bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary culture of microvascular endothelial cells from human benign prostatic hyperplasia
Authors: Stachon Axel , Schlüter Tanja , Köller Manfred , Weisser Heike , Krieg Michael 
Published: August 2002

AbstractBackgroundProstate growth seems to be influenced by paracrine factors like IL‐6 originating from the microvascular endothelium. Therefore, our efforts were focused on the primary culture and behavior of microvascular endothelial cells (HPEC) derived from tissue of human benign prostatic hyperplasia (BPH). Until now, the isolation and culture of HPEC from BPH have not been reported.MethodsBPH tissue was cut into small cubes and gently squeezed after incubation with dispase. HPEC were cultured from the resulting cell suspension after a stepwise selection by use of superparamagnetic beads coated with antibodies against endothelial specific antigens. HPEC were characterized by flow cytometry and immunohistochemistry. γ‐Glutamyl transpeptidase activity (specific for microvascular endothelium) was measured after dissolution of the HPEC with Triton X‐100. After the incubation of HPEC either with ATP, VEGF, or TNF‐α, the release of IL‐6 was measured by enzyme linked immunosorbent assay (ELISA).ResultsHPEC showed a typical endothelial morphology. They were positive for von Willebrand factor, CD31, CD62E (after stimulation with TNF‐α), α‐actin and were negative for fibroblastic antigens and PSA. Proliferation was stimulated by vascular endothelial growth factor (VEGF). γ‐Glutamyl transpeptidase activity in HPEC was 6.3 μIU/μg protein, whereas in human umbilical vein endothelial cells (HUVEC) no γ‐glutamyl transpeptidase activity was detectable. The IL‐6 secretion of HPEC was stimulated by VEGF and TNF‐α, but not by ATP and bradykinin.ConclusionsFor the first time, the primary culture of microvascular endothelial cells from BPH tissue was successfully performed. Our results suggest that HPEC may be actively involved in prostate growth, due to the secretion of regulatory factors such as IL‐6. Prostate 48:156–164, 2001. © 2001 Wiley‐Liss, Inc.
Hypermethylation of the CD44 gene is associated with progression and metastasis of human prostate cancer
Authors: Kito Hiroki , Suzuki Hiroyoshi , Ichikawa Tomohiko , Sekita Nobuyuki , Kamiya Naoto , Akakura Koichiro , Igarashi Tatsuo , Nakayama Tsuyoshi , Watanabe Masatoshi , Harigaya Kenichi , Ito Haruo 
Published: August 2002

AbstractBackgroundCD44 is a metastasis suppressor gene for prostate cancer and the down‐regulation of CD44 and its variants is associated with the progression of prostate cancer. Also, hypermethylation of the CpG islands of the CD44 gene is closely associated with transcriptional inactivation, resulting in the decreased expression of CD44. To clarify the exact role of methylation status of CpG islands of CD44 gene in the progression and metastasis of prostate cancer, we investigated the methylation status of this gene in primary and metastatic human prostate tumors obtained from surgery or autopsy.MethodsWe examined 97 samples from 40 Japanese patients with adenocarcinoma of the prostate. Tumor tissues were obtained from radical prostatectomy specimens from eight patients with stage B, 12 patients with stage C and three patients with stage D1 and at autopsy from 17 hormone‐refractory metastatic cases, who had initially responded to the therapy and thereafter relapsed. Distant metastatic tissues were also obtained at autopsy (i.e., liver, lung, kidney, mammary gland, and pelvic lymph nodes) from 10 of 17 hormone‐refractory cases. We analyzed the hypermethylation status of CD44 promotor region by PCR using genomic DNAs digested with the m5C‐sensitive restriction enzyme HpaII.ResultsThe correlation between the methylation status of CD44 gene and the stage progression of prostate cancer was statistically significant (P = 0.0438). In two of 10 hormone‐refractory cases, a comparison of the methylation status of the CD44 gene in metastases to that in primary tumors revealed interfocal heterogeneity of CD44 methylation status.ConclusionsThese results indicate an important role of CD44 methylation in the progression and metastasis of prostate cancer, although the amount of methylational heterogeneity is substantial among metastatic sites within the same patient. Prostate 49:110–115, 2001. © 2001 Wiley‐Liss, Inc.
Dynamic and structural analysis of isotropically distributed molecular ensembles
Authors: Prompers Jeanine J. , Brüschweiler Rafael 
Published: August 2002

