bluuebunny/crossref_metadata_2025_split huggingface dataset:
CpG Island hypermethylation in cell‐free serum DNA identifies patients with localized prostate cancer
Authors: Ellinger Jörg , Haan Kim , Heukamp Lukas C. , Kahl Philip , Büttner Reinhard , Müller Stefan C. , von Ruecker Alexander , Bastian Patrick J. 
Published: November 2007

AbstractBACKGROUNDOne of the earliest and most common epigenetic events in prostate carcinogenesis is DNA CpG island (CGI) hypermethylation. Our aim was to analyze the diagnostic and prognostic possibilities of multigene methylation analysis in cell‐free serum DNA of prostate cancer (PCA) patients.METHODSWe analyzed serum samples from 226 consecutive patients (168 PCA; 42 benign prostatic hyperplasia (BPH); 5 incidental PCA; 11 healthy individuals). Cell‐free DNA was digested with methylation‐sensitive restriction endonucleases (HpaII and HinP1I). Subsequently, CGI hypermethylation at GSTP1, PTGS2, Reprimo, and TIG1 was assessed using real‐time PCR.RESULTSCGI hypermethylation at GSTP1, TIG1, PTGS2, and Reprimo was more frequent in PCA (42.3%, 9.5%, 2.4%, and 1.2%, respectively) compared to BPH (7.7%, 0%, 0%, and 0%, respectively) and healthy individuals (all 0%) with a statistical significant difference of GSTP1 (P < 0.0001) and TIG1 (P = 0.038). GSTP1 hypermethylation was also detected in four patients with incidental PCA. Hypermethylation in serum DNA at GSTP1 and hypermethylation at any gene site distinguished between PCA and BPH patients in a highly specific (92%) but less sensitive (42–47%) manner. Neither CGI hypermethylation at a single gene loci nor the combination of multiple gene sites was correlated to the pathological stage, grade or biochemical recurrence following radical prostatectomy.CONCLUSIONSThe detection of aberrant hypermethylation in cell‐free serum DNA allows the highly specific diagnosis of PCA. A test based on GSTP1 hypermethylation in serum samples of patients with suspected PCA may help to identify men with increased risk of harboring PCA despite negative prostate biopsy. Prostate 68: 42–49, 2008. © 2007 Wiley‐Liss, Inc.
Molecular imaging of NF‐kappaB in prostate tissue after systemic administration of IL‐1β
Authors: Vykhovanets Eugene V. , Shukla Sanjeev , MacLennan Gregory T. , Resnick Martin I. , Carlsen Harald , Blomhoff Rune , Gupta Sanjay 
Published: November 2007

AbstractBACKGROUNDActivation of nuclear‐factor kappaB (NF‐κB) influences the transcription of number of genes, many of which participate in inflammatory responses and tumor development. A wide range of human cancers and inflammatory disorders express inappropriate regulation of NF‐κB. The role of NF‐κB in intraprostatic inflammation has not been elucidated.METHODSUsing transgenic NF‐κB‐Luciferase Tag mice coupled to the luciferase reporter gene, we performed serial, noninvasive in vivo and ex vivo molecular imaging of NF‐κB activation in the mouse body after systemic administration of mouse pro‐inflammatory cytokines: TNF‐α, IL‐6, and IL‐1β at 10 µg/kg body weights. In some experiments, pretreatment with dexamethasone (10 mg/kg) was used to modulate the cytokine‐induced NF‐κB‐dependent luminescence in vivo.RESULTSTreatment of NF‐κB‐Luc mice with cytokines increased luminescence in a time‐ and organ‐ specific manner. Highest levels of NF‐κB‐dependent luminescence were observed approximately 3–4 hr after IL‐1β administration. An important finding was the cumulative effect of IL‐1β to activate NF‐κB in the prostate during chronic administration.CONCLUSIONSThe molecular imaging of NF‐κB activity might be an attractive approach to distinguish the role of cytokine‐induced NF‐κB signaling in intraprostatic inflammation and prostate cancer development. Since dexamethasone, a known NF‐κB inhibitor, could reduce the IL‐1β‐induced NF‐κB‐dependent luminescence in the prostate, NF‐κB‐Luc mice might be useful tool to screen potential candidate drugs for treatment of inflammation and tumor associated with aberrant NF‐κB activity. Prostate 68: 34–41, 2008. © 2007 Wiley‐Liss, Inc.
Evolution of binding sites for zinc and calcium ions playing structural roles
Authors: Torrance James W. , MacArthur Malcolm W. , Thornton Janet M. 
Published: November 2007

