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Intrinsically disordered

Matilde M Vaghi, Petra E Vértes, Manfred G Kitzbichler, Annemieke M Apergis-Schoute, Febe E van der Flier, Naomi A Fineberg, Akeem Sule, Rashid Zaman, Valerie Voon, Prantik Kundu, Edward T Bullmore, Trevor W Robbins
BACKGROUND: A recent hypothesis has suggested that core deficits in goal-directed behavior in obsessive-compulsive disorder (OCD) are caused by impaired frontostriatal function. We tested this hypothesis in OCD patients and control subjects by relating measures of goal-directed planning and cognitive flexibility to underlying resting-state functional connectivity. METHODS: Multiecho resting-state acquisition, combined with micromovement correction by blood oxygen level-dependent sensitive independent component analysis, was used to obtain in vivo measures of functional connectivity in 44 OCD patients and 43 healthy comparison subjects...
August 11, 2016: Biological Psychiatry
Durga Mahor, Anu Priyanka, Gandham S Prasad, Krishan Gopal Thakur
Consumption of foods and beverages with high purine content increases the risk of hyperuricemia, which causes gout and can lead to cardiovascular, renal, and other metabolic disorders. As patients often find dietary restrictions challenging, enzymatically lowering purine content in popular foods and beverages offers a safe and attractive strategy to control hyperuricemia. Here, we report structurally and functionally characterized purine nucleoside phosphorylase (PNP) from Kluyveromyces lactis (KlacPNP), a key enzyme involved in the purine degradation pathway...
2016: PloS One
Zhi-Long Yu, Sen Xin, Ya You, Le Yu, Yue Lin, Da-Wei Xu, Chan Qiao, Zhi-Hong Huang, Ning Yang, Shu-Hong Yu, John B Goodenough
Hard carbons attract myriad interests as anode materials for high-energy rechargeable batteries due to their low costs and high theoretical capacities; practically they deliver unsatisfied performance due to their intrinsically disordered microarchitecture. Here we report a facile ion-catalyzed synthesis of phenol-formaldehyde resin-based hard carbon aerogel by taking advantages of the chelation effect of phenol and Fe3+, which consists of a three-dimensionally interconnected carbon network embedded with hydrogen-rich, ordered microstructures of expanded nanographites and carbon micropores...
October 21, 2016: Journal of the American Chemical Society
Alexander S Falk, Ansgar B Siemer
Several amyloid fibrils have cores framed by highly dynamic, intrinsically disordered, domains that can play important roles for function and toxicity. To study these domains in detail using solid-state NMR spectroscopy, site-specific resonance assignments are required. Although the rapid dynamics of these domains lead to considerable averaging of orientation-dependent NMR interactions and thereby line-narrowing, the proton linewidths observed in these samples is far larger than what is regularly observed in solution...
October 20, 2016: Journal of Biomolecular NMR
Christoph Göbl, Moritz Resch, Madeleine Strickland, Christoph Hartlmüller, Martin Viertler, Nico Tjandra, Tobias Madl
The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical-shift assignments, and data analysis that relies on well-separated resonances. We present a covalent paramagnetic lanthanide-binding tag (LBT) for increasing the chemical-shift dispersion and facilitating the chemical-shift assignment of challenging, repeat-containing IDPs. Linkage of the DOTA-based LBT to a cysteine residue induces pseudo-contact shifts (PCS) for resonances more than 20 residues from the spin-labeling site...
October 20, 2016: Angewandte Chemie
Satoshi Izumi, Guang Hong, Koh Iwasaki, Masayuki Izumi, Yusuke Matsuyama, Mirei Chiba, Takashi Toda, Tada-Aki Kudo
The taste detection system for oral fatty acid may be related to obesity. In addition, sleep is intrinsically and closely related to food intake and metabolism. However, the association of gustatory salivation with body mass index (BMI), daytime sleepiness, or sleep habits is largely unknown. Therefore, we evaluated the relationship between gustatory salivation and BMI, Epworth sleepiness scale (ESS, a daytime sleepiness scale) or sleep habits among 26 healthy young individuals (20 males and 6 females; mean age: 26...
2016: Tohoku Journal of Experimental Medicine
Qin Qiao, Ruxi Qi, Guanghong Wei, Xuhui Huang
Amyloid deposits of human islet amyloid polypeptide (hIAPP) are identified in 95% of type II diabetes patients. The oligomers during the early stage of hIAPP aggregation are believed to be more cytotoxic than the mature fibrils. However, the structural details during the initial stage of hIAPP aggregation are still under debate experimentally. To understand its initial nucleation mechanism, we investigate the thermodynamics and kinetics of hIAPP(11-25) dimerization, which is the first manifestation of the interplay between intra- and inter-molecular interactions, via the construction of Markov state models from extensive molecular dynamics simulations...
October 19, 2016: Physical Chemistry Chemical Physics: PCCP
Shengwei Hou, Ulrike Pfreundt, Dan Miller, Ilana Berman-Frank, Wolfgang R Hess
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5' ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities...