AbstractAn efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between “rigid” and “mobile” parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5‐ns molecular dynamics trajectory of native ubiquitin and a 40‐ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10‐fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules. Proteins 2002;46:177–189. © 2001 Wiley‐Liss, Inc.
Role of hydrophilic and hydrophobic contacts in folding of the second β‐hairpin fragment of protein G: Molecular dynamics simulation studies of an all‐atom model
Authors: Zhou Yaoqi , Linhananta Apichart 
Published: August 2002

AbstractPredicting the folding mechanism of the second β‐hairpin fragment of the Ig‐binding domain B of streptococcal protein G is unexpectedly challenging for simplified reduced models because the models developed so far indicated a different folding mechanism from what was suggested from high‐temperature unfolding and equilibrium free‐energy surface analysis based on established all‐atom empirical force fields in explicit or implicit solvent. This happened despite the use of empirical residue‐based interactions, multibody hydrophobic interactions, and inclusions of hydrogen bonding effects in the simplified models. This article employs a recently developed all‐atom (except nonpolar hydrogens) model interacting with simple square‐well potentials to fold the peptide fragment by molecular dynamics simulation methods. In this study, 193 out of 200 trajectories are folded at two reduced temperatures (3.5 and 3.7) close to the transition temperature T* ∼ 4.0. Each simulation takes <7 h of CPU time on a Pentium 800‐MHz PC. Folding of the new all‐atom model is found to be initiated by collapse before the formation of main‐chain hydrogen bonds. This verifies the mechanism proposed from previous all‐atom unfolding and equilibrium simulations. The new model further predicts that the collapse is initiated by two nucleation contacts (a hydrophilic contact between D46 and T49 and a hydrophobic contact between Y45 and F52), in agreement with recent NMR measurements. The results suggest that atomic packing and native contact interactions play a dominant role in folding mechanism. Proteins 2002;47:154–162. © 2002 Wiley‐Liss, Inc.
Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation
Authors: Zhao Shanrong , Goodsell David S. , Olson Arthur J. 
Published: August 2002

AbstractWe compiled and analyzed a data set of paired protein structures containing proteins for which multiple high‐quality uncomplexed atomic structures were available in the Protein Data Bank. Side‐chain flexibility was quantified, yielding a set of residue‐ and environment‐specific confidence levels describing the range of motion around χ1 and χ2 angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side‐chain motion and estimating the extent of side‐chain motion in protein structure prediction. We compare the performance of a simple 40° threshold with these quantitative confidence levels in a critical evaluation of side‐chain prediction with the program SCWRL. Proteins 2001;43:271–279. © 2001 Wiley‐Liss, Inc.
Optimization of solvation models for predicting the structure of surface loops in proteins
Authors: Das Bedamati , Meirovitch Hagai 
Published: August 2002

