bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apoptotic impact of α1‐blockers on prostate cancer growth: A myth or an inviting reality?
Authors: Tahmatzopoulos Anastasios , Kyprianou Natasha 
Published: February 2004

AbstractBACKGROUNDPharmacological manipulation or genetic targeting of the major apoptosis regulators, such as bcl‐2, caspases, and inhibitors of apoptosis (IAPs), represent clinically attractive avenues towards effective therapeuti strategies for advanced prostate cancer. A wealth of evidence established the α1‐adrenoceptor antagonists to be clinically effective in relieving the symptoms associated with benign prostatic hyperplasia (BPH) by relaxing prostatic smooth muscle tone. This action alone however does not fully account for the long‐term clinical response to these drugs in BPH patients.METHODSExperimental and retrospective clinical studies provided new evidence supporting a differential growth‐suppressing function of two α1‐adrenoceptor antagonists against prostate cancer, independent of an α1‐adrenoceptor mechanism.RESULTSThe quinazoline‐based antagonists, doxazosin and terazosin, induce apoptosis, inhibit cell adhesion to the extracellular matrix (by activating anoikis), and prevent cell invasion and migration of prostate tumor epithelial cells and vascular endothelial cells. Tamsulosin, a sulphonamide‐based, clinically effective α1‐adrenoceptor antagonist for BPH treatment, fails to exert a similar apoptotic action against prostate cells. Furthermore, at pharmacologically relevant doses, doxazosin suppresses benign and malignant prostate growth in in vivo experimental models. The effect is characterized by three intriguing features: (a) it is mediated by an α1‐adrenoceptor‐independent action, (possibly related to the quinazoline nucleus); (b) it is targeted at the apoptotic process without affecting cell proliferation; and (c) the elevated apoptotic index correlated with symptom score improvement in BPH patients.CONCLUSIONSThis evidence challenges conventional knowledge of the mechanism of action of α1‐adrenoceptor antagonists, and points to a new therapeutic value for these drugs by providing a differential molecular basis for their anti‐tumor efficacy. The present review focuses on the characterization of the apoptotic/anti‐angiogenic effect of quinazoline‐based α1‐adrenoceptor antagonists against prostate cancer cells and discusses the clinical significance of this action in the prevention and treatment of prostate cancer. © 2003 Wiley‐Liss, Inc.
Expression of bone morphogenetic protein‐7 (BMP‐7) in human prostate
Authors: Masuda Hiroshi , Fukabori Yoshitatsu , Nakano Katsuya , Shimizu Nobuaki , Yamanaka Hidetoshi 
Published: February 2004

AbstractBACKGROUNDIt is known that BMP is a factor that strongly induces bone formation in muscle tissue. However, the expression of BMP‐7 is not detected in normal bone tissues. Recently, we reported that the level of BMP‐7 expression was significantly higher in metastatic bone lesions than in normal bone and that the high expression of BMP‐7 in metastatic bone lesions was related to osteoblastic metastasis. The aim of this study was to investigate the level of BMP‐7 gene expression in normal prostate glandular tissues, newly diagnosed prostate cancer tissues, and local recurrent prostate cancer tissues.METHODSTotal RNA was extracted from 23 samples of normal prostate glandular tissues, 28 samples of newly diagnosed prostate cancer tissues, and 23 samples of local recurrent prostate cancer tissues. We also examined the expression of BMP‐7 in human prostatic epithelial cells (HPECs) under conditions of androgen replacement. After reverse transcription of the RNA samples, the expression of BMP‐7 was measured by real‐time quantitative polymerase chain reaction (PCR). Glyceraldehyde phosphate dehydrogenase (GAPDH) was used as an internal standard.RESULTSThe level of BMP‐7 expression was highest in the normal prostate glandular tissue (P < 0.05). The expression of BMP‐7 tended to be lower during the development and progression of prostate cancer. The expression of BMP‐7 in prostate epithelial cells treated with 10−7 M dihydrotestosterone (DHT) was significantly higher than in the DHT‐free control (P = 0.0285).CONCLUSIONSIt has been reported that the BMP‐7 mRNA level is androgen‐dependent in the mouse prostate. The present results suggest that the BMP‐7 mRNA level is androgen‐dependent in the human prostate, since the expression of BMP‐7 was decreased in local recurrent prostate cancer tissues after hormonal therapy and was increased by DHT. © 2004 Wiley‐Liss, Inc.
Free energy simulations and MM–PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody
Authors: Laitinen Tuomo , Kankare Jussi A. , Peräkylä Mikael 
Published: February 2004