AbstractThe geometry of metal coordination by proteins is well understood, but the evolution of metal binding sites has been less studied. Here we present a study on a small number of well‐documented structural calcium and zinc binding sites, concerning how the geometry diverges between relatives, how often nonrelatives converge towards the same structure, and how often these metal binding sites are lost in the course of evolution. Both calcium and zinc binding site structure is observed to be conserved; structural differences between those atoms directly involved in metal binding in related proteins are typically less than 0.5 Å root mean square deviation, even in distant relatives. Structural templates representing these conserved calcium and zinc binding sites were used to search the Protein Data Bank for cases where unrelated proteins have converged upon the same residue selection and geometry for metal binding. This allowed us to identify six “archetypal” metal binding site structures: two archetypal zinc binding sites, both of which had independently evolved on a large number of occasions, and four diverse archetypal calcium binding sites, where each had evolved independently on only a handful of occasions. We found that it was common for distant relatives of metal‐binding proteins to lack metal‐binding capacity. This occurred for 13 of the 18 metal binding sites we studied, even though in some of these cases the original metal had been classified as “essential for protein folding.” For most of the calcium binding sites studied (seven out of eleven cases), the lack of metal binding in relatives was due to point mutation of the metal‐binding residues, whilst for zinc binding sites, lack of metal binding in relatives always involved more extensive changes, with loss of secondary structural elements or loops around the binding site. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Effects of glycerol on the compaction and stability of the wild type and mutated rabbit muscle creatine kinase
Authors: Feng Shan , Yan Yong‐Bin 
Published: November 2007

AbstractAll organisms have developed detect, repair, regulation, and stabilization mechanisms to survive from cellular and molecular damage induced by diverse stresses. Among them, the accumulation of osmolytes is a common mechanism evolved by cells to maintain cell volume and stabilize macromolecules against various environmental stresses. The molecular mechanisms by which osmolytes stabilize proteins and prevent aggregation have been well‐established. However, little is known about the effects of osmolytes on mutated or damaged proteins. In this research, we investigated the effects of glycerol on the activity, structure, and stability of the wild type (WT) and D54G CK under normal and extreme (high temperature) conditions. It was found that glycerol had similar effects on the suppression of the aggregation during the refolding of both proteins. Under native conditions, the effect of glycerol on the mutated protein was more obvious than on the WT protein. Glycerol could efficiently force the mutated protein to fold to a state close to the WT protein, and thus stabilize the native state of the mutated protein. Glycerol could also protect both the WT and mutated proteins against heat‐induced denaturation. However, the change in the transition free energy of heat‐induced inactivation of the WT protein was larger than that of the mutated protein. These results suggested that glycerol might have differential effects on the changes of the chemical potential and the transition free energy of the WT and mutated proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structure–function relationships in the 2‐oxo acid dehydrogenase family: Substrate‐specific signatures and functional predictions for the 2‐oxoglutarate dehydrogenase‐like proteins
Authors: Bunik Victoria I. , Degtyarev Dmitry 
Published: November 2007

AbstractStructural relationship within the family of the thiamine diphosphate‐dependent 2‐oxo acid dehydrogenases was analyzed by combining different methods of sequence alignment with crystallographic and enzymological studies of the family members. For the first time, the sequence similarity of the homodimeric 2‐oxoglutarate dehydrogenase to heterotetrameric 2‐oxo acid dehydrogenases is established. The presented alignment of the catalytic domains of the dehydrogenases of pyruvate, branched‐chain 2‐oxo acids and 2‐oxoglutarate unravels the sequence markers of the substrate specificity and the essential residues of the family members without the 3D structures resolved. Predicted dual substrate specificity of some of the 2‐oxo acid dehydrogenases was confirmed experimentally. The results were used to decipher functions of the two hypothetical proteins of animal genomes, OGDHL and DHTKD1, similar to the 2‐oxoglutarate dehydrogenase. Conservation of all the essential residues confirmed their catalytic competence. Sequence analysis indicated that OGDHL represents a previously unknown isoform of the 2‐oxoglutarate dehydrogenase, whereas DHTKD1 differs from the homologs at the N‐terminus and substrate binding pocket. The differences suggest changes in heterologous protein interactions and accommodation of more polar and/or bulkier structural analogs of 2‐oxoglutarate, such as 2‐oxoadipate, 2‐oxo‐4‐hydroxyglutarate, or products of the carboligase reaction between a 2‐oxodicarboxylate and glyoxylate or acetaldehyde. The signatures of the Ca2+‐binding sites were found in the Ca2+‐activated 2‐oxoglutarate dehydrogenase and OGDHL, but not in DHTKD1. Mitochondrial localization was predicted for OGDHL and DHTKD1, with DHTKD1 probably localized also to nuclei. Medical implications of the obtained results are discussed in view of the possible associations of the 2‐oxo acid dehydrogenases and DHTKD1 with neurodegeneration and cancer. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Sequence‐similar, structure‐dissimilar protein pairs in the PDB
Authors: Kosloff Mickey , Kolodny Rachel 
Published: November 2007