AbstractA novel procedure for optimizing the atomic solvation parameters (ASPs) σi developed recently for cyclic peptides is extended to surface loops in proteins. The loop is free to move, whereas the protein template is held fixed in its X‐ray structure. The energy is Etot = EFF(ϵ = nr) + ∑ σiAi, where EFF(ϵ = nr) is the force‐field energy of the loop–loop and loop–template interactions, ϵ = nr is a distance‐dependent dielectric constant, and n is an additional parameter to be optimized. Ai is the solvent‐accessible surface area of atom i. The optimal σi and n are those for which the loop structure with the global minimum of Etot(n, σi) becomes the experimental X‐ray structure. Thus, the ASPs depend on the force field and are optimized in the protein environment, unlike commonly used ASPs such as those of Wesson and Eisenberg (Protein Sci 1992;1:227–235). The latter are based on the free energy of transfer of small molecules from the gas phase to water and have been traditionally combined with various force fields without further calibration. We found that for loops the all‐atom AMBER force field performed better than OPLS and CHARMM22. Two sets of ASPs [based on AMBER (n = 2)], optimized independently for loops 64–71 and 89–97 of ribonuclease A, were similar and thus enabled the definition of a best‐fit set. All these ASPs were negative (hydrophilic), including those for carbon. Very good (i.e., small) root‐mean‐square‐deviation values from the X‐ray loop structure were obtained with the three sets of ASPs, suggesting that the best‐fit set would be transferable to loops in other proteins as well. The structure of loop 13–24 is relatively stretched and was insensitive to the effect of the ASPs. Proteins 2001;43:303–314. © 2001 Wiley‐Liss, Inc.
How to guarantee optimal stability for most representative structures in the protein data bank
Authors: Bastolla Ugo , Farwer Jochen , Knapp Ernst Walter , Vendruscolo Michele 
Published: August 2002

AbstractWe proposed recently an optimization method to derive energy parameters for simplified models of protein folding. The method is based on the maximization of the thermodynamic average of the overlap between protein native structures and a Boltzmann ensemble of alternative structures. Such a condition enforces protein models whose ground states are most similar to the corresponding native states. We present here an extensive testing of the method for a simple residue‐residue contact energy function and for alternative structures generated by threading. The optimized energy function guarantees high stability and a well‐correlated energy landscape to most representative structures in the PDB database. Failures in the recognition of the native structure can be attributed to the neglect of interactions between different chains in oligomeric proteins or with cofactors. When these are taken into account, only very few X‐ray structures are not recognized. Most of them are short inhibitors or fragments and one is a structure that presents serious inconsistencies. Finally, we discuss the reasons that make NMR structures more difficult to recognize. Proteins 2001;44:79–96. © 2001 Wiley‐Liss, Inc.
Role of non‐glycine residues in left‐handed helical conformation for the conformational stability of human lysozyme
Authors: Takano Kazufumi , Yamagata Yuriko , Yutani Katsuhide 
Published: August 2002

AbstractTo understand the role of non‐Gly residues in the left‐handed helical conformation for the conformational stability of a protein, the non‐Gly to Gly and Ala mutations at six left‐handed residues (R21, Y38, R50, Q58, H78, and N118) of the human lysozyme were examined. The thermodynamic parameters for denaturation were determined using a differential scanning calorimeter, and the crystal structures were analyzed by X‐ray crystallography. If a left‐handed non‐Gly had an unfavorable steric interaction between the side‐chain Cβ and backbone, the Gly mutation would be expected to stabilize more than the Ala mutation at the same position. For the mutant human lysozymes, however, there were few differences in the denaturation Gibbs energy (ΔG) between the Gly and Ala mutants, except for the substitution at position 58. Analysis of the changes in stability (ΔΔG) based on the structures of the wild‐type and mutant proteins showed that the experimental ΔΔG value of Q58G was ∼7 kJ/mol higher than the estimated value without consideration of any local steric interaction. These results indicate that only Q58G increased the stability by elimination of local constraints. The residue 58 is located at the most rigid position in the left‐handed non‐Gly residues and is involved in its enzymatic function. It can be concluded that the left‐handed non‐Gly residues do not always have unfavorable strain energies as compared with Gly at the same position. Proteins 2001;44:233–243. © 2001 Wiley‐Liss, Inc.
Role of amino acid residues in left‐handed helical conformation for the conformational stability of a protein
Authors: Takano Kazufumi , Yamagata Yuriko , Yutani Katsuhide 
Published: August 2002

