal‐specific proteins and the possible role of the aromatic amino acid to ensure proper positioning and orientation of galactose in the binding site have been discussed.
Interactions and chaperone function of αA‐crystallin with T5P γC‐crystallin mutant
Authors: Liang Jack J‐N 
Published: August 2004

AbstractT5P γC‐crystallin mutation is associated with Coppock‐like cataract, one of the autosomal dominant congenital cataracts. It is not known why the abundant α‐crystallin cannot prevent the mutation‐related aggregation. Our previous studies indicate that the mutation changes conformation and reduces solubility and stability, but it is not known whether it is these events or the loss of interaction with other crystallins that causes the cataract. It is also not known whether the α‐crystallin can protect T5P mutant as effectively from heat‐induced aggregation as the wild‐type (WT) γC‐crystallin. To investigate the mechanism of interactions and chaperone function between αA‐ and γC‐crystallin, human αA‐crystallin and W9F mutant as well as WT γC‐crystallin and T5P mutant were cloned. Interactions between αA‐ and γC‐crystallin were studied with fluorescence resonance energy transfer (FRET), and chaperone activity was assessed by the suppression of heat‐induced aggregation of substrate proteins. Conformational changes of substrate proteins were studied by spectroscopic measurements. The results indicate that the T5P mutant showed a slightly greater FRET than WT γC‐crystallin with αA‐crystallin, and αA‐crystallin could effectively prevent both WT and T5P γC‐crystallin from heat‐induced aggregation. Spectroscopic measurements show that both αA‐crystallin and γC‐crystallin underwent only slight conformational change after chaperone binding. Together with previous results obtained with a two‐hybrid system assay of interactions between αA‐ and γC‐crystallin, the present FRET and chaperone results indicate that loss of interactions of T5P mutant with other crystallins may play a larger role than the protection afforded by chaperone‐like activity in Coppock‐like cataract.
Substrate‐induced asymmetry and channel closure revealed by the apoenzyme structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase
Authors: Morris Van K. , Izard Tina 
Published: August 2004

AbstractPhosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in prokaryotic coenzyme A (CoA) biosynthesis, directing the transfer of an adenylyl group from ATP to 4′‐phosphopantetheine (Ppant) to yield dephospho‐CoA (dPCoA). The crystal structures of Escherichia coli PPAT bound to its substrates, product, and inhibitor revealed an allosteric hexameric enzyme with half‐of‐sites reactivity, and established an in‐line displacement catalytic mechanism. To provide insight into the mechanism of ligand binding we solved the apoenzyme (Apo) crystal structure of PPAT from Mycobacterium tuberculosis. In its Apo form, PPAT is a symmetric hexamer with an open solvent channel. However, ligand binding provokes asymmetry and alters the structure of the solvent channel, so that ligand binding becomes restricted to one trimer.
Investigation of the nature of the methionine–π interaction in β‐hairpin peptide model systems
Authors: Tatko Chad D. , Waters Marcey L. 
Published: August 2004

AbstractThere are frequent contacts between aromatic rings and sulfur atoms in proteins. However, it is unclear to what degree this putative interaction is stabilizing and what the nature of the interaction is. We have investigated the aryl–sulfur interaction by placing a methionine residue diagonal to an aromatic ring on the same face of a β‐hairpin, which places the methionine side chain in close proximity to the aryl side chain. The methionine (Met)–aryl interaction was compared with an equivalent hydrophobic and cation–π interaction in the context of the β‐hairpin. The interaction between phenylalanine (Phe), tryptophan (Trp), or cyclohexylalanine (Cha) and Met stabilized the β‐hairpin by −0.3 to −0.5 kcal mole−1, as determined by double‐mutant cycles. The peptides were subjected to thermal denaturations that suggest a hydrophobic driving force for the interactions between Met and Trp or Cha. The observed interaction of Met or norleucine (Nle) with Trp or Cha are quite similar, implying a hydrophobic driving force for the Met–π interaction. However, the thermodynamic data suggest that there may be some differences between the interaction of Met with Trp and Phe and that there may be a small thermodynamic component to the Met•••Phe interaction.
Structure of the XPC binding domain of hHR23A reveals hydrophobic patches for protein interaction
Authors: Kamionka Mariusz , Feigon Juli 
Published: August 2004

