bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome analysis of human colon cancer by two‐dimensional difference gel electrophoresis and mass spectrometry
Authors: Friedman David B. , Hill Salisha , Keller Jeffrey W. , Merchant Nipun B. , Levy Shawn E. , Coffey Robert J. , Caprioli Richard M. 
Published: February 2004

AbstractTwo‐dimensional difference gel electrophoresis (2‐D DIGE) coupled with mass spectrometry (MS) was used to investigate tumor‐specific changes in the proteome of human colorectal cancers and adjacent normal mucosa. For each of six patients with different stages of colon cancer, Cy5‐labeled proteins isolated from tumor tissue were combined with Cy3‐labeled proteins isolated from neighboring normal mucosa and separated on the same 2‐D gel along with a Cy2‐labeled mixture of all 12 normal/tumor samples as an internal standard. Over 1500 protein spot‐features were analyzed in each paired normal/tumor comparison, and using DIGE technology with the mixed‐sample internal standard, statistically significant quantitative comparisons of each protein abundance change could be made across multiple samples simultaneously without interference due to gel‐to‐gel variation. Matrix‐assisted laser desorption/ionization‐time of flight (MALDI‐TOF) and tandem (TOF/TOF) MS provided sensitive and accurate mass spectral data for database interrogation, resulting in the identification of 52 unique proteins (including redundancies due to proteolysis and post‐translationally modified isoforms) that were changing in abundance across the cohort. Without the benefit of the Cy2‐labeled 12 sample mixture internal standard, 42 of these proteins would have been overlooked due to the large degree of variation inherent between normal and tumor samples.
Extensive analysis of the human platelet proteome by two‐dimensional gel electrophoresis and mass spectrometry
Authors: García Angel , Prabhakar Sripadi , Brock Chris J. , Pearce Andrew C. , Dwek Raymond A. , Watson Steve P. , Hebestreit Holger F. , Zitzmann Nicole 
Published: February 2004

AbstractPlatelets play a key role in the control of bleeding and wound healing, contributing to the formation of vascular plugs. Under pathologic circumstances, they are involved in thrombotic disorders, including heart disease. Since platelets do not have a nucleus, proteomics offers a powerful alternative approach to provide data on protein expression in these cells, helping to address their biology. In this publication we extend the previously reported analysis of the pI 4–5 region of the human platelet proteome to the pI 5–11 region. By using narrow pI range two‐dimensional electrophoresis (2‐DE) for protein separation followed by high‐throughput tandem mass spectrometry (MS/MS) for protein identification, we were able to identify 760 protein features, corresponding to 311 different genes, resulting in the annotation of 54% of the pI 5–11 range 2‐DE proteome map. We evaluated the physicochemical properties and functions of the identified platelet proteome. Importantly, the main group of proteins identified is involved in intracellular signalling and regulation of the cytoskeleton. In addition, 11 hypothetical proteins are reported. In conclusion, this study provides a unique inventory of the platelet proteome, contributing to our understanding of platelet function and building the basis for the identification of new drug targets.
Chemical Kinetics of the Thermal Decomposition of NTO
Authors: Kondrikov Boris N. , Smirnov S. P. , Minakin A. V. , Doherty Ruth M. 
Published: February 2004

