bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation and Structural Characterization of Mono‐Ru‐Substituted α2‐Dawson‐Type Phosphotungstate with a Carbonyl Ligand and Other Ru(CO)‐Substituted Heteropolytungstates
Authors: Nishiki Kensuke , Ota Hiromi , Ogo Shuhei , Sano Tsuneji , Sadakane Masahiro 
Published: May 2015

AbstractIn our previous article (Dalton Trans. 2008, 6692–6698) we reported that hydrothermal reaction of a mono‐lacunary Keggin‐type silicotungstate, [SiW11O39]8–, and Ru(acac)3 (acac: acetylacetonate) for 5–24 h produced a mono‐Ru‐substituted Keggin‐type silicotungstate with a terminal aqua ligand, [SiW11O39RuIII(H2O)]5–, which was further converted into a carbonyl (CO) derivative, [SiW11O39RuII(CO)]6–, by increasing the reaction time for several days. Here, reactions of Ru(acac)3 with other mono‐lacunary heteropolytungstates for the formation of other mono‐Ru(CO)‐substituted heteropolytungstates, including Keggin derivatives, [GeW11O39RuII(CO)]6– and [PW11O39RuII(CO)]5–, and Dawson‐type phosphotungstates, [α1‐P2W17O61RuII(CO)]8– and [α2‐P2W17O61RuII(CO)]8–, are presented. The desired α2‐isomer of Dawson‐type phosphotungstate, [α2‐P2W17O61RuII(CO)]8–, was produced in high purity and was fully characterized by CV, 31P NMR, 13C NMR, IR, UV/Vis, elemental analysis, mass spectroscopy, TG‐DTA, TPD‐MS, and single‐crystal structure analysis. On the other hand, Keggin‐type complexes, [GeW11O39RuII(CO)]6– and [PW11O39RuII(CO)]5–, were formed together with their aqua derivatives, [GeW11O39RuIII(H2O)]5– and [PW11O39RuIII(H2O)]4–, respectively, and the α1‐isomer of Dawson‐type phosphotungstate, [α1‐P2W17O61RuII(CO)]8–, was produced together with the α2‐derivative, as confirmed by CV, IR, mass spectroscopy, and 31P NMR spectroscopy.
Cooperative and alternate functions for STIM1 and STIM2 in macrophage activation and in the context of inflammation
Authors: Sogkas Georgios , Stegner David , Syed Shahzad N. , Vögtle Timo , Rau Eduard , Gewecke Britta , Schmidt Reinhold E. , Nieswandt Bernhard , Gessner Johannes Engelbert 
Published: May 2015

AbstractCalcium (Ca2+) signaling in immune cells, including macrophages, controls a wide range of effector functions that are critical for host defense and contribute to inflammation and autoimmune diseases. However, receptor‐mediated Ca2+ responses consist of complex mechanisms that make it difficult to identify the pathogenesis and develop therapy. Previous studies have revealed the importance of the Ca2+ sensor STIM1 and store‐operated Ca2+‐entry (SOCE) for Fcγ‐receptor activation and IgG‐induced inflammation. Here, we identify the closely related STIM2 as mediator of cell migration and cytokine production downstream of GPCR and TLR4 activation in macrophages and show that mice lacking STIM2 are partially resistant to inflammatory responses in peritonitis and LPS‐induced inflammation. Interestingly, STIM2 modulates the migratory behavior of macrophages independent from STIM1 and without a strict requirement for Ca2+ influx. While STIM2 also contributes in part to FcγR activation, the C5a‐induced amplification of IgG‐mediated phagocytosis is mainly dependent on STIM1. Blockade of STIM‐related functions limits mortality in experimental models of AIHA and LPS‐sepsis in normal mice. These results suggest benefits of Ca2+‐inhibition for suppression of exacerbated immune reactions and illustrate the significance of alternate functions of STIM proteins in macrophage activation and in the context of innate immune inflammation.
Novel organic dyes for multicolor localization‐based super‐resolution microscopy
Authors: Lehmann Martin , Lichtner Gregor , Klenz Haider , Schmoranzer Jan 
Published: May 2015