AbstractIt is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which “redundant” structures have been removed, based on a sequence‐based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence‐similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence‐based structural superpositions and geometry‐based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence‐based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry‐based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence‐based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry‐based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence‐similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm). Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structural disorder serves as a weak signal for intracellular protein degradation
Authors: Tompa P. , Prilusky J. , Silman I. , Sussman J. L. 
Published: November 2007

AbstractTargeted turnover of proteins is a key element in the regulation of practically all basic cellular processes. The underlying physicochemical and/or sequential signals, however, are not fully understood. This issue is particularly pertinent in light of the recent recognition that intrinsically unstructured/disordered proteins, common in eukaryotic cells, are extremely susceptible to proteolytic degradation in vitro. The in vivo half‐lives of proteins were determined recently in a high‐throughput study encompassing the entire yeast proteome; here we examine whether these half‐lives correlate with the presence of classical degradation motifs (PEST region, destruction‐box, KEN‐box, or the N‐terminal residue) or with various physicochemical characteristics, such as the size of the protein, the degree of structural disorder, or the presence of low‐complexity regions. Our principal finding is that, in general, the half‐life of a protein does not depend on the presence of degradation signals within its sequence, even of ubiquitination sites, but correlates mainly with the length of its polypeptide chain and with various measures of structural disorder. Two distinct modes of involvement of disorder in degradation are proposed. Susceptibility to degradation of longer proteins, containing larger numbers of residues in conformational disorder, suggests an extensive function, whereby the effect of disorder can be ascribed to its mere physical presence. However, after normalization for protein length, the only signal that correlates with half‐life is disorder, which indicates that it also acts in an intensive manner, that is, as a specific signal, perhaps in conjunction with the recognition of classical degradation motifs. The significance of correlation is rather low; thus protein degradation is not determined by a single characteristic, but is a multi‐factorial process that shows large protein‐to‐protein variations. Protein disorder, nevertheless, plays a key signalling role in many cases. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Protein structure mining using a structural alphabet
Authors: Tyagi M. , de Brevern A. G. , Srinivasan N. , Offmann B. 
Published: November 2007

AbstractWe present a comprehensive evaluation of a new structure mining method called PB‐ALIGN. It is based on the encoding of protein structure as 1D sequence of a combination of 16 short structural motifs or protein blocks (PBs). PBs are short motifs capable of representing most of the local structural features of a protein backbone. Using derived PB substitution matrix and simple dynamic programming algorithm, PB sequences are aligned the same way amino acid sequences to yield structure alignment. PBs are short motifs capable of representing most of the local structural features of a protein backbone. Alignment of these local features as sequence of symbols enables fast detection of structural similarities between two proteins. Ability of the method to characterize and align regions beyond regular secondary structures, for example, N and C caps of helix and loops connecting regular structures, puts it a step ahead of existing methods, which strongly rely on secondary structure elements. PB‐ALIGN achieved efficiency of 85% in extracting true fold from a large database of 7259 SCOP domains and was successful in 82% cases to identify true super‐family members. On comparison to 13 existing structure comparison/mining methods, PB‐ALIGN emerged as the best on general ability test dataset and was at par with methods like YAKUSA and CE on nontrivial test dataset. Furthermore, the proposed method performed well when compared to flexible structure alignment method like FATCAT and outperforms in processing speed (less than 45 s per database scan). This work also establishes a reliable cut‐off value for the demarcation of similar folds. It finally shows that global alignment scores of unrelated structures using PBs follow an extreme value distribution. PB‐ALIGN is freely available on web server called Protein Block Expert (PBE) athttp://bioinformatics.univ‐reunion.fr/PBE/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Binding similarity network of ligand
Authors: Park Keunwan , Kim Dongsup 
Published: November 2007