AbstractOur previous study of six non‐Gly to Gly/Ala mutant human lysozymes in a left‐handed helical region showed that only one non‐Gly residue at a rigid site had unfavorable strain energy as compared with Gly at the same position (Takano et al., Proteins 2001; 44:233–243). To further examine the role of left‐handed residues in the conformational stability of a protein, we constructed ten Gly to Ala mutant human lysozymes. Most Gly residues in human lysozyme are located in the left‐handed helix region. The thermodynamic parameters for denaturation and crystal structures were determined by differential scanning calorimetry and X‐ray analysis, respectively. The difference in denaturation Gibbs energy (ΔΔG) for the ten Gly to Ala mutants ranged from + 1.9 to −7.5 kJ/mol, indicating that the effect of the mutation depends on the environment of the residue. We confirm that Gly in a left‐handed region is more favorable at rigid sites than non‐Gly, but there is little difference in energetic cost between Gly and non‐Gly at flexible sites. The present results indicate that dihedral angles in the backbone conformation and also the flexibility at the position should be considered for analyses of protein stability, and protein structural determination, prediction, and design. Proteins 2001;45:274–280. © 2001 Wiley‐Liss, Inc.
Crystal structure of non‐allosteric L‐lactate dehydrogenase from Lactobacillus pentosus at 2.3 Å resolution: Specific interactions at subunit interfaces
Authors: Uchikoba Hiroyuki , Fushinobu Shinya , Wakagi Takayoshi , Konno Michiko , Taguchi Hayao , Matsuzawa Hiroshi 
Published: August 2002

AbstractL‐Lactate dehydrogenase (LDH) from Lactobacillus pentosus is a non‐allosteric enzyme, which shows, however, high sequence similarity to allosteric LDHs from certain bacteria. To elucidate the structural basis of the absence of allostery of L. pentosus LDH (LPLDH), we determined the crystal structure of LPLDH at 2.3 Å resolution. Bacterial LDHs are tetrameric enzymes composed of identical subunits and exhibit 222 symmetry. The quaternary structure of LPLDH was similar to the active conformation of allosteric LDHs. Structural analysis revealed that the subunit interfaces of LPLDH are optimized mainly through hydrophilic interactions rather than hydrophobic interactions, compared with other LDHs. The subunit interfaces of LPLDH are more specifically stabilized by increased numbers of intersubunit salt bridges and hydrogen bonds, and higher geometrical complementarity. Such high specificity at the subunit interfaces should hinder the rearrangement of the quaternary structure needed for allosteric regulation and thus explain the “non‐allostery” of LPLDH. Proteins 2002;46:206–214. © 2001 Wiley‐Liss, Inc.
Metabolism of the phosphonate herbicide glyphosate by a non‐nitrate‐utilizing strain of Penicillium chrysogenum
Authors: Klimek Magdalena , Lejczak Barbara , Kafarski Paweł , Forlani Giuseppe 
Published: August 2002

AbstractA Penicillium chrysogenum strain was isolated for its ability to grow in minimal medium containing the herbicide glyphosate as the only nitrogen source. The presence of concentrations up to 25 mM progressively stimulated the fungal growth rate, which was negligible in media lacking reduced nitrogen. However, glyphosate utilization never exceeded 1 mmol g−1 mycelial dry mass, and below a threshold concentration both herbicide uptake and fungal growth were subject to a lag phase, suggesting that the herbicide may enter the cell by either simple passive diffusion or inducible carriers. Amino acids, possible products of glyphosate breakdown, as well as ammonia, were found to replace the herbicide in restoring mycelial growth. Cells were devoid of detectable nitrate reductase activity, thus the isolate seems to be impaired in its ability to convert nitrate to ammonium. In vitro activity of 5‐enol‐pyruvyl‐shikimate‐3‐phosphate synthase, the target site of glyphosate action, was highly sensitive to the herbicide. Fungal growth rate was considerably lower when the herbicide was also the only phosphorus source, whereas glyphosate utilization was substantially unaffected, suggesting an unusual route for its degradation. Herbicide metabolism was strongly reduced when other sources of organic nitrogen were made available.© 2001 Society of Chemical Industry
Wild salmonids and sea louse infestations on the west coast of Scotland: sources of infection and implications for the management of marine salmon farms
Authors: Butler James R A 
Published: August 2002

