bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis of allele variation of human thiopurine‐S‐methyltransferase
Authors: Wu Hong , Horton John R. , Battaile Kevin , Allali‐Hassani Abdellah , Martin Fernando , Zeng Hong , Loppnau Peter , Vedadi Masoud , Bochkarev Alexey , Plotnikov Alexander N. , Cheng Xiaodong 
Published: January 2007

AbstractHuman thiopurine S‐methyltransferase (TPMT) exhibits considerable person‐to‐person variation in activity to thiopurine drugs. We have produced an N‐terminal truncation of human TPMT protein, crystallized the protein in complex with the methyl donor product S‐adenosyl‐L‐homocysteine, and determined the atomic structure to the resolution of 1.58 and 1.89 Å, respectively, for the seleno‐methionine incorporated and wild type proteins. The structure of TPMT indicates that the naturally occurring amino acid polymorphisms scatter throughout the structure, and that the amino acids whose alteration have the most influence on function are those that form intra‐molecular stabilizing interactions (mainly van der Waals contacts). Furthermore, we have produced four TPMT mutant proteins containing variant alleles of TPMT*2, *3A, *3B, and *3C and examined the structure‐function relationship of the mutant proteins based on their expression and solubility in bacteria and their thermostability profile. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Indel‐based targeting of essential proteins in human pathogens that have close host orthologue(s): Discovery of selective inhibitors forLeishmania donovanielongation factor‐1α
Authors: Nandan Devki , Lopez Martin , Ban Fuqiang , Huang Meilan , Li Yvonne , Reiner Neil E. , Cherkasov Artem 
Published: January 2007

AbstractWe propose a novel strategy for selective targeting of essential pathogen proteins that contain sizable indels (insertions/deletions) in their sequences compared with their host orthologues. This approach has been tested on elongation factor‐1α (EF‐1α) from the protozoan pathogenLeishmania donovani. Leishmania EF‐1α is 82% identical to the corresponding human orthologue, but possesses a 12 aminoacid sequence deletion compared with human EF‐1α. We used this indel‐differentiated region to design small molecules that selectively bind to leishmania EF‐1α and not to the human protein. Three unrelated molecules were identified with the capacity to inhibit protein synthesis in leishmania by up to 75% while exhibiting no effect on human protein translation. These candidates may serve as prototypes for future development of antiprotozoan therapeutics. More generally, these findings provide a basis for a novel drug design platform. This platform targets essential pathogen proteins that are highly conserved across species, and consequently would not typically be considered to be conventional drug targets. We anticipate that such indel‐directed targeting of essential proteins in microbial pathogens may help address the growing problem of antibiotic resistance. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Chaperone‐mediated inhibition of tubulin self‐assembly
Authors: Mitra Gopa , Saha Abhik , Gupta Twishasri Das , Poddar Asim , Das Kali P. , Das Gupta Sujoy K. , Bhattacharyya Bhabatarak 
Published: January 2007

AbstractMolecular chaperones are known to play an important role in facilitating the proper folding of many newly synthesized proteins. Here, we have shown that chaperone proteins exhibit another unique property to inhibit tubulin self‐assembly efficiently. Chaperones tested include α‐crystallin from bovine eye lenses, HSP16.3, HSP70 from Mycobacterium tuberculosis and α s‐casein from milk. All of them inhibit polymerization in a dose‐dependent manner independent of assembly inducers used. The critical concentration of MTP polymerization increases with increasing concentration of HSP16.3. Increase in chaperone concentration lowers the extent of polymerization and increases the lag time of self‐assembly reaction. Although the addition of a chaperone at the early stage of elongation phase shows no effect on polymerization, the same concentration of chaperone inhibits polymerization completely when added before the initiation of polymerization. Bindings of HSP16.3 and α s‐casein to tubulin have been confirmed using isothermal titration calorimetry. Affinity constants of tubulin are 5.3 ×× 104 and 9.8 ×× 105 M−1 for HSP16.3 and α s‐casein, respectively. Thermodynamic parameters indicate favourable entropy and enthalpy changes for both chaperones‐tubulin interactions. Positive entropy change suggests that the interaction is hydrophobic in nature and desolvation occurring during formation of tubulin‐chaperone complex. On the basis of thermodynamic data and observations made upon addition of chaperone at early elongation phase or before the initiation of polymerization, we hypothesize that chaperones bind tubulin at the protein‐protein interaction site involved in the nucleation phase of self‐assembly. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A protein‐specifically adapted scoring function for the reranking of docking solutions
Authors: Müller Wolfgang , Sticht Heinrich 
Published: January 2007