AbstractThe kinetics of thermal decomposition of 3‐nitro‐2,4‐dihydro‐3H‐1,2,4‐triazol‐5‐one (NTO) in the temperature interval from 200 °C to 260 °C was investigated using a glass Bourdon gauge. The overall decomposition reaction includes two distinct stages: the fast first‐order decomposition and the subsequent autocatalytic reaction. The importance of the first stage increases with increasing decomposition temperature and decreasing loading density of the Bourdon gauge (m/V). A period of preliminary heating, at a lower temperature, strongly influences the autocatalytic stage when the decomposition is carried out at a higher temperature. In the temperature domain 200–220 °C, the Arrhenius constants of the decomposition reaction are found to be close to the values usually observed for nitrocompounds: E=173 kJ/mol and log10 k≈12.5 (s−1). It is shown that a simple model of NTO decomposition based on an autocatalytic reaction of the m‐th order can describe the course of the decomposition at high temperature but the m number appears to be excessively high, up to 4. A new model of the decomposition is developed, including an initial monomolecular reaction, decomposition of the crystalline substance, and an autocatalytic reaction of NTO dissolved in liquid decomposition products. This model gives the common order of autocatalysis, m=1.
Antitumor activity of irofulven monotherapy and in combination with mitoxantrone or docetaxel against human prostate cancer models
Authors: Van Laar Emily S. , Weitman Steven , MacDonald John R. , Waters Stephen J. 
Published: February 2004

AbstractBACKGROUNDIrofulven (6‐hydroxymethylacylfulvene, HMAF, MGI 114) is a novel antitumor agent currently undergoing clinical trials in hormone‐refractory prostate cancer. This report examines the efficacy of irofulven alone or in combination with mitoxantrone or docetaxel against androgen‐independent prostate cancer cell lines.METHODSTo elucidate the activity of irofulven monotherapy and in combination, PC‐3 and DU‐145 cell lines were utilized in cellular viability assessments and tumor growth inhibition studies.RESULTSViability assays with irofulven and mitoxantrone show additive to synergistic activity. Furthermore, irofulven and mitoxantrone in combination exhibit enhanced antitumor activity against PC‐3 and DU‐145 xenografts. Additive combination effects are also observed when irofulven and docetaxel were tested against PC‐3 xenografts and curative activity (8/10 CR) is observed in DU‐145 xenografts.CONCLUSIONSThese studies demonstrate that irofulven displays strong activity as monotherapy and in combination with mitoxantrone or docetaxel against androgen‐independent prostate cancer in vitro and in vivo; thus, supporting the clinical investigation of irofulven against hormone‐refractory prostate cancer. © 2003 Wiley‐Liss, Inc.
Phenylephrine‐induced neurogenic prostatitis facilitates the promotion of PIN‐like lesions in rats
Authors: Rosenzweig N. , Horodniceanu J. , Abramovici A. 
Published: February 2004

AbstractBACKGROUNDAtypical prostate hyperplasia, resembling PIN lesions in men, together with chronic inflammatory exudates, have been reported after chronic administration of phenylephrine (PE). The present study aims to characterize the evolution of the expression of typical leukocyte markers immunohistochemically as correlated to the promotion of PIN lesions.METHODSAdolescent rats received injections of PE (subcutaneously) (10 mg/kg BW/per day) and were euthanized 3, 8 hr, 1, 3, 7, 14 days thereafter. The dissected prostates were fixed in formalin, and paraffin embedded sections were cut and immunoreacted.RESULTSPE exerted a time related bi‐phasic effect on the rat prostate. A first inflammatory reaction phase took place at 3–8 hr post injection characterized by vascular dilatation, congestion, edema, and massive leukocytic infiltrate, mainly of ED1+ cells. At 24 hr, the amount of ED1+ cells decreased approaching the equivalent values of ED2+, CD8+ cells, and mastocytes. Their values remained relatively high for the rest of the experimental period. A second phase of proliferative changes, consisting of healing fibrosis as well as dysplastic epithelial lesions, similar to human PIN lesions, appeared on the 7th day.CONCLUSIONSNeuro‐immune interactions promote prostatic fibrosis and dysplastic changes; these being preceded by an acute and transient inflammatory reaction. © 2003 Wiley‐Liss, Inc.
Gain of androgen receptor gene copies in primary prostate cancer due to X chromosome polysomy
Authors: Röpke Albrecht , Erbersdobler Andreas , Hammerer Peter , Palisaar Jüri , John Kerstin , Stumm Markus , Wieacker Peter 
Published: February 2004