AbstractAntiestradiol antibody 57‐2 binds 17β‐estradiol (E2) with moderately high affinity (Ka = 5 × 108 M−1). The structurally related natural estrogens estrone and estriol as well synthetic 17‐deoxy‐estradiol and 17α‐estradiol are bound to the antibody with 3.7–4.9 kcal mol−1 lower binding free energies than E2. Free energy perturbation (FEP) simulations and the molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) method were applied to investigate the factors responsible for the relatively low cross‐reactivity of the antibody with these four steroids, differing from E2 by the substituents of the steroid D‐ring. In addition, computational alanine scanning of the binding site residues was carried out with the MM–PBSA method. Both the FEP and MM–PBSA methods reproduced the experimental relative affinities of the five steroids in good agreement with experiment. On the basis of FEP simulations, the number of hydrogen bonds formed between the antibody and steroids, which varied from 0 to 3 in the steroids studied, determined directly the magnitude of the steroid–antibody interaction free energies. One hydrogen bond was calculated to contribute about 3 kcal mol−1 to the interaction energy. Because the relative binding free energies of estrone (two antibody‐steroid hydrogen bonds), estriol (three hydrogen bonds), 17‐deoxy‐estradiol (no hydrogen bonds), and 17α‐estradiol (two hydrogen bonds) are close to each other and clearly lower than that of E2 (three hydrogen bonds), the water–steroid interactions lost upon binding to the antibody make an important contribution to the binding free energies. The MM–PBSA calculations showed that the binding of steroids to the antiestradiol antibody is driven by van der Waals interactions, whereas specificity is solely due to electrostatic interactions. In addition, binding of steroids to the antiestradiol antibody 57‐2 was compared to the binding to the antiprogesterone antibody DB3 and antitestosterone antibody 3‐C4F5, studied earlier with the MM–PBSA method. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Probing the α‐complementing domain of E. coli β‐galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition
Authors: Poussu Eini , Vihinen Mauno , Paulin Lars , Savilahti Harri 
Published: February 2004

AbstractProtein structure‐function relationships can be studied by using linker insertion mutagenesis, which efficiently identifies essential regions in target proteins. Bacteriophage Mu in vitro DNA transposition was used to generate an extensive library of pentapeptide insertion mutants within the α‐complementing domain 1 of Escherichia coli β‐galactosidase, yielding mutants at 100% efficiency. Each mutant contained an accurate 15‐bp insertion that translated to five additional amino acids within the protein, and the insertions were distributed essentially randomly along the target sequence. Individual mutants (α‐donors) were analyzed for their ability to restore (by α‐complementation) β‐galactosidase activity of the M15 deletion mutant (α‐acceptor), and the data were correlated to the structure of the β‐galactosidase tetramer. Most of the insertions were well tolerated, including many of those disrupting secondary structural elements even within the protein's interior. Nevertheless, certain sites were sensitive to mutations, indicating both known and previously unknown regions of functional importance. Inhibitory insertions within the N‐terminus and loop regions most likely influenced protein tetramerization via direct local effects on protein–protein interactions. Within the domain 1 core, the insertions probably caused either lateral shifting of the polypeptide chain toward the protein's exterior or produced more pronounced structural distortions. Six percent of the mutant proteins exhibited temperature sensitivity, in general suggesting the method's usefulness for generation of conditional phenotypes. The method should be applicable to any cloned protein‐encoding gene. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Protein conformer selection by sequence‐dependent packing contacts in crystals of 3‐phosphoglycerate kinase
Authors: Kovári Zoltán , Vas Mária 
Published: February 2004

