bluuebunny/crossref_metadata_2025_split huggingface dataset:
pH‐dependent molecular dynamics of vesicular stomatitis virus glycoprotein G
Authors: Rücker Pia , Wieninger Silke A. , Ullmann G. Matthias , Sticht Heinrich 
Published: February 2013

AbstractVesicular stomatitis virus glycoprotein G (VSV‐G) belongs to a new class of viral fusion proteins (Class III). The structure of VSV‐G has been solved in two different conformations and fusion is known to be triggered by low pH. To investigate Class III fusion mechanisms, molecular dynamics simulations were performed on the VSV‐G prefusion structure in two different protonation states: at physiological pH (pH 7) and low pH present in the endosome (pH 5). Domain IV containing the fusion loops, which need to interact with the target membrane, exhibits the highest mobility. Energetic analyses revealed weakened interaction between Domain IV and the protein core at pH 5, which can be attributed to two pairs of structurally neighboring conserved and differentially protonated residues in the Domain IV–core interface. Energetic calculations also demonstrated that the interaction between the subunits in the core of the trimeric VSV‐G is strengthened at pH 5, mainly due to newly formed interactions between the C‐terminal loop of Domain II and the N‐terminus of the adjacent subunit. A pair of interacting residues in this interface that is affected by differential protonation was shown to be the main effectors of this phenomenon. The results of this study thus enhance the mechanistic understanding of the effects of protonation changes in VSV‐G. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Shape evolution with temperature of a thermotolerant protein (PeaT1) in solution detected by small angle X‐ray scattering
Authors: Xing Xueqing , Liu Quan , Wang Wei , Zhang Kunhao , Li Tang , Cai Quan , Mo Guang , Cheng Weidong , Wang Dehong , Gong Yu , Chen Zhongjun , Qiu Dewen , Wu Zhonghua 
Published: February 2013

AbstractThe protein elicitor from Alternaria tenuissima (PeaT1) presented excellent thermotolerance and potential application in agriculture as a pesticide. Previous synchrotron radiation circular dichroism study demonstrated that the secondary structures in PeaT1 protein are reversible with temperature change. To further clarify the mechanism of its thermotolerance, synchrotron radiation small angle x‐ray scattering (SAXS) technique was used to study the shape change of PeaT1 protein with temperature in this article. Ab initio structure restorations based on the SAXS data revealed that PeaT1 protein has a prolate shape with a P2 symmetry axis along the prolate anisometric direction. With temperature increase, a gooseneck vase‐like (25°C), to jug‐like (55°C), then to oval (85°C) shape change can be found, and these shape changes are also approximately reversible with temperature decrease. PeaT1 protein contains two homogenous molecules, and each of them consists of F, NAC, T, and UBA domains. The structures of the four domains were predicted. Simulated annealing algorithm was used to superimpose the domain structures onto the SAXS shapes. It was found that all the structural domains have position rotation and translation with temperature change, but the NAC domains are relatively stable, playing a role of frame. This shape change information provides clues for further exploring its biological function and application. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity‐creating mutations
Authors: Roche Julien , Caro Jose A. , Dellarole Mariano , Guca Ewelina , Royer Catherine A. , García‐Moreno E. Bertrand , Garcia Angel E. , Roumestand Christian 
Published: February 2013

AbstractThe effects of cavity‐creating mutations on the structural flexibility, local and global stability, and dynamics of the folded state of staphylococcal nuclease (SNase) were examined with NMR spectroscopy, MD simulations, H/D exchange, and pressure perturbation. Effects on global thermodynamic stability correlated well with the number of heavy atoms in the vicinity of the mutated residue. Variants with substitutions in the C‐terminal domain and the interface between α and β subdomains showed large amide chemical shift variations relative to the parent protein, moderate, widespread, and compensatory perturbations of the H/D protection factors and increased local dynamics on a nanosecond time scale. The pressure sensitivity of the folded states of these variants was similar to that of the parent protein. Such observations point to the capacity of the folded proteins to adjust to packing defects in these regions. In contrast, cavity creation in the β‐barrel subdomain led to minimal perturbation of the structure of the folded state, However, significant pressure dependence of the native state amide resonances, along with strong effects on native state H/D exchange are consistent with increased probability of population of excited state(s) for these variants. Such contrasted responses to the creation of cavities could not be anticipated from global thermodynamic stability or crystal structures; they depend on the local structural and energetic context of the substitutions. © 2012 Wiley Periodicals, Inc.
High resolution crystal structure of dengue‐3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition
Authors: Elahi Montasir , Islam Monirul M. , Noguchi Keiichi , Yohda Masafumi , Kuroda Yutaka 
Published: February 2013