AbstractRad23 proteins are involved both in the ubiquitin‐proteasome pathway and in nucleotide excision repair (NER), but the relationship between these two pathways is not yet understood. The two human homologs of Rad23, hHR23A and B, are functionally redundant in NER and interact with xeroderma pigmentosum complementation group C (XPC) protein. The XPC–hHR23 complex is responsible for the specific recognition of damaged DNA, which is an early step in NER. The interaction of the XPC binding domain (XPCB) of hHR23A/B with XPC protein has been shown to be important for its optimal function in NER. We have determined the solution structure of XPCB of hHR23A. The domain consists of five amphipathic helices and reveals hydrophobic patches on the otherwise highly hydrophilic domain surface. The patches are predicted to be involved in interaction with XPC. The XPCB domain has limited sequence homology with any proteins outside of the Rad23 family except for sacsin, a protein involved in spastic ataxia of Charlevoix‐Saguenay, which contains a domain with 35% sequence identity.
A ‘Continuous Meeting’ Type of Biomedical Education in Rijeka, Croatia
Authors: Volarević S. 
Published: August 2004

AbstractDuring the second half of 2002 and the first half of 2003, several top international scientists gave guest courses, each in their own research field of expertise, as a part of a postgraduate (PhD) programme in biomedical education at the Medical school in Rijeka, Croatia. Due to its structure, the programme is a ‘continuous meeting’ type of learning. Courses attracted not only local medical doctors and dentists but also from the surrounding region as well as neighbouring countries in southeastern Europe. The highlights from presentations of several selected scientists were reported here as some might bear relevance to contemporary immunological research. I also describe the programme's structure and contents that could, if proved attractive, greatly stimulate an almost lacking interest in biomedical sciences in these areas of Europe.
Epitope DNA Vaccines Against Tuberculosis: Spacers and Ubiquitin Modulates Cellular Immune Responses Elicited by Epitope DNA Vaccine
Authors: Wang Q.‐M. , Sun S.‐H. , Hu Z.‐L. , Zhou F.‐J. , Yin M. , Xiao C.‐J. , Zhang J.‐C. 
Published: August 2004

AbstractCell‐mediated immune responses are crucial in the protection against tuberculosis. In this study, we constructed epitope DNA vaccines (p3‐M‐38) encoding cytotoxic T lymphocyte (CTL) epitopes of MPT64 and 38 kDa proteins of Mycobacterium tuberculosis. In order to observe the influence of spacer sequence (Ala‐Ala‐Tyr) or ubiquitin (UbGR) on the efficacy of the two CTL epitopes, we also constructed DNA vaccines, p3‐M‐S(spacer)‐38, p3‐Ub (UbGR)‐M‐S‐38 and p3‐Ub‐M‐38. The immune responses elicited by the four DNA vaccines were tested in C57BL/6 (H‐2b) mice. The cytotoxicity of T cells was detected by LDH‐release method and by enzyme‐linked immunospot assay for epitope‐specific cells secreting interferon‐γ. The results showed that DNA immunization with p3‐M‐38 vaccine could induce epitope‐specific CD8+ CTL response and that the spacer sequence (AAY) only enhanced M epitope presentation. The protein‐targeting sequence (UbGR) enhanced the immunogenicity of the two epitopes. The finding that defined spacer sequences at C‐terminus and protein‐targeting degradation modulated the immune response of epitope string DNA vaccines will be of importance for the further development of multi‐epitope DNA vaccines against tuberculosis.
The Receptor for Interleukin‐17E is Induced by Th2 Cytokines in Antigen‐Presenting Cells
Authors: Gratchev A. , Kzhyshkowska J. , Duperrier K. , Utikal J. , Velten F. W. , Goerdt S. 
Published: August 2004