AbstractIn several crystal structures of 3‐phosphoglycerate kinase (PGK), the two domains occupy different relative positions. It is intriguing that the two extreme (open and closed) conformations have never been observed for the enzyme from the same species. Furthermore, in certain cases, these different crystalline conformations represent the enzyme‐ligand complex of the same composition, such as the ternary complex containing either the substrate 3‐phosphoglycerate (3‐PG) and β,γ‐imido‐adenosine‐5′‐triphosphate (AMP‐PNP), an analogue of the substrate MgATP, or 3‐PG and the product MgADP. Thus, the protein conformation in the crystal is apparently determined by the origin of the isolated enzyme: PGK from pig muscle has only been crystallized in open conformation, whereas PGK from either Thermotoga maritima or Trypanosoma brucei has only been reported in closed conformations. A systematic analysis of the underlying sequence differences at the crucial hinge regions of the molecule and in the protein–protein contact surfaces in the crystal, in two independent pairs of open and closed states, have revealed that 1) sequential differences around the molecular hinges do not explain the appearance of fundamentally different conformations and 2) the species‐specific intermolecular contacts between the nonconserved residues are responsible for stabilizing one conformation over the other in the crystalline state. A direct relationship between the steric position of the contacts in the three‐dimensional structure and the conformational state of the protein has been demonstrated. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Funnel‐like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution
Authors: Xia Yu , Levitt Michael 
Published: February 2004

AbstractTo understand the physical and evolutionary determinants of protein folding, we map out the complete organization of thermodynamic and kinetic properties for protein sequences that share the same fold. The exhaustive nature of our study necessitates using simplified models of protein folding. We obtain a stability map and a folding rate map in sequence space. Comparison of the two maps reveals a common organizational principle: optimality decreases more or less uniformly with distance from the optimal sequence in the sequence space. This gives a funnel‐shaped optimality surface. Evolutionary dynamics of a sequence population on these two maps reveal how the simple organization of sequence space affects the distributions of stability and folding rate preferred by evolution. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Prediction of α‐turns in proteins using PSI‐BLAST profiles and secondary structure information
Authors: Kaur Harpreet , Raghava G.P.S. 
Published: February 2004

AbstractIn this paper a systematic attempt has been made to develop a better method for predicting α‐turns in proteins. Most of the commonly used approaches in the field of protein structure prediction have been tried in this study, which includes statistical approach “Sequence Coupled Model” and machine learning approaches; i) artificial neural network (ANN); ii) Weka (Waikato Environment for Knowledge Analysis) Classifiers and iii) Parallel Exemplar Based Learning (PEBLS). We have also used multiple sequence alignment obtained from PSIBLAST and secondary structure information predicted by PSIPRED. The training and testing of all methods has been performed on a data set of 193 non‐homologous protein X‐ray structures using five‐fold cross‐validation. It has been observed that ANN with multiple sequence alignment and predicted secondary structure information outperforms other methods. Based on our observations we have developed an ANN‐based method for predicting α‐turns in proteins. The main components of the method are two feed‐forward back‐propagation networks with a single hidden layer. The first sequence‐structure network is trained with the multiple sequence alignment in the form of PSI‐BLAST‐generated position specific scoring matrices. The initial predictions obtained from the first network and PSIPRED predicted secondary structure are used as input to the second structure–structure network to refine the predictions obtained from the first net. The final network yields an overall prediction accuracy of 78.0% and MCC of 0.16. A web server AlphaPred (http://www.imtech.res.in/raghava/alphapred/) has been developed based on this approach. Proteins 2004. © 2004 Wiley‐Liss, Inc.
The role of carbon‐donor hydrogen bonds in stabilizing tryptophan conformations
Authors: Petrella Robert J. , Karplus Martin 
Published: February 2004

AbstractAlthough most side‐chain torsion angles correspond to low‐energy rotameric positions, deviations occur with significant frequency. One striking example arises in Trp residues, which have an important role in stabilizing protein structures because of their size and mixed hydrophobic/hydrophilic character. Ten percent of Trp side‐chains have unexplained conformations with χ2 near 0° instead of the expected 90°. The current work is a structural and energetic analysis of these conformations. It is shown that many Trp residues with these orientations are stabilized by three‐center carbon‐donor hydrogen bonds of the form CH…X…HC, where X is a polar hydrogen‐bond acceptor in the environment of the side‐chain. The bridging hydrogen bonds occur both within the Trp side‐chain and between the side‐chain and the local protein backbone. Free energy maps of an isolated Trp residue in an explicit water environment show a minimum corresponding to the off‐rotamer peak observed in the crystallographic data. Bridging carbon‐donor hydrogen bonds are also shown to stabilize on‐rotamer Trp conformations, and similar bridging hydrogen bonds also stabilize some off‐rotamer Asp conformations. The present results suggest a previously unrecognized role for three‐center carbon‐donor hydrogen bonds in protein structures and support the view that the off‐rotamer Trp side‐chain orientations are real rather than artifacts of crystallographic refinements. Certain of the off‐rotamer Trp conformations appear to have a functional role. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations
Authors: Hudáky Ilona , Gáspári Zoltán , Carugo Oliviero , Čemažar Maša , Pongor Sándor , Perczel András 
Published: February 2004