AbstractDengue viruses are classified into four serotypes. Here, we report a 1.7 Å crystal structure of a recombinant dengue‐3 envelope protein domain III (ED3), which contains most of the putative epitopes. Although the fold was well conserved, we found that a local backbone deformation in the first β‐strand, which contains the putative epitope‐1, occurred upon domain isolation. Furthermore, a comparison with dengue‐2 ED3 indicated a large structural change by as much as 4.0 Å at Asp662, located in epitope‐2. These minute structural and surface properties changes observed in the high resolution ED3 structure represent potential determinants for serospecificity and epitope recognition by antibodies. © 2012 Wiley Periodicals, Inc.
Identification of a cation transport pathway in Neisseria meningitidis PorB
Authors: Kattner Christof , Zaucha Jan , Jaenecke Frank , Zachariae Ulrich , Tanabe Mikio 
Published: February 2013

AbstractNeisseria meningitidis is the main causative agent of bacterial meningitis. In its outer membrane, the trimeric Neisserial porin PorB is responsible for the diffusive transport of essential hydrophilic solutes across the bilayer. Previous molecular dynamics simulations based on the recent crystal structure of PorB have suggested the presence of distinct solute translocation pathways through this channel. Although PorB has been electrophysiologically characterized as anion‐selective, cation translocation through nucleotide‐bound PorB during pathogenesis is thought to be instrumental for host cell death. As a result, we were particularly interested in further characterizing cation transport through the pore. We combined a structural approach with additional computational analysis. Here, we present two crystal structures of PorB at 2.1 and 2.65 Å resolution. The new structures display additional electron densities around the protruding loop 3 (L3) inside the pore. We show that these electron densities can be identified as monovalent cations, in our case Cs+, which are tightly bound to the inner channel. Molecular dynamics simulations reveal further ion interactions and the free energy landscape for ions inside PorB. Our results suggest that the crystallographically identified locations of Cs+ form a cation transport pathway inside the pore. This finding suggests how positively charged ions are translocated through PorB when the channel is inserted into mitochondrial membranes during Neisserial infection, a process which is considered to dissipate the mitochondrial transmembrane potential gradient and thereby induce apoptosis. Proteins 2013. © 2012 Wiley Periodicals, Inc.
ACA‐specific RNA sequence recognition is acquired via the loop 2 region of MazF mRNA interferase
Authors: Park Jung‐Ho , Yoshizumi Satoshi , Yamaguchi Yoshihiro , Wu Kuen‐Phon , Inouye Masayori 
Published: February 2013

AbstractMazF is an mRNA interferase that cleaves mRNAs at a specific RNA sequence. MazF from E. coli (MazF‐ec) cleaves RNA at A and CA. To date, a large number of MazF homologs that cleave RNA at specific three‐ to seven‐base sequences have been identified from bacteria to archaea. MazF‐ec forms a dimer, in which the interface between the two subunits is known to be the RNA substrate‐binding site. Here, we investigated the role of the two loops in MazF‐ec, which are closely associated with the interface of the MazF‐ec dimer. We examined whether exchanging the loop regions of MazF‐ec with those from other MazF homologs, such as MazF from Myxococcus xanthus (MazF‐mx) and MazF from Mycobacterium tuberculosis (MazF‐mt3), affects RNA cleavage specificity. We found that exchanging loop 2 of MazF‐ec with loop 2 regions from either MazF‐mx or MazF‐mt3 created a new cleavage sequence at (A/U)(A/U)AA and C in addition to the original cleavage site, A and CA, whereas exchanging loop 1 did not alter cleavage specificity. Intriguingly, exchange of loop 2 with 8 or 12 consecutive Gly residues also resulted in a new RNA cleavage site at (A/U)(A/U)AA and C. The present study suggests a method for expanding the RNA cleavage repertoire of mRNA interferases, which is crucial for potential use in the regulation of specific gene expression and for biotechnological applications. Proteins 2013. © 2012 Wiley Periodicals, Inc.
First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina
Authors: Kushwaha Gajraj Singh , Yamini Shavait , Kumar Mukesh , Sinha Mau , Kaur Punit , Sharma Sujata , Singh Tej P. 
Published: February 2013