AbstractIn this work, we developed a protein‐specifically adapted scoring function and applied it to the reranking of protein–protein docking solutions generated with a conventional docking program. The approach was validated using experimentally determined structures of the bacterial HPr–protein in complex with four structurally nonhomologous binding partners as an example. A sufficiently large data basis for the generation of protein‐specifically adapted pair potentials was generated by modeling all orthologous complexes for each type of interaction resulting in a total of 224 complexes. The parameters for potential generation were systematically varied and resulted in a total of 66,132 different scoring functions that were tested for their ability of successful reranking of 1000 docking solutions generated from modeled structures of the unbound binding partners. Parameters that proved critical for the generation of good scoring functions were the distance cutoff used for the generation of the pair potential, and an additional cutoff that allows a proper weighting of conserved and nonconserved contacts in the interface. Compared to the original scoring function, application of this novel type of scoring functions resulted in a significant accumulation of acceptable docking solutions within the first 10 ranks. Depending on the type of complex investigated one to five acceptable complex geometries are found among the 10 highest‐ranked solutions and for three of the four systems tested, an acceptable solution was placed on the first rank. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Characterization and identification of diarylheptanoids in ginger (Zingiber officinale Rosc.) using high‐performance liquid chromatography/electrospray ionization mass spectrometry
Authors: Jiang Hongliang , Timmermann Barbara N. , Gang David R. 
Published: January 2007

AbstractIn our continuing investigation of diarylheptanoids in Zingiberaceae plants using liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS/MS), 26 diarylheptanoids were identified from fresh ginger rhizome. Of the 26 compounds, 15 diarylheptanoids appear to be new compounds. In addition, the majority of these compounds (18) were acetylated, which is different from our investigation of diarylheptanoids from turmeric, another member of the Zingiberaceae, which did not possess any acetylated diarylheptanoids. In all, five distinct groups (homologous series) of diarylheptanoids were found in extracts from ginger rhizome. These groups were differentiated by structural differences on the heptane skeletons, whereas homologs within each group differed by substitution patterns on the aromatic rings. Diagnostic fragmentation behavior in (+)‐ and (−)ESI‐MS/MS analyses for each group of homologs, as well as information regarding polarity obtained from retention time data, allowed us to classify compounds by group and identify them based on key structural features. Copyright © 2007 John Wiley & Sons, Ltd.
Estimating risk of breast cancer in carriers of BRCA1 and BRCA2 mutations: a meta‐analytic approach
Authors: Fu Rongwei , Harris Emily L. , Helfand Mark , Nelson Heidi D. 
Published: January 2007

AbstractEstimates of penetrance (or risk) of breast cancer among BRCA mutation carriers in published studies are heterogeneous, prohibiting direct combined estimates. Estimates of prevalence of BRCA mutations are more homogeneous and could allow combined estimates of prevalence. We propose a combined estimator of penetrance from combined estimates of the prevalence of BRCA mutations in women with and without breast cancer and from the probability of breast cancer by using Bayes' Theorem. The relative risk of having breast cancer with positive family history and the prevalence of positive family history contribute to the combined estimate of penetrance if family history is present. The combined estimate incorporates variation in estimates from different resources. The method is illustrated by using data from Ashkenazi Jewish women unselected for family history and for those with family history. Risks of breast cancer conferred by BRCA1 and BRCA2 mutations are estimated to be 8.39 per cent (6.56, 10.68 per cent) and 2.66 per cent (1.85, 3.82 per cent) by 40 years old, and 47.45 per cent (37.39, 57.72 per cent) and 31.85 per cent (23.72, 41.26 per cent) by 75 years old, respectively. For those with family history, risks of breast cancer conferred by BRCA mutations appear to be higher. Copyright © 2007 John Wiley & Sons, Ltd.
Enhanced neural differentiation of neural stem cells and neurite growth by amniotic epithelial cell co‐culture
Authors: Meng Xiao‐ting , Chen Dong , Dong Zhi‐yong , Liu Jia‐mei 
Published: January 2007