Precise multicolor single molecule localization‐based microscopy (SMLM) requires bright probes with compatible photo‐chemical and spectral properties to resolve distinct molecular species at the nanoscale. The accuracy of multicolor SMLM is further challenged by color channel crosstalk and chromatic alignment errors. These constrains limit the applicability of known reversibly switchable organic dyes for optimized multicolor SMLM. Here, we tested 28 commercially available dyes for their suitability to super‐resolve a known cellular nanostructure. We identified eight novel dyes in different spectral regimes that enable high quality dSTORM imaging. Among those, the spectrally close dyes CF647 and CF680 comprise an optimal dye pair for spectral demixing‐based, registration free multicolor dSTORM with low crosstalk. Combining this dye pair with the separately excited CF568 we performed 3‐color dSTORM to image the relative nanoscale distribution of components of the endocytic machinery and the cytoskeleton.
A major limitation of multicolor single molecule localization based super‐resolution microscopy (SMLM) is the availability of suitable photo‐switchable fluorescent dyes. By screening 28 commercially available dyes, novel dyes in different spectral regimes were identified that are well suited for dual and triple color SMLM with low crosstalk. These novel dyes are employed to image the relative nanoscale distribution of sub‐cellular components.magnified imageA major limitation of multicolor single molecule localization based super‐resolution microscopy (SMLM) is the availability of suitable photo‐switchable fluorescent dyes. By screening 28 commercially available dyes, novel dyes in different spectral regimes were identified that are well suited for dual and triple color SMLM with low crosstalk. These novel dyes are employed to image the relative nanoscale distribution of sub‐cellular components.
The Epigenetic Regulation of the Opioid System: New Individualized Prompt Prevention and Treatment Strategies
Authors: Muñoa Iraia , Urizar Itziar , Casis Luis , Irazusta Jon , Subirán Nerea 
Published: May 2015

ABSTRACTThe most well‐known physiological effect associated with opiod system is their efficacy in pain reduction or analgesia, although their effect on a variety of other physiological and physiophological functions has become apparent in recent years. This review is an attempt to clarify in more detail the epigenetic regulation of opioid system to understand with more precision their transcriptional and posttranscriptional regulation in multiple pyisiological and pharmacological contexts. The opioid receptors show an epigenetic regulation and opioid peptide precursors by methylation, chromatin remodeling and microRNA. Although the opioid receptor promoters have similarity between them, they use different epigenetic regulation forms and they exhibit different pattern of expression during the cell differentiation. DNA methylation is also confirmed in opioid peptide precursors, being important for gene expression and tissue specificity. Understanding the epigenetic basis of those physiological and physiopathological procesess is essential for the development of individualized prompt prevention and treatment strategies. J. Cell. Biochem. 116: 2419–2426, 2015. © 2015 Wiley Periodicals, Inc.
Tumor Necrosis Factor Related Apoptosis Inducing Ligand (Trail) in Endothelial Response to Biomechanical and Biochemical Stresses in Arteries
Authors: D'Auria F , Centurione L , Centurione MA , Angelini A , Di Pietro R 
Published: May 2015