AbstractInterleukin‐17E (IL‐17E) (IL‐25) is a recently identified cytokine capable to induce Th2‐associated cytokine production (IL‐5 and IL‐13) and T helper 2 (Th2)‐type pathologies in animal models. The IL‐17E‐responsive cell population in vivo was described to be a further uncharacterized non‐T‐, non‐B‐splenic accessory cell. Despite the identification of IL‐17BR as the receptor for IL‐17E, the cell population expressing IL‐17BR has hitherto not been identified. Here, we show that human monocyte‐derived Th2‐skewed antigen‐presenting cells (APC2) express membrane‐bound and soluble forms of IL‐17BR on the mRNA and protein level upon stimulation with IL‐4, IL‐10, IL‐13 or transforming growth factor‐βin vitro. These results indicate that IL‐17BR‐expressing APC2s may mediate the development of the IL‐17E‐mediated immunological reaction patterns observed in vivo.
Induction of Systemic Tolerance in Normal but not in Transgenic Mice Through Continuous Feeding of Ovalbumin
Authors: Simioni P. U. , Fernandes L. G. R. , Gabriel D. L. , Tamashiro W. M. S. C. 
Published: August 2004

AbstractThe ingestion of most dietary protein can cause systemic tolerance, and such tolerance is easier to induce in younger than in older mice. In this study, we examined whether oral tolerance to ovalbumin (OVA) could be induced in OVA‐T‐cell receptor (OVA‐TCR)‐specific transgenic mice. Continuous feeding or gavage with OVA induced tolerance, measured as reduced antibody production, in young and aged BALB/c mice, in a dose‐dependent manner, but this effect was not observed in transgenic mice. Once BALB/c mice became tolerant, this state was maintained for over 44 weeks, although the tolerant state could be reversed by adoptive cell transfer. DO11.10 mice did not become tolerant upon continuous feeding with OVA, and the adoptive transfer of naïve cells increased the levels of specific antibodies in their sera after antigenic challenge. The immunization schedule used here leads to a Th2‐dependent antibody response in normal BALB/c mice. However, the same schedule induced both Th1‐ and Th2‐antibody responses in transgenic mice. Dendritic cells (DC) from tolerant BALB/c mice were less efficient in the induction of the proliferation of cocultured T cells from both BALB/c and DO11.10 mice, as well as Th1 [interleukin (IL)‐2 and interferon (IFN)‐γ] and Th2 (IL‐4 and IL‐10) cytokine production. The DC from DO11.10 transgenic mice were equally efficient in the induction of T‐cell proliferation in both normal and transgenic mice, as well as in the induction of Th1 and Th2 cytokines, whether or not the mice consumed OVA. Transforming growth factor (TGF)‐β secretion was significantly lower in the supernatants of T cells from both normal and transgenic mice cocultured with DC from DO11.10 mice that had consumed OVA, while it was significantly higher in the presence of DC from normal tolerant mice, thus implicating TGF‐β as a regulatory cytokine in oral tolerance in the murine model.
Single‐Base Oligodeoxyguanosine‐Binding Proteins on Nonspecific Cytotoxic Cells: Identification of a New Class of Pattern‐Recognition Receptors
Authors: Kaur H. , Jaso‐Friedmann L. , Leary J. H. , Evans D. L. 
Published: August 2004

AbstractThe present study was designed to identify a possible new class of pathogen‐recognition proteins that bind single‐base oligodeoxynucleotide (ODN) ligands. Binding by the teleost natural killer cell equivalent [referred to as nonspecific cytotoxic cells (NCC)] was compared with mammalian cells (mouse RAW264.7 cells and human THP‐1 cells). The ODN analysed were composed of 20‐mers of guanosine (dG20), adenosine (dA20), thymidine (dT20) or cytosine (dC20). Binding studies first determined the 50% saturation levels for NCC (1.25 µg/ml), RAW264.7 (0.2 µg/ml) and THP‐1 (0.8 µg/ml). Binding by dG20 to all the three cell types was saturable. Ligand blots of NCC membrane lysates with biotinylated dG20 revealed two different major molecular weight species (16–18 and 29 kDa) of binding proteins. The 29‐kDa protein was identified with the help of Western blot analysis using a polyclonal antibody specific to an NCC antimicrobial protein (ncamp‐1). The membrane expression of the 29‐kDa ncamp‐1 was determined by the binding of surface‐biotinylated NCC membrane proteins with digoxigenin dG20 followed by immunoprecipitation using anti‐digoxigenin agarose beads. The 29 and 14–18 kDa NCC membrane proteins were cross‐reactive using Western blot examination with a polyclonal anti‐histone 1 antibody. Function studies revealed that dG20 activated a twofold upregulation of membrane binding by homologous dG20‐biotin. dG20 also stimulated NCC‐increased membrane expression of NCC receptor protein 1. Additional experiments were performed to determine the DNase sensitivity of the different ODN. dG20 appeared to be more resistant to DNase treatment, compared to dC20, dA20 and dT20. The single‐base ODN‐binding proteins may represent a new class of pattern‐recognition receptors that are involved in innate anti‐bacterial resistance mediated by NCC.
Active Synthesis of Mouse Polymeric Immunoglobulin Receptor in the Epithelial Cells of the Distal Urinary Tubule in Kidney
Authors: Asano M. , Saito M. , Suguro H. , Nomura H. , Inage T. , Moro I. 
Published: August 2004