AbstractA systematic comparison is made between experimental and computational data gained on vicinal disulfide bridges in proteins and peptides. Structural and stability data of ab initio and density functional theory (DFT) calculations on the model compound 4,5‐ditiaheptano‐7‐lactam and the model peptide HCOox‐[CysCys]NH2 at RHF/3‐21G*, B3LYP/6‐31+G(d), and B3LYP/6‐311++G(d,p) levels of theory are presented. The data on XxxCysCysYyy type amino acid sequence units retrieved from PDB SELECT, along with data on sequence units that have vicinal disulfide bridge, taken from the Brookhaven Protein Data Bank, are conformationally characterized. Amino acid backbone conformations, cis‐trans isomerism of the amide bond between the two cysteine residues, and ring puckering are studied. Ring puckers are characterized by their relation to the conformers of the parent 4,5‐ditiaheptano‐7‐lactam. Computational precision and accuracy are proved by frequency calculation and solvent model optimization on selected conformers. It is found that the ox‐[CysCys] unit is able to accept types I, II, VIa, VIb, and VIII β‐turn structures. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Squeezed exponential kinetics to describe a nonglassy downhill folding as observed in a lattice protein model
Authors: Nakamura Hironori K. , Sasai Masaki , Takano Mitsunori 
Published: February 2004

AbstractWe previously studied the so‐called strange kinetics in the two‐dimensional lattice HP model. To further study the strange kinetics, folding processes of a 27‐mer cubic lattice protein model with Gō potential were investigated by simulating how the bundle of folding trajectories, consisting of a number of independent Monte Carlo simulations, evolves as the folding reaction proceeds, covering a wide range of temperature. Three realms of folding kinetics were observed depending on temperature. Although at temperatures where folding was two‐state‐like, the kinetics was conventional single exponential, we found that the time course data were well represented by a squeezed (or “shrunken”) exponential function, exp [−(t/τ)β] with β > 1, at temperatures lower than the folding temperature, where folding was fastest and of a nonglassy downhill type. The squeezed exponential kinetics was found to pertain to the subdiffusion on the nonglassy downhill free energy surface and presents a marked contrast both to the single exponential kinetics and to the stretched exponential kinetics that was observed at lower temperatures where folding was also downhill but topological frustration came into effect. The observed temperature dependence of the folding kinetics suggests that some small single‐domain proteins may follow the squeezed exponential kinetics at about the room temperature. Proteins 2004;55:99–106. © 2004 Wiley‐Liss, Inc.
A structural and dynamic model for the interaction of interleukin‐8 and glycosaminoglycans: Support from isothermal fluorescence titrations
Authors: Krieger Elmar , Geretti Elena , Brandner Barbara , Goger Birgit , Wells Timothy N. , Kungl Andreas J. 
Published: February 2004