AbstractThe protein and ligand interaction takes an important part in protein function. Both ligand and its binding site are essential components for understanding how the protein–ligand complex functions. Until now, there have been many studies about protein function and evolution, but they usually lacked ligand information. Accordingly, in this study, we tried to answer the following questions: how much ligand and binding site are associated with protein function, and how ligands themselves are related to each other in terms of binding site. To answer the questions, we presented binding similarity network of ligand. Through the network analysis, we attempted to reveal systematic relationship between the ligand and binding site. The results showed that ligand binding site and function were closely related (conservation ratio, 81%). We also showed conservative tendency of function in line with ligand structure similarity with some exceptional cases. In addition, the binding similarity network of ligand revealed scale‐free property to some degree like other biological networks. Since most nodes formed highly connected cluster, a clustering coefficient was very high compared with random. All the highly connected ligands (hubs) were involved in various functions forming large cluster and tended to act as a bridge between modular clusters in the network. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Modeling ensembles of transmembrane β‐barrel proteins
Authors: Waldispühl Jérôme , O'Donnell Charles W. , Devadas Srinivas , Clote Peter , Berger Bonnie 
Published: November 2007

AbstractTransmembrane β‐barrel (TMB) proteins are embedded in the outer membrane of Gram‐negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few nonhomologous TMB structures have been determined by X‐ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane proteins. We introduce the program partiFold to investigate the folding landscape of TMBs. By computing the Boltzmann partition function, partiFold estimates inter‐β‐strand residue interaction probabilities, predicts contacts and per‐residue X‐ray crystal structure B‐values, and samples conformations from the Boltzmann low energy ensemble. This broad range of predictive capabilities is achieved using a single, parameterizable grammatical model to describe potential β‐barrel supersecondary structures, combined with a novel energy function of stacked amino acid pair statistical potentials. PartiFold outperforms existing programs for inter‐β‐strand residue contact prediction on TMB proteins, offering both higher average predictive accuracy as well as more consistent results. Moreover, the integration of these contact probabilities inside a stochastic contact map can be used to infer a more meaningful picture of the TMB folding landscape, which cannot be achieved with other methods. Partifold's predictions of B‐values are competitive with recent methods specifically designed for this problem. Finally, we show that sampling TMBs from the Boltzmann ensemble matches the X‐ray crystal structure better than single structure prediction methods. A webserver running partiFold is available at http://partiFold.csail.mit.edu/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Intrinsically disordered protein from a pathogenic mesophile Mycobacterium tuberculosis adopts structured conformation at high temperature
Authors: Kumar Niti , Shukla Swati , Kumar Sanjiv , Suryawanshi Anju , Chaudhry Uma , Ramachandran Srinivasan , Maiti Souvik 
Published: November 2007

AbstractCompared to eukaryotes, the occurrence of “intrinsically disordered” or “natively unfolded” proteins in prokaryotes has not been explored extensively. Here, we report the occurrence of an intrinsically disordered protein from the mesophilic human pathogen Mycobacterium tuberculosis. The Histidine‐tagged recombinant Rv3221c biotin‐binding protein is intrinsically disordered at ambient and physiological growth temperatures as revealed by circular dichroism and Fourier transform infrared (FTIR) spectroscopic studies. However, an increase in temperature induces a transition from disordered to structured state with a folding temperature of ≈53°C. Addition of a structure inducing solvent trifluoroethanol (TFE) causes the protein to fold at lower temperatures suggesting that TFE fosters hydrophobic interactions, which drives protein folding. Differential Scanning Calorimetry studies revealed that folding is endothermic and the transition from a disordered to structured state is continuous (higher‐order), implying existence of intermediates during folding process. Secondary structure analysis revealed that the protein has propensity to form β‐sheets. This is in conformity with FTIR spectrum that showed an absorption peak at wave number of 1636 cm−1, indicative of disordered β‐sheet conformation in the native state. These data suggest that although Rv3221c may be disordered under ambient or optimal growth temperature conditions, it has the potential to fold into ordered structure at high temperature driven by increased hydrophobic interactions. In contrast to the generally known behavior of other intrinsically disordered proteins folding at high temperature, Rv3221c does not appear to oligomerize or aggregate as revealed through numerous experiments including Congo red binding, Thioflavin T‐binding, turbidity measurements, and examining molar ellipticity as a function of protein concentration. The amino acid composition of Rv3221c reveals that it has 24% charged and 54.9% hydrophobic amino acid residues. In this respect, this protein, although belonging to the class of intrinsically disordered proteins, has distinct features. The intrinsically disordered state and the biotin‐binding feature of this protein suggest that it may participate in many biochemical processes requiring biotin as a cofactor and adopt suitable conformations upon binding other folded targets. Proteins 2008. © 2007 Wiley‐Liss, Inc.