AbstractBACKGROUNDProstate cancer is an androgen dependent tumor. In advanced prostate cancers androgen deprivation has proved to be an effective therapy, but 25% show no response. In this study prostatectomy specimens from patients without preoperative therapy were analyzed to determine the possible mechanism of primary antiandrogen resistance.METHODSThe number of androgen receptor (AR) gene copies and X‐centromeres were investigated from 80 prostate cancer specimens by FISH analysis.RESULTSIn 9 out of 80 prostate cancers additional X‐chromosomes with the corresponding AR gene could be detected. Polysomy of the X‐chromosome correlates with pathological classification and tumor volume.CONCLUSIONSAdditional AR genes due to polysomy of the X‐chromosome are present in a subgroup of primary prostate cancers prior to antiandrogen therapy. Because the growth of prostate cancers is androgen dependent, these specimens may have an advantage in low concentrations of androgens. This may be a factor for initial antiandrogen resistance. © 2003 Wiley‐Liss, Inc.
Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the AR
Authors: Cicek Mine S. , Conti David V. , Curran Anthony , Neville Phillippa J. , Paris Pamela L. , Casey Graham , Witte John S. 
Published: February 2004

AbstractBACKGROUNDThe prostate is an androgen‐regulated organ and polymorphisms in genes involved in testosterone synthesis, in particular, SRD5A2 (A49T and V89L variants), CYP17 (MspAI variant), and the AR (CAG, GGC repeats), represent candidate risk factors for prostate cancer incidence and aggressiveness.METHODSWe evaluated the relationship between these five polymorphisms and prostate cancer risk in a family‐based case‐control study (N = 920). Cases were diagnosed at major medical institutions in Cleveland Ohio, and Detroit Michigan, and their unaffected brothers were used as controls. Associations were investigated with regard to prostate cancer risk, and clinical characteristics at diagnosis (i.e., tumor stage/grade, age, family history).RESULTSThe SRD5A2 V89L variant was associated with an increased risk of prostate cancer (OR = 1.56, P = 0.02). This association was driven primarily by men diagnosed at an earlier age (OR = 2.35, P = 0.001), or with more aggressive disease (OR = 1.63, P = 0.06). None of the other variants exhibited noteworthy associations with disease.CONCLUSIONSThese findings suggest that the SRD5A2 V89L variant may influence risk of developing prostate cancer, especially among men with a younger age of diagnosis or more aggressive disease. © 2003 Wiley‐Liss, Inc.
Molecular modeling study of the editing active site of Escherichia coli leucyl‐tRNA synthetase: Two amino acid binding sites in the editing domain
Authors: Lee Keun Woo , Briggs James M. 
Published: February 2004

AbstractAminoacyl‐tRNA synthetases (aaRSs) strictly discriminate their cognate amino acids. Some aaRSs accomplish this via proofreading and editing mechanisms. Mursinna and coworkers recently reported that substituting a highly conserved threonine (T252) with an alanine within the editing domain of Escherichia coli leucyl‐tRNA synthetase (LeuRS) caused LeuRS to cleave its cognate aminoacylated leucine from tRNALeu (Mursinna et al., Biochemistry 2001;40:5376–5381). To achieve atomic level insight into the role of T252 in LeuRS and the editing reaction of aaRSs, a series of molecular modeling studies including homology modeling and automated docking simulations were carried out. A 3D structure of E. coli LeuRS was constructed via homology modeling using the X‐ray structure of Thermus thermophilus LeuRS as a template because the E. coli LeuRS structure is not available from X‐ray or NMR studies. However, both the X‐ray T. thermophilus and homology‐modeled E. coli structures were used in our studies. Amino acid binding sites in the proposed editing domain, which is also called the connective polypeptide 1 (CP1) domain, were investigated by automated docking studies. The root mean square deviation (RMSD) for backbone atoms between the X‐ray and homology‐modeled structures was 1.18 Å overall and 0.60 Å for the editing (CP1) domain. Automated docking studies of a leucine ligand into the editing domain were performed for both structures: homology structure of E. coli LeuRS and X‐ray structure of T. thermophilus LeuRS for comparison. The results of the docking studies suggested that there are two possible amino acid binding sites in the CP1 domain for both proteins. The first site lies near a threonine‐rich region that includes the highly conserved T252 residue, which is important for amino acid discrimination. The second site is located in a flexible loop region surrounded by residues E292, A293, M295, A296, and M298. The important T252 residue is at the bottom of the first binding pocket. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Computer modeling of the rhamnogalacturonase–“hairy” pectin complex
Authors: Choi Jong Keun , Lee Beom Hyoung , Chae Chong Hak , Shin Whanchul 
Published: February 2004