AbstractAmniotic epithelial cells (AECs) were reported to show a neuroprotective effect on neurons, but there was no direct evidence for a functional relationship between neural stem cells (NSCs) and AECs. The aim of this study was to determine whether AECs could stimulate differentiation and expand neurogenesis of NSCs, and whether the roles were due to a diffusible factor or required direct cell‐cell contact. AECs were isolated from rat amnion on E14–16 and NSCs were isolated from neocortical tissue. The growth and differentiation of NSCs were compared under different conditions. The results showed that NSCs cultured with FGF‐2 proliferated and formed floating neurospheres while those grown in B27 without FGF‐2 failed to thrive. Those grown either with AEC conditioned medium or in transwells showed significantly improved survival. Moreover, the neural differentiation and length of neurite were greater in exogenous FGF groups when NSCs were allowed direct contact with AECs. Western blotting, immunocytochemistry and RT‐PCR indicated that rat AECs could secrete NT‐3 and BDNF. Furthermore, the presence of FGF‐2 enhanced the function of AECs. These findings identified that AECs may be regarded as a critical component of NSCs niche and suggested that direct cell‐to‐cell contact may provide additional and independent support. Such information would circumvent the need for AECs‐NSCs co‐culture and could potentially facilitate the production of neurons for future clinical applications.
Enrichment of epidermal stem cells by rapid adherence and analysis of the reciprocal interaction of epidermal stem cells with neighboring cells using an organotypic system
Authors: Dong Rui , Liu Xiaoliang , Liu Yuan , Deng Zhihong , Nie Xin , Wang Xinwen , Jin Yan 
Published: January 2007

AbstractKeratinocytes have the ability to adhere to extracellular matrix rapidly. With this in mind, in this study we isolated keratinocytes known as rapidly adhering (RA) cells. To compare epidermal regenerative abilities, skin substitutes were reconstructed by adding keratinocytes or RA cells to two groups of bioengineered dermis made by fibroblasts and hair follicle dermal cells respectively. After transplantation, the results illustrated that the skin substitutes including RA cells were integrated into the host tissue. Furthermore, with hair follicle dermal cells’ influences, the RA cells could form structures very similar to normal hair follicles. These results indicate that RA cells are predominately comprised of epidermal stem cells. The results also demonstrated that besides the reciprocal interaction of epidermal stem cells with dermal cells, the interaction of epidermal stem cells with keratinocytes were critical in epidermis morphogenesis and self‐renewal, and application of RA cells could optimize engineering of skin substitutes.
Detection of potassium currents and regulation of multidrug resistance by potassium channels in human gastric cancer cells
Authors: Han Ying , Shi Yongquan , Han Zheyi , Sun Li , Fan Daiming 
Published: January 2007

AbstractThe present study aimed to investigate the potassium currents and further explore the role of potassium channels in drug response of gastric cancer cells. By patch‐clamp technique, potassium currents of human gastric cancer cell SGC7901 were recorded in the mode of voltage clamp. Both 4‐aminopyridine (4‐AP) and tetraethylammonium (TEA) could almost completely block this current. The chemotherapeutic drugs, adriamycin or 5‐fluorouracil could significantly increase the K+ current density on SGC7901 cells in a dose‐dependent manner. 4‐AP or TEA was found to restrain adriamycin‐induced apoptosis and enhance multidrug‐resistant phenotype of SGC7901 cells. Up‐regulation of Kv1.5, which has been found widely expressed in gastric cancer cells including SGC7901, increased the K+ current density and sensitivity of SGC7901 cells to multiple chemotherapeutic drugs, whereas down‐regulation of Kv1.5 enhanced the drug‐resistant phenotype of SGC7901 cells. In conclusion, potassium channels may exert regulatory effects on multidrug resistance by regulating drug‐induced apoptosis in gastric cancer cells.
Long interstitial (TTAGGG)n arrays do not colocalize with repressive chromatin modifications in Chinese hamster cells
Authors: Svetlova M.P. , Solovjeva L.V. , Smirnova A.N. , Tomilin N.V. 
Published: January 2007