ABSTRACTShear stress is determined by three physical components described in a famous triad: blood flow, blood viscosity and vessel geometry. Through the direct action on endothelium, shear stress is able to radically interfere with endothelial properties and the physiology of the vascular wall. Endothelial cells (ECs) have also to sustain biochemical stresses represented by chemokines, growth factors, cytokines, complement, hormones, nitric oxide (NO), oxygen and reactive oxygen species (ROS). Many growth factors, cytokines, chemokines, hormones, and chemical substances, like NO, act and regulate endothelium functions and homeostasis. Among these cytokines Tumor Necrosis Factor Related Apoptosis Inducing Ligand (TRAIL) has been assigned a regulatory role in ECs physiology and physiopathology. Thus, the aim of this review is to provide a general overview of the endothelial response pathways after different types of biomechanical and biochemical stress in in vitro models and to analyze the crucial role of TRAIL under pathological conditions of the cardiocirculatory system like atherosclerosis, coronary artery disease, and diabetes. J. Cell. Biochem. 116: 2427–2434, 2015. © 2015 Wiley Periodicals, Inc.
Outcome of vulvar reconstruction by anterolateral thigh flap in patients with advanced and recurrent vulvar malignancy
Authors: Zhang Wei , Zeng Ang , Yang Jiaxin , Cao Dongyan , Huang Huifang , Wang Xiaojun , You Yan , Chen Jie , Lang Jinghe , Shen Keng 
Published: May 2015

BackgroundTo evaluate the outcomes of vulvar reconstruction using anterolateral thigh (ALT) flaps in patients with advanced and recurrent vulvar malignancies.MethodsTotally 24 patients who received ALT‐based vulvar reconstruction were retrospectively reviewed to evaluate the outcome focusing on quality of life and prognosis.ResultsFour patients received vulvar reconstruction at the time of primary surgery due to advanced stage, and 20 patients underwent vulvar reconstruction after recurrence. No patient experienced complete flap loss. Major complications happened in five patients (20.83%). Minor complications occurred in three patients (12.5%). All wounds healed favorable after appropriate treatment. The mean scale of verbal rating scale (VRS‐4) was 1.58 before reconstruction while decreased to 0.13 after surgery (P < 0.0001). Mean performance status was 1.67 before surgery compared to 0.13 after surgery (P < 0.0001). Fourteen patients (58.33%) developed recurrence with a median interval of recurrence of 5 months after vulvar reconstruction. Ten patients (41.67%) are living with disease free in a median follow‐up of 19.5 months. Overall 5 years survival was 56.4%.ConclusionALT flap based vulvar reconstruction method can improve the quality of life and might be considered as an appropriate option for reconstructing the vulvar defects in patients with advanced or recurrent vulvar malignancy. J. Surg. Oncol. 2015 111:985–991. © 2015 Wiley Periodicals, Inc.
Nonspecific yet decisive: Ubiquitination can affect the native‐state dynamics of the modified protein
Authors: Gavrilov Yulian , Hagai Tzachi , Levy Yaakov 
Published: May 2015

AbstractUbiquitination is one of the most common post‐translational modifications of proteins, and mediates regulated protein degradation among other cellular processes. A fundamental question regarding the mechanism of protein ubiquitination is whether and how ubiquitin affects the biophysical nature of the modified protein. For some systems, it was shown that the position of ubiquitin within the attachment site is quite flexible and ubiquitin does not specifically interact with its substrate. Nevertheless, it was revealed that polyubiquitination can decrease the thermal stability of the modified protein in a site‐specific manner because of alterations of the thermodynamic properties of the folded and unfolded states. In this study, we used detailed atomistic simulations to focus on the molecular effects of ubiquitination on the native structure of the modified protein. As a model, we used Ubc7, which is an E2 enzyme whose in vivo ubiquitination process is well characterized and known to lead to degradation. We found that, despite the lack of specific direct interactions between the ubiquitin moiety and Ubc7, ubiquitination decreases the conformational flexibility of certain regions of the substrate Ubc7 protein, which reduces its entropy and thus destabilizes it. The strongest destabilizing effect was observed for systems in which Lys48‐linked tetra‐ubiquitin was attached to sites used for in vivo degradation. These results reveal how changes in the configurational entropy of the folded state may modulate the stability of the protein's native state. Overall, our results imply that ubiquitination can modify the biophysical properties of the attached protein in the folded state and that, in some proteins, different ubiquitination sites will lead to different biophysical outcomes. We propose that this destabilizing effect of polyubiquitin on the substrate is linked to the functions carried out by the modification, and in particular, regulatory control of protein half‐life through proteasomal degradation.
ChSeq: A database of chameleon sequences
Authors: Li Wenlin , Kinch Lisa N. , Karplus P. Andrew , Grishin Nick V. 
Published: May 2015