AbstractBinding of interleukin‐8 (IL‐8) to glycosaminoglycans (GAGs) on the surface of endothelial cells is crucial for the recruitment of neutrophils to an inflammatory site. Deriving structural knowledge about this interaction from in silico docking experiments has proved difficult because of the high flexibility and the size of GAGs. Therefore, we developed a docking method that takes into account ligand and protein flexibility by running ∼15,000 molecular dynamics simulations of the docking event with different initial orientations of the binding partners. The method was shown to successfully reproduce the residues of basic fibroblast growth factor involved in GAG binding. Docking of a heparin hexasaccharide to IL‐8 gave an interaction interface involving the basic residues His18, Lys20, Arg60, Lys64, Lys67, and Arg68. By subjecting IL‐8 single‐site mutants, in which these amino acids were replaced by alanine, to isothermal fluorescence titrations, the affinities for heparin were determined to be wtIL‐8 > IL‐8(H18A) ≫ IL‐8(R68A) > IL‐8(K67A) ≫ IL‐8(K20A) > IL‐8(R60A) ≫ IL‐8(K64A). A comparison with the binding energies calculated from the model revealed high values for wtIL‐8 and the H18A mutant and significantly lower but similar energies for the remaining mutants. Connecting the two fully sulfated hexasaccharides bound to each of the two IL‐8 monomers in the dimeric chemokine by an N‐acetylated dodecasaccharide gave a complex structure in which the GAG molecule aligned in a parallel fashion to the N‐terminal α‐helices of IL‐8 like a horseshoe. A 5‐ns molecular dynamics simulation of this complex confirmed its structural stability and revealed a reorientation in both binding sites where a disaccharide became the central binding unit. Isothermal fluorescence titration experiments using differently sulfated heparin disaccharides confirmed that a single disaccharide can indeed bind IL‐8 with high affinity. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: Close structural resemblance to E. coli pantothenate kinase
Authors: Li de La Sierra‐Gallay Ines , Collinet Bruno , Graille Marc , Quevillon‐Cheruel Sophie , Liger Dominique , Minard Philippe , Blondeau Karine , Henckes Gilles , Aufrère Robert , Leulliot Nicolas , Zhou Cong‐Zhao , Sorel Isabelle , Ferrer Jean‐Luc , Poupon Anne , Janin Joël , van Tilbeurgh Herman 
Published: February 2004

AbstractThe protein product of the YGR205w gene of Saccharomyces cerevisiae was targeted as part of our yeast structural genomics project. YGR205w codes for a small (290 amino acids) protein with unknown structure and function. The only recognizable sequence feature is the presence of a Walker A motif (P loop) indicating a possible nucleotide binding/converting function. We determined the three‐dimensional crystal structure of Se‐methionine substituted protein using multiple anomalous diffraction. The structure revealed a well known mononucleotide fold and strong resemblance to the structure of small metabolite phosphorylating enzymes such as pantothenate and phosphoribulo kinase. Biochemical experiments show that YGR205w binds specifically ATP and, less tightly, ADP. The structure also revealed the presence of two bound sulphate ions, occupying opposite niches in a canyon that corresponds to the active site of the protein. One sulphate is bound to the P‐loop in a position that corresponds to the position of β‐phosphate in mononucleotide protein ATP complex, suggesting the protein is indeed a kinase. The nature of the phosphate accepting substrate remains to be determined. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
Immunoglobulin kappa light chain and its amyloidogenic mutants: A molecular dynamics study
Authors: Nowak Mateusz 
Published: February 2004

AbstractAL amyloidosis and LCDD are pathological conditions caused by extracellural deposition of monoclonal Ig light chain variable domains. In the former case, deposits have a form of amyloid fibrils, in the latter, amorphous aggregates. 1REI κ light chain variable domain and its two point mutants, R61N and D82I, were chosen for the analysis in this work. Wild 1REI does not create deposits in vitro, while R61N aggregates as amyloid fibrils and D82I creates amorphous aggregates. Both mutated residues create a conserved salt bridge; thus, substitution of any of them should decrease VL domain stability. For these three proteins, 5 ns MD simulations were conducted in temperatures of 300 K and 400 K, with protonated and unprotonated acidic residues, mimicking acidic and neutral experimental pH conditions (3 sets: N300, N400, and A400). The analysis of trajectories focused on characterization of changes in conformational behavior and stability of Ig κ light chain variable domain caused by single aminoacid substitutions that were experimentally proved to enhance aggregation propensity, both in the form of amyloid and amorphous aggregates. Residue D82 turns out to be involved not only in R61–D82 but also in K45–D82 interaction, which was not observed in the X‐ray structure, but frequently populated simulations of 1REI. The substitution D82I excludes both interactions, resulting in substantial destabilization (i.e., easier aggregation). Examination of behavior of edge regions of VL β‐sandwich reveals significant alterations in D82I mutant compared to wild 1REI, while relatively small changes occur in R61N. This suggests that mild and slow destabilization is the reason of the conversion of VL to partially folded amyloidogenic intermediate structure. Proteins 2004. © 2004 Wiley‐Liss, Inc.