AbstractThe sea louse (Lepeophtheirus salmonis Krøyer) is a major health problem for both farmed and wild salmonids. This paper investigates louse epidemiology and management in the salmon‐farming zone of western Scotland. Based on a review of the marine ecology of wild salmon (Salmo salar L) and sea trout (Salmo trutta L), and catch and farm production statistics, best estimates were made for numbers of wild and farm hosts present in coastal waters in March–June 2000. Applying data for ovigerous female louse infections and fecundity, the sources and risks of larval transmission to wild salmon and sea trout were modelled. Farm salmon in the second spring of production were the primary host group (98% of fish), while numbers of wild salmonids (<1%) and escaped farm salmon (2%) were relatively insignificant. Farm salmon produced 97% of louse eggs at high levels (eight ovigerous lice per fish), and 78% at low levels (one per fish). Wild salmonids produced <1% of eggs under both scenarios, but escaped farm salmon produced 3% and 21%, respectively. All hosts potentially cross‐infect one another, but farm salmon are more likely to infect wild and farm smolts, and also other farm salmon. Monitoring of lice on sea trout in June 1998–2000 by the Association of West Coast Fisheries Trusts corroborated the model's conclusions. Localised epizootics occurred every year and coincided with the presence of ovigerous lice on local farms. In areas of mixed‐year class production on farms, epizootics were evident every spring, but occurred every second spring in areas of single‐year class production. In 1998–2000 at least 14–40% of sea trout were infected with potentially lethal infestations of lice. Ovigerous louse levels of <0.005 per fish were required on farm salmon in the spring of 2000 to produce less eggs than those emitted by wild salmonids. With the industry's continued expansion, and thus increased numbers of farm salmon, a target of zero ovigerous lice will be required on farms to minimise impacts on wild salmonids. Due to the limited long‐term efficacy and availability of louse medicines, management strategies are discussed which will improve control, including single‐year class production over large areas, alternate S1–S1/2 smolt inputs, and 11‐month production cycles.© 2002 Society of Chemical Industry
Traffic load models for bridge design: recent developments and research
Authors: Prat Michel 
Published: August 2002

AbstractThe processes and methods used to achieve the load models of the Eurocode for traffic loads on road bridges pREN1991‐2 is now widely accepted. Various universities (Aaachen, Delft, Trinity College, Dublin, Liège, Pisa), consulting engineers (Flint & Neill Partnership) and organizations, notably the TRL (Transport Research Laboratory) and the BRE (British Research Establishement, Ltd), the main centres for civil engineering research in the United Kingdom, together with the SETRA and the LCPC who cover the major aspects of road transport for the Ministry of Transport in France, lead studies involving civil engineering companies, industrial manufacturers of heavy vehicles and manufacturers of tyres for the determination of loading levels for bridge design. This paper presents an overview of recent developments and some envisaged research.
Hypocholesterolaemic effect of the oleoresin of Capsicum annum L. in gerbils (Meriones hurrianae Jerdon)
Authors: Gupta R. S. , Dixit V. P. , Dobhal M. P. 
Published: August 2002

AbstractThe effect of capsicum oleoresin (CO) on dietary hypercholeterolaemia were observed in male gerbils at a dose of 75 mg/kg body wt/day. The oleoresin reduced serum cholesterol and triglycerides by 70% and 66%, whereas, liver cholesterol and triglycerides were lowered by 70.9% and 68.7% respectively, in comparison with atherogenic fed controls. CO feeding prevented the accumulation of cholesterol and triglycerides in the liver and aorta. The faecal excretion of cholesterol and triglycerides were significantly increased in oleoresin fed gerbils. Copyright © 2002 John Wiley & Sons, Ltd.
Antiulcerogenic effect of Hippophae rhamnoides L.
Authors: Süleyman H. , Demirezer L. Ö. , Büyükokuroglu M. E. , Akcay M. F. , Gepdiremen A. , Banoglu Z. N. , Göçer F. 
Published: August 2002

AbstractThe antiulcerogenic effect of a hexane extract (HRe‐1) from Hippophae rhamnoides (Eleagnaceae) was tested on indomethacin‐ and stress‐induced ulcer models. As a result HRe‐1 was found to be active in preventing gastric injury. Copyright © 2001 John Wiley & Sons, Ltd.