AbstractChameleon sequences (ChSeqs) refer to sequence strings of identical amino acids that can adopt different conformations in protein structures. Researchers have detected and studied ChSeqs to understand the interplay between local and global interactions in protein structure formation. The different secondary structures adopted by one ChSeq challenge sequence‐based secondary structure predictors. With increasing numbers of available Protein Data Bank structures, we here identify a large set of ChSeqs ranging from 6 to 10 residues in length. The homologous ChSeqs discovered highlight the structural plasticity involved in biological function. When compared with previous studies, the set of unrelated ChSeqs found represents an about 20‐fold increase in the number of detected sequences, as well as an increase in the longest ChSeq length from 8 to 10 residues. We applied secondary structure predictors on our ChSeqs and found that methods based on a sequence profile outperformed methods based on a single sequence. For the unrelated ChSeqs, the evolutionary information provided by the sequence profile typically allows successful prediction of the prevailing secondary structure adopted in each protein family. Our dataset will facilitate future studies of ChSeqs, as well as interpretations of the interplay between local and nonlocal interactions. A user‐friendly web interface for this ChSeq database is available at prodata.swmed.edu/chseq.
Chemical ligation of the influenza M2 protein for solid‐state NMR characterization of the cytoplasmic domain
Authors: Kwon Byungsu , Tietze Daniel , White Paul B. , Liao Shu Y. , Hong Mei 
Published: May 2015

AbstractSolid‐state NMR‐based structure determination of membrane proteins and large protein complexes faces the challenge of limited spectral resolution when the proteins are uniformly 13C‐labeled. A strategy to meet this challenge is chemical ligation combined with site‐specific or segmental labeling. While chemical ligation has been adopted in NMR studies of water‐soluble proteins, it has not been demonstrated for membrane proteins. Here we show chemical ligation of the influenza M2 protein, which contains a transmembrane (TM) domain and two extra‐membrane domains. The cytoplasmic domain, which contains an amphipathic helix (AH) and a cytoplasmic tail, is important for regulating virus assembly, virus budding, and the proton channel activity. A recent study of uniformly 13C‐labeled full‐length M2 by spectral simulation suggested that the cytoplasmic tail is unstructured. To further test this hypothesis, we conducted native chemical ligation of the TM segment and part of the cytoplasmic domain. Solid‐phase peptide synthesis of the two segments allowed several residues to be labeled in each segment. The post‐AH cytoplasmic residues exhibit random‐coil chemical shifts, low bond order parameters, and a surface‐bound location, thus indicating that this domain is a dynamic random coil on the membrane surface. Interestingly, the protein spectra are similar between a model membrane and a virus‐mimetic membrane, indicating that the structure and dynamics of the post‐AH segment is insensitive to the lipid composition. This chemical ligation approach is generally applicable to medium‐sized membrane proteins to provide site‐specific structural constraints, which complement the information obtained from uniformly 13C, 15N‐labeled proteins.
A comparison of pathway‐independent and pathway‐dependent methods in the calculation of conformational free enthalpy differences
Authors: Lin Zhixiong , van Gunsteren Wilfred F. 
Published: May 2015