AbstractInterstitial tandem (TTAGGG)n repeats (ITRs) in Chinese hamster (CH) cells are mostly arranged into the long (>100 kb) continuous pericentric arrays which do not contain HindIII sites (Faravelli M, Azzalin CM, Bertoni L, Chernova O, Attolini C, Mondello C, et al. Molecular organization of internal telomeric sequences in Chinese hamster chromosomes, Gene 2002;283,11–16), are free of protein‐coding genes, and can formally be classified as heterochromatin. ITRs dynamically interact with (TTAGGG)n‐binding protein TRF1 and can be visualized using Green Fluorescent Protein (GFP)‐tagged TRF1. Here we examined whether mobility of GFP‐TRF1 associated with ITRs in CH cells is affected by inhibitors of transcription and whether ITRs colocalize with known repressive chromatin modifications hallmarked by histone H3 trimethylated at lysine‐9 (H3K9m3) or lysine‐27 (H3K27m3). We found that GFP‐TRF1 bodies do not colocalize in the nuclei of V79 cells with H3K9m3 or H3K27m3 indicating that ITRs do not represent typical constitutive or facultative heterochromatin. Mobility of ITR‐bound GFP‐TRF1 is suppressed by inhibitors of transcription consistent with the view that TRF1 is exchanged during transcription of ITRs. However, GFP‐TRF1 bodies do not colocalize with nuclear hubs of intensive transcription detected through in vivo incorporation of 5‐bromouridine triphosphate. Using real‐time PCR, we also examined transcription of unique sequences adjacent to (TTAGGG)n arrays in CH genome and found that they are transcribed, indicating that these arrays do not generally inhibit transcription in cis. Together, our results suggest that ITRs represent a special kind of moderately transcribed heterochromatin which possible function remains to be established.
Changes in composition and activities of 26S proteasomes under the action of doxorubicin—apoptosis inductor of erythroleukemic K562 cells
Authors: Tsimokha Anna S. , Mittenberg Alexey G. , Kulichkova Valentina A. , Kozhukharova Irina V. , Gause Larisa N. , Konstantinova Irina M. 
Published: January 2007

AbstractChanges in the subunit composition, phosphorylation of the subunits, and regulation of the activities of 26S proteasomes in proliferating cells undergoing programmed cell death have not been studied so far. Moreover, there are no reports on phosphorylation of proteasome subunits both in normal and in neoplastic cells during apoptosis. The data of the present study show for the first time that apoptosis inductor doxorubicin regulates subunit composition, enzymatic activities, and phosphorylation state of 26S proteasomes in neoplastic (proerythroleukemic K562) cells or, in other words, induces reprogramming of proteasome population. Furthermore, the phosphorylation state of proteasomes is found to be the mechanism controlling specificity of proteasomal proteolytic and endoribonuclease activities.
Phosphoinositide 3‐kinase inhibitor LY294002 but not serum withdrawal suppresses proliferation of murine embryonic stem cells
Authors: Lianguzova Maria S. , Chuykin Ilia A. , Nordheim Alfred , Pospelov Valery A. 
Published: January 2007