AbstractThis is the first structural evidence of recognition of mRNA cap structures by a ribosome inactivating protein. It is well known that a unique cap structure is formed at the 5′ end of mRNA for carrying out various processes including mRNA maturation, translation initiation, and RNA turnover. The binding studies and crystal structure determinations of type 1 ribosome inactivating protein (RIP‐1) from Momordica balsamina (MbRIP‐1) were carried out with mRNA cap structures including (i) N7‐methyl guanine (m7G), (ii) N7‐methyl guanosine diphosphate (m7GDP), and (iii) N7‐methyl guanosine triphosphate (m7GTP). These compounds showed affinities to MbRIP‐1 at nanomolar concentrations. The structure determinations of the complexes of MbRIP‐1 with m7G, m7GDP, and m7GTP at 2.65, 1.77, and 1.75 Å resolutions revealed that all the three compounds bound to MbRIP‐1 in the substrate binding site at the positions which are slightly shifted towards Glu85 as compared to those of rRNA substrates. In this position, Glu85 forms several hydrogen bonds with guanine moiety while N‐7 methyl group forms van der Waals contacts. However, the guanine rings are poorly stacked in these complexes. Thus, the mode of binding by MbRIP‐1 to mRNA cap structures is different which results in the inhibition of depurination. Since some viruses are known to exploit the capping property of the host, this action of MbRIP‐1 may have implications for the antiviral activity of this protein in vivo. The understanding of the mode of binding of MbRIP‐1 to cap structures may also assist in the design of anti‐viral agents. Proteins 2012. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Multiple factor analysis: principal component analysis for multitable and multiblock data sets
Authors: Abdi Hervé , Williams Lynne J. , Valentin Domininique 
Published: February 2013

AbstractMultiple factor analysis (MFA, also called multiple factorial analysis) is an extension of principal component analysis (PCA) tailored to handle multiple data tables that measure sets of variables collected on the same observations, or, alternatively, (in dual‐MFA) multiple data tables where the same variables are measured on different sets of observations. MFA proceeds in two steps: First it computes a PCA of each data table and ‘normalizes’ each data table by dividing all its elements by the first singular value obtained from its PCA. Second, all the normalized data tables are aggregated into a grand data table that is analyzed via a (non‐normalized) PCA that gives a set of factor scores for the observations and loadings for the variables. In addition, MFA provides for each data table a set of partial factor scores for the observations that reflects the specific ‘view‐point’ of this data table. Interestingly, the common factor scores could be obtained by replacing the original normalized data tables by the normalized factor scores obtained from the PCA of each of these tables. In this article, we present MFA, review recent extensions, and illustrate it with a detailed example. WIREs Comput Stat 2013, 5:149–179. doi: 10.1002/wics.1246This article is categorized under:

Data: Types and Structure > Categorical Data
Statistical Learning and Exploratory Methods of the Data Sciences > Exploratory Data Analysis
Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Six million years of magnetic grain-size records reveal that temperature and precipitation were decoupled on the Chinese Loess Plateau during ~ 4.5–2.6 Ma
Authors: Nie Junsheng , Song Yougui , King John W. , Zhang Rui , Fang Xiaomin 
Published: February 2013

AbstractMagnetic grain-size variations have been used as sensitive paleoclimate proxies to investigate the evolution of the East Asian summer monsoon, but their relationship with temperature and precipitation is not entirely clear. Here we find that two magnetic grain-size proxy records (χARM/χLF and χARM/SIRM, where χARM, χLF and SIRM are anhysteretic remanent magnetization susceptibility, magnetic susceptibility measured at 470 Hz and saturation isothermal remanent magnetization, respectively) of Chinese loess and red-clay sediments co-vary during the last 6 Ma, except between ~ 4.5 and 2.6 Ma, when these two records had opposite trends. We attribute this disparate behavior to the different responses of χARM/χLF and χARM/SIRM to temperature and precipitation during ~ 4.5–2.6 Ma, when temperature and precipitation on the Chinese Loess Plateau were decoupled. A comparison of the loess and red-clay χARM/χLF and χARM/SIRM records with the global ice-volume proxy records reveals that χARM/χLF is more sensitive to temperature variations than χARM/SIRM. The results suggest that temperature on the Chinese Loess Plateau had a cooling trend from ~ 4.5 to ~ 2.6 Ma, whereas rainfall tended to increase. Our studies demonstrate that joint analysis of loess χARM/χLF and χARM/SIRM records can reveal paleoclimatic information that cannot be revealed by a single parameter.
A comparison of charcoal measurements for reconstruction of Mediterranean paleo-fire frequency in the mountains of Corsica
Authors: Leys Bérangère , Carcaillet Christopher , Dezileau Laurent , Ali Adam A. , Bradshaw Richard H.W. 
Published: February 2013