AbstractThe structure of a pectin‐bound complex of rhamnogalacturonase was modeled to identify the amino acid residues involved in catalysis and substrate binding. The “hairy” region of pectin, represented by six repeating stretches of (1→4)‐D‐galacturonate‐(1→2)‐L‐rhamnose dimer, was flexibly docked into the putative binding site of rhamnogalacturonase from Aspergillus aculeatus whose X‐ray structure is known. A search of the complex configurational space was performed using AutoDock for the dimeric and tetrameric sugar units in which the −1 galacturonate residue has various ring conformations. Then the plausible AutoDock solutions were manually extended to the dodecameric pectin models. Subsequently, the resulting complex models were subjected to solvated molecular dynamics using AMBER. In the best model, the substrate has an extended pseudo‐threefold helix with the −1 ring in a 4H3 half‐chair that approaches the transition state conformation. The catalytic machinery is clearly defined: Asp197 is a general acid and the activated water bound between Asp177 and Glu198 is a nucleophile. The active site is similar, with a small yet significant difference, to that of polygalacturonase that degrades the pectic “smooth” region of linear homopolymer of D‐(1→4)‐linked galacturonic acid. Rhamnogalacturonase has ten binding subsites ranging from −3 to +7, while polygalacturonase has eight subsites from −5 to +3. The model suggests that the eight amino acids including three arginine and three lysine residues, all of which are invariantly conserved in the rhamnogalacturonase family of proteins, are important in substrate binding. The present study may aid in designing mutational studies to characterize rhamnogalacturonase. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Roles of physical interactions in determining protein‐folding mechanisms: Molecular simulation of protein G and α spectrin SH3
Authors: Yup Lee Seung , Fujitsuka Yoshimi , Kim Do Hyun , Takada Shoji 
Published: February 2004

AbstractProtein‐folding mechanisms of two small globular proteins, IgG binding domain of protein G and α spectrin SH3 domain are investigated via Brownian dynamics simulations with a model made of coarse‐grained physical energy functions responsible for sequence‐specific interactions and weak Gō‐like energies. The folding pathways of α spectrin SH3 are known to be mainly controlled by the native topology, while protein G folding is anticipated to be more sensitive to the sequence‐specific effects than native topology. We found in the folding of protein G that the C terminal β hairpin is formed earlier and is rigid, once ordered, in the presence of an intact C terminal turn. The α helix is found to exhibit repeated partial formations/deformations during folding and to be stabilized via the tertiary contact with preformed β sheets. This predicted scenario is fully consistent with experimental ϕ value data. Moreover, we found that the folding route is critically affected when the hydrophobic interaction is excluded from physical energy terms, suggesting that the hydrophobicity critically contributes to the folding propensity of protein G. For the folding of α spectrin SH3, we found that the distal β hairpin and diverging turn are parts formed early, fully in harmony with previous results of simple Gō‐like and experimental analysis, supporting that the folding route of SH3 domain is robust and coded by the native topology. The hybrid method provides useful tools for analyzing roles of physical interactions in determining folding mechanisms. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Missense mutations in transmembrane domains of proteins: Phenotypic propensity of polar residues for human disease
Authors: Partridge Anthony W. , Therien Alex G. , Deber Charles M. 
Published: February 2004