AbstractThe tissue distribution of mouse polymeric immunoglobulin receptor (pIgR) has been demonstrated. By Northern blot hybridization, pIgR mRNA expression was detected in liver, intestine, stomach, lung and kidney. A weak expression was also detected in thymus by reverse transcriptase‐polymerase chain reaction. The pIgR expression in kidney was further studied and confirmed that pIgR protein was actively synthesized in the epithelial cells of distal urinary tubule and of Henle's loop. Immunoelectron microscopical analysis showed the accumulation of pIgR‐containing vesicles in the apical portion of distal urinary tubule epithelial cells.
Tolerability and Anti‐Inflammatory Effects of Glucuronoxylomannan in Collagen‐Induced Arthritis
Authors: Mirshafiey A. , Ngoc Dzung D. T. , Murphy J. W. , Khorramizadeh M. R. , Saadat F. , Mehrabian F. , Larsson P. 
Published: August 2004

AbstractThis investigation was planned to assess the therapeutic efficacy of glucuronoxylomannan (GXM) in collagen‐induced arthritis (CIA). GXM was isolated from culture filtrate of Cryptococcus neoformans var. gattii, serotype C. CIA was induced by the immunization of Dark Agouti rats with bovine type II collagen in incomplete Freund's adjuvant. GXM solution at two doses, 25 and 50 mg/kg, was administered intraperitoneally. Onset of i.p. injections of GXM to prevention and treatment groups was days 0 and 10 postimmunization, respectively. The WEHI‐164 cell line was used for assaying tolerability, matrix metalloproteinase type 2 (MMP‐2) activity and apoptosis. MMP‐2 activity was assessed using zymography. For assessment of apoptosis, the terminal deoxyribonucleotidyl transferase‐mediated dUTP nick‐end labelling method was used. The results of this experiment showed that the treatment of CIA with GXM at a dose of 50 mg/kg could suppress disease development both prophylactically and therapeutically. This beneficial effect of GXM was associated with a significant decrease in the anti‐CII antibody response compared with untreated rats. Moreover, GXM therapy could diminish MMP‐2 activity, but it had no notable effect on apoptosis. GXM also showed a high tolerability compared with certain steroidal and non‐steroidal anti‐inflammatory drugs. We conclude that GXM suppresses the development of disease in CIA and it could be recommended as a new immunosuppressive and anti‐inflammatory agent for further investigations.
The Influence of Remaining Live BCG Organisms in Vaccinated Mice on the Maintenance of Immunity to Tuberculosis
Authors: Olsen A. W. , Brandt L. , Agger E. M. , Van Pinxteren L. A. H. , Andersen P. 
Published: August 2004

AbstractThe only available vaccine against Mycobacterium tuberculosis, the bacille Calmette‐Guérin (BCG) vaccine, is at present being used as a reference for the efficacy of novel vaccines. Herein, we demonstrate that viable BCG can be detected at late time points after vaccination in C57BL/6J mice. If BCG is cleared by antibiotic treatment, the number of mycobacteria‐reactive effector cells in the spleen gradually reverts to low levels and consequently immunity in this organ wanes, while resistance in the lung remains stable. The implications for comparing BCG vaccination with experimental vaccines including non‐replicating vaccines are discussed.