AbstractFire-history reconstructions inferred from sedimentary charcoal records are based on measuring sieved charcoal fragment area, estimating fragment volume, or counting fragments. Similar fire histories are reconstructed from these three approaches for boreal lake sediment cores, using locally defined thresholds. Here, we test the same approach for a montane Mediterranean lake in which taphonomical processes might differ from boreal lakes through fragmentation of charcoal particles. The Mediterranean charcoal series are characterized by highly variable charcoal accumulation rates. Results there indicate that the three proxies do not provide comparable fire histories. The differences are attributable to charcoal fragmentation. This could be linked to fire type (crown or surface fires) or taphonomical processes, including charcoal transportation in the catchment area or in the sediment. The lack of correlation between the concentration of charcoal and of mineral matter suggests that fragmentation is not linked to erosion. Reconstructions based on charcoal area are more robust and stable than those based on fragment counts. Area-based reconstructions should therefore be used instead of the particle-counting method when fragmentation may influence the fragment abundance.
Augmenting cognitive behaviour therapy for post-traumatic stress disorder with emotion tolerance training: a randomized controlled trial
Authors: Bryant R. A. , Mastrodomenico J. , Hopwood S. , Kenny L. , Cahill C. , Kandris E. , Taylor K. 
Published: February 2013

BackgroundMany patients do not adhere to or benefit from cognitive behaviour therapy (CBT) for post-traumatic stress disorder (PTSD). This randomized controlled trial evaluates the extent to which preparing patients with emotion regulation skills prior to CBT enhances treatment outcome.MethodA total of 70 adult civilian patients with PTSD were randomized to 12 sessions of either supportive counselling followed by CBT (Support/CBT) or emotion regulation training followed by CBT (Skills/CBT).ResultsSkills/CBT resulted in fewer treatment drop-outs, less PTSD and anxiety, and fewer negative appraisals at 6 months follow-up than Support/CBT. Between-condition effect size was moderate for PTSD severity (0.43, 95% confidence interval −0.04 to 0.90). More Skills/CBT (31%) patients achieved high end-state functioning at follow-up than patients in Support/CBT (12%) [χ2(n = 70) = 3.67, p < 0.05].ConclusionsThis evidence suggests that response to CBT may be enhanced in PTSD patients by preparing them with emotion regulation skills. High attrition of participants during the study limits conclusions from this study.
Throwing the Baby Out With the Bathwater: Can the Military's Role in Global Health Crises be Redeemed?
Authors: Burkle Frederick M. 
Published: February 2013

AbstractFor decades, military humanitarian assistance programs have avoided empirical scrutiny, leaving researchers, the humanitarian community and decision makers without proof of outcome. This Editorial highlights the findings of three major studies that disclose deficits in the quality of the performance and reporting of humanitarian missions, and offer guidance for change. The author suggests that, contrary to current plans to limit the military's role in humanitarian assistance, emerging crises actually increase civilian security risks and that it is time for a new partnership of military and civilian humanitarian resources to evolve in the interest of human security.BurkleFM. Throwing the baby out with the bathwater: can the military's role in global health crises be redeemed?. Prehosp Disaster Med.2013;28(3):1–3..
Can Risk-Taking Be an Endophenotype for Bipolar Disorder? A Study on Patients with Bipolar Disorder Type I and Their First-Degree Relatives
Authors: Hıdıroğlu Ceren , Demirci Esen Özlem , Tunca Zeliha , Neslihan Gűrz Yalçìn Şehnaz , Lombardo Lauren , Glahn David C. , Özerdem Ayşegül 
Published: February 2013

AbstractRisk-taking behavior and impulsivity are core features of bipolar disorder. Whether they are part of the inherited aspect of the illness is not clear. We aimed to evaluate risk-taking behavior as a potential endophenotype for bipolar disorders, and its relationship with impulsivity and illness features. The Balloon Analogue Risk Task (BART) and Barratt Impulsiveness Scale-11 (BIS-11) were used to assess risk-taking behavior and impulsivity respectively in 30 euthymic bipolar I patients (BD), their 25 asymptomatic first-degree relatives (BD-R), and 30 healthy controls (HC). The primary BART outcome measure was the behavioral adjustment score (number of pumps after trials where the balloon did not pop minus the number of pumps after trials where the balloon popped). BD (p< .001) and BD-R (p= .001) had similar and significantly lower adjustment scores than HC. Only BD scored significantly higher on BIS-11 total (p= .01) and motor (p= .04) subscales than HC. Neither the BART, nor impulsivity scores associated with illness features. A limitation of this study is medicated patients and a heterogeneous BD-R were included. Riskiness may be a candidate endophenotype for bipolar disorder as it appears independently from illness features, presents similarly in BD and BD-R groups and differs from impulsivity. (JINS, 2013,19, 1–9)
Structure and function of a cyanophage-encoded peptide deformylase
Authors: Frank Jeremy A , Lorimer Don , Youle Merry , Witte Pam , Craig Tim , Abendroth Jan , Rohwer Forest , Edwards Robert A , Segall Anca M , Burgin Alex B 
Published: February 2013

Abstract
Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal α-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.