AbstractThe multistep umbrella sampling method, which belongs to pathway‐dependent methods to calculate conformational free enthalpy differences, is used to calculate the free enthalpy difference between a right‐handed 2.710/12‐helix and a left‐handed 314‐helix of a hexa‐β‐peptide in methanol solution. The same conformational free enthalpy difference was previously investigated using pathway‐independent methods such as direct counting and enveloping distribution sampling. Our results show that the pathway‐dependent simulations are sensitive to the choice of the pathway and its parameter values. A pathway based on restraining distances of hydrogen‐bonding atom pairs shows poor sampling for two different values of the restraining force constant. Another pathway based on restraining backbone dihedral angles did smoothly sample the transition between the two helical conformations, but only with a proper choice of the restraining force constant. The results illustrate that if, and only if, a proper pathway and proper parameters are chosen, the multistep umbrella sampling can be almost 50 times more efficient than the pathway‐independent methods in this case. The analysis illustrates the advantages and pitfalls of the much used multistep umbrella sampling methodology.
Marginally hydrophobic transmembrane α‐helices shaping membrane protein folding
Authors: De Marothy Minttu T. , Elofsson Arne 
Published: May 2015

AbstractCells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices—implying a dynamic relationship between membrane proteins and their environment.
Molecular mechanisms of transcriptional control by Rev‐erbα: An energetic foundation for reconciling structure and binding with biological function
Authors: Vaissière Anaïs , Berger Sylvie , Harrus Deborah , Dacquet Catherine , Le Maire Albane , Boutin Jean A. , Ferry Gilles , Royer Catherine A. 
Published: May 2015

AbstractRev‐erbα and β are nuclear receptors that function as transcriptional repressors of genes involved in regulating circadian rhythms, glucose, and cholesterol metabolism and the inflammatory response. Given these key functions, Rev‐erbs are important drug targets for treatment of a number of human pathologies, including cancer, heart disease, and type II diabetes. Transcriptional repression by the Rev‐erbs involves direct competition with transcriptional activators for target sites, but also recruitment by the Rev‐erbs of the NCoR corepressor protein. Interestingly, Rev‐erbs do not appear to interact functionally with a very similar corepressor, Smrt. Transcriptional repression by Rev‐erbs is thought to occur in response to the binding of heme, although structural, and ligand binding studies in vitro show that heme and corepressor binding are antagonistic. We carried out systematic studies of the ligand and corepressor interactions to address the molecular basis for corepressor specificity and the energetic consequences of ligand binding using a variety of biophysical approaches. Highly quantitative fluorescence anisotropy assays in competition mode revealed that the Rev‐erb specificity for the NCoR corepressor lies in the first two residues of the β‐strand in Interaction Domain 1 of NCoR. Our studies confirmed and quantitated the strong antagonism of heme and corepressor binding and significant stabilization of the corepressor complex by a synthetic ligand in vitro. We propose a model which reconciles the contradictory observations concerning the effects of heme binding in vitro and in live cells.
Structures of potent anticancer compounds bound to tubulin
Authors: McNamara Dan E. , Senese Silvia , Yeates Todd O. , Torres Jorge Z. 
Published: May 2015

AbstractSmall molecules that bind to tubulin exert powerful effects on cell division and apoptosis (programmed cell death). Cell‐based high‐throughput screening combined with chemo/bioinformatic and biochemical analyses recently revealed a novel compound MI‐181 as a potent mitotic inhibitor with heightened activity towards melanomas. MI‐181 causes tubulin depolymerization, activates the spindle assembly checkpoint arresting cells in mitosis, and induces apoptotic cell death. C2 is an unrelated compound previously shown to have lethal effects on microtubules in tumorigenic cell lines. We report 2.60 Å and 3.75 Å resolution structures of MI‐181 and C2, respectively, bound to a ternary complex of αβ‐tubulin, the tubulin‐binding protein stathmin, and tubulin tyrosine ligase. In the first of these structures, our crystallographic results reveal a unique binding mode for MI‐181 extending unusually deep into the well‐studied colchicine‐binding site on β‐tubulin. In the second structure the C2 compound occupies the colchicine‐binding site on β‐tubulin with two chemical moieties recapitulating contacts made by colchicine, in combination with another system of atomic contacts. These insights reveal the source of the observed effects of MI‐181 and C2 on microtubules, mitosis, and cultured cancer cell lines. The structural details of the interaction between tubulin and the described compounds may guide the development of improved derivative compounds as therapeutic candidates or molecular probes to study cancer cell division.