AbstractMouse embryonic stem (mES) cells have short duration of their cell cycle and are capable of proliferating in the absence of growth factors. To find out which signaling pathways contribute to the regulation of the mES cell cycle, we used pharmacological inhibitors of MAP and PI3 kinase cascades. The MAP kinase inhibitors as well as serum withdrawal did not affect mES cell cycle distribution, whereas the inhibitor of PI3K activity, LY294002, induced accumulation of cells in G1 phase followed by apoptotic cell death. Serum withdrawal also causes apoptosis, but it does not change the content and activity of cell cycle regulators. In contrast, in mES cells treated with LY294002, the activities of Cdk2 and E2F were significantly decreased. Interestingly, LY294002 had a much stronger effect on cell cycle distribution in low serum conditions, implying that serum can promote G1 → S transition of mES cells by a LY294002‐resistant mechanism. Thus, proliferation of mES cells is maintained by at least two separate mechanisms: a LY294002‐sensitive pathway, which is active even in the absence of serum, and LY294002‐resistant, but serum‐dependent, pathway.
Extra‐cellular matrix proteins induce re‐distribution of α‐actinin‐1 and α‐actinin‐4 in A431 cells
Authors: Bolshakova Anastasia , Petukhova Olga , Turoverova Lidia , Tentler Dmitri , Babakov Vladimir , Magnusson Karl‐Eric , Pinaev George 
Published: January 2007

AbstractAlpha‐actinins are actin‐binding proteins of non‐muscle cells, which can participate in the regulation of transcription factor activity. We describe the distribution of α‐actinin‐1 and −4 depending on different actin cytoskeleton formed as a result of cell adhesion to extracellular matrix proteins, such as fibronectin and laminin 2/4. Immunofluorescent studies show a difference in the distribution of α‐actinin and −4. Both isoforms localise along stress‐fibres, but α‐actinin‐1 localises in the perinuclear region more abundantly than α‐actinin‐4. Western blot analysis demonstrated existence of truncated forms of both isoforms. Truncated α‐actinin‐1 appears in cells spread on fibronectin or laminin. Cell spreading also correlated with more tight association of α‐actinin‐4 with chromatin. Basing on our previous finding of an interaction of α‐actinin‐4 with p65 subunit of the NF‐κB, we checked the possible influence of immobilised ligands on its redistribution in nuclear complexes containing p65. α‐Actinin‐4 seems to be present in some but not all nuclear complexes containing p65. Immobilised ligands may affect the interaction of α‐actinin‐4/p65 complexes with chromatin. The data suggest that adhesion to extra‐cellular matrix may interfere in cellular reactions mediated by α‐actinin‐1 and −4.
Different disturbances—one pathway of protein unfolding. Actin folding‐unfolding and misfolding
Authors: Povarova Olga I. , Kuznetsova Irina M. , Turoverov Konstantin K. 
Published: January 2007

AbstractThis review summarizes the results of our investigations of actin unfolding‐refolding and presents the notion that protein unfolding pathway, the number and the appearance order of intermediate states do not dependent on denaturing agents. To place our concept in the context of current knowledge of protein folding, we review in brief the development of general ideas of protein folding mechanisms, paying special attention to some key points of this process. Thus we focus on the characteristics of amino acid sequences that provide the existence of protein native structure, and on the interactions that compensate the increase of free energy due to the decrease of entropy on the way from multitude unfolded conformations to unique native state. In particular, we emphasize that ordered structures can arise both due to intramolecular and intermolecular interactions which lead to the formation of native and misfolded (associates, amorphous aggregates amyloid and amyloid‐like fibrils) states, respectively.
Caldesmon inhibits both force development and transition of actin monomers from “OFF” to “ON” conformational state by changing its position in thin filaments
Authors: Pronina Olga E. , Makuch Robert , Wrzosek Antoni , Dąbrowska Renata , Borovikov Yurii S. 
Published: January 2007

AbstractWe have investigated the effect of caldesmon on the actin conformational state and its position at force generation in glycerinated fibers upon transformation from relaxation to rigor. F‐actin and caldesmon were labeled with TRITC‐phalloidin or acrylodan, respectively, and the orientation and mobility of the probes were calculated. Transition from relaxation to rigor was accompanied by force development and by the changes in orientation and mobility of TRITC‐phalloidin that were typical for actin monomer transformation from the “OFF” to the “ON” conformational state. In the presence of caldesmon, both the force developed by the fibers and the changes in the orientation and mobility of TRITC‐phalloidin were markedly decreased. In contrast, the orientation and mobility of acrylodan change essentially showed the displacement of the caldesmon molecules and the changes in its mobility. The results are evidence that structure and/or mode of the attachment of caldesmon to actin modulates both the force production and transition of actin monomers from “OFF” to “ON” conformations in the ATPase cycle.