AbstractPrevious experiments on the cystic fibrosis transmembrane conductance regulator suggested that non‐native polar residues within membrane domains can compromise protein structure/function. However, depending on context, replacement of a native residue by a non‐native residue can result either in genetic disease or in benign effects (e.g., polymorphisms). Knowledge of missense mutations that frequently cause protein malfunction and subsequent disease can accordingly reveal information as to the impact of these residues in local protein environments. We exploited this concept by performing a statistical comparison of disease‐causing mutations in protein membrane‐spanning domains versus soluble domains. Using the Human Gene Mutation Database of 240 proteins (including 80 membrane proteins) associated with human disease, we compared the relative phenotypic propensity to cause disease of the 20 naturally occurring amino acids when removed from—or inserted into—native protein sequences. We found that in transmembrane domains (TMDs), mutations involving polar residues, and ionizable residues in particular (notably arginine), are more often associated with protein malfunction than soluble proteins. To further test the hypothesis that interhelical cross‐links formed by membrane‐embedded polar residues stabilize TMDs, we compared the occurrence of such residues in the TMDs of mesophilic and thermophilic prokaryotes. Results showed a significantly higher proportion of ionizable residues in thermophilic organisms, reinforcing the notion that membrane‐embedded electrostatic interactions play critical roles in TMD stability. Proteins 2004;54:000.000. © 2004 Wiley‐Liss, Inc.
Novel approaches for modeling of the A1 adenosine receptor and its agonist binding site
Authors: Gutiérrez‐de‐Terán Hugo , Centeno Nuria B. , Pastor Manuel , Sanz Ferran 
Published: February 2004

AbstractThe present work describes the building of a human A1 adenosine receptor (hA1AR) model, based on the X‐ray crystal structure of bovine rhodopsin, and its use as a basis for the investigation of some important structural characteristics of the receptor. One of the issues investigated was the protonation position of two histidine residues known to influence ligand binding, with protonation of His251 (6.52) in epsilon position and His278 (7.43) in delta position showing the best agreement with experimental evidence. The model was also used to study the position and structural role of water molecules present in the helical bundle. Finally, the binding site location and the ligand docking were investigated using an objective strategy. A suitable site for the binding of the ribose moiety of adenosine was first postulated and further confirmed by means of a novel chemometric strategy based on GRIND descriptors. Using this position as an anchor point, the binding of adenosine was studied by docking and molecular dynamics simulations obtaining two putative binding positions in good agreement with experimental data. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Flexibility of β‐sheets: Principal component analysis of database protein structures
Authors: Emberly Eldon G. , Mukhopadhyay Ranjan , Tang Chao , Wingreen Ned S. 
Published: February 2004

AbstractProtein folds are built primarily from the packing together of two types of structures: α‐helices and β‐sheets. Neither structure is rigid, and the flexibility of helices and sheets is often important in determining the final fold (e.g., coiled coils and β‐barrels). Recent work has quantified the flexibility of α‐helices using a principal component analysis (PCA) of database helical structures (J. Mol. Bio. 2003, 327, pp. 229–237). Here, we extend the analysis to β‐sheet flexibility using PCA on a database of β‐sheet structures. For sheets of varying dimension and geometry, we find two dominant modes of flexibility: twist and bend. The distributions of amplitudes for these modes are found to be Gaussian and independent, suggesting that the PCA twist and bend modes can be identified as the soft elastic normal modes of sheets. We consider the scaling of mode eigenvalues with sheet size and find that parallel β‐sheets are more rigid than antiparallel sheets over the entire range studied. Finally, we discuss the application of our PCA results to modeling and design of β‐sheet proteins. Proteins 2004. © 2004 Wiley‐Liss, Inc.
A novel approach to predict active sites of enzyme molecules
Authors: Chou Kuo‐Chen , Cai Yu‐dong 
Published: February 2004

AbstractEnzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. Proteins 2004. © 2004 Wiley‐Liss, Inc.