October 19, 2016: Scientific Reports
Alberto Baggioli, Carlo A Cavallotti, Antonino Famulari
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other...
October 18, 2016: Physical Chemistry Chemical Physics: PCCP
Amanda L Mansouri, Laura N Grese, Erica L Rowe, James C Pino, S Chakra Chennubhotla, Arvind Ramanathan, Hugh M O'Neill, Valerie Berthelier, Christopher B Stanley
Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR) separate from their mutual binding. Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR...
October 18, 2016: Molecular BioSystems
Bin Zhang, Shijia Li, Chuanjun Zhuo, Meng Li, Adam Safron, Axel Genz, Wen Qin, Chunshui Yu, Martin Walter
BACKGROUND: Major depressive disorder (MDD) is a highly prevalent psychiatric condition in which patients often have difficulties regulating their emotions. Prior studies have shown that attention bias towards negative emotion is linked to activation in regions of the default mode network (DMN) in MDD individuals. Furthermore, MDD patients showed increased resting-state functional connectivity (FC) between the medial prefrontal cortex and other DMN structures. METHODS: Twenty-one MDD patients that currently experiencing depressive episodes and twenty-five healthy control participants performed the current emotional expectancy paradigm in a gradient-echo SENSE-SPIRAL fMRI...
October 7, 2016: Journal of Affective Disorders
Merve Cikili Uytun, Emel Karakaya, Didem Behice Oztop, Serife Gengec, Kazım Gumus, Sevgi Ozmen, Selim Doğanay, Semra Icer, Esra Demirci, Saliha Demirel Ozsoy
It is known that patients with Attention Deficit and Hyperactivity disorder (ADHD) and Conduct disorder (CD) commonly shows greater symptom severity than those with ADHD alone and worse outcomes. This study researches whether Default mode network (DMN) is altered in adolescents with ADHD + CD, relative to ADHD alone and controls or not. Ten medication-naïve boys with ADHD + CD, ten medication-naïve boys with ADHD and 10-age-matched typically developing (TD) controls underwent functional magnetic resonance imaging (fMRI) scans in the resting state and neuropsychological tasks such as the Wisconsin Card Sorting Test (WCST), Stroop Test TBAG Form (STP), Auditory Verbal learning Test (AVLT), Visual Auditory Digit Span B (VADS B) were applied to all the subjects included...
October 13, 2016: Brain Imaging and Behavior
Peng Liu, Yanfei Liu, Geliang Wang, Xuejuan Yang, Lingmin Jin, Jinbo Sun, Wei Qin
Primary dysmenorrhea (PDM), characterized by cramping pain in the lower abdomen, is a common gynecological disorder in women of child-bearing age. An increasing number of neuroimaging studies have emphasized that PDM is associated with functional and structural abnormalities in the regions related to the default mode network (DMN). Based on resting-state functional magnetic resonance imaging (fMRI), the aim of this study was to use amplitude of low-frequency fluctuation (ALFF) and functional connectivity (FC) to investigate changes of the intrinsic brain activity in the DMN in PDM...
October 13, 2016: Brain Imaging and Behavior
Matteo Ziacchi, Pietro Palmisano, Ernesto Ammendola, Gabriele Dell'era, Federico Guerra, Stefano Aquilani, Vittorio Aspromonte, Giuseppe Boriani, Michele Accogli, Giuseppe Del Giorno, Eraldo Occhetta, Alessandro Capucci, Renato Pietro Ricci, Giampiero Maglia, Mauro Biffi
AIM: The aim of this multicentre, observational, transversal study was to evaluate pacemaker (PM) choice and setting in a large number of patients, in order to understand their relationship with the patients' clinical characteristics. METHODS AND RESULTS: The study enrolled a total of 1858 patients (71 ± 14 years, 54% male), consecutively evaluated during scheduled PM follow-up visits in 7 Italian cardiac arrhythmia centres. To evaluate the appropriateness of PM choice in relation to the patients' clinical characteristics, we analysed their rhythm disorders at the time of device implantation and the characteristics of the devices implanted...
October 13, 2016: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
Mike Reppert, Anish R Roy, Jeremy O B Tempkin, Aaron R Dinner, Andrei Tokmakoff
The characterization of intrinsically disordered protein (IDP) ensembles is complicated both by inherent heterogeneity and by the fact that many common experimental techniques function poorly when applied to IDPs. For this reason, the development of alternative structural tools for probing IDP ensembles has attracted considerable attention. Here we describe our recent work in developing experimental and computational tools for characterizing IDP ensembles using Amide I (backbone carbonyl stretch) vibrational spectroscopy...
October 13, 2016: Journal of Physical Chemistry. B
Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, Junichi Higo
The C-terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non-neutralized. Because of the flexibility of the unbound CTD, a free-energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized...
December 5, 2016: Journal of Computational Chemistry
Kenna Degner, Ronald R Magness, Dinesh M Shah
The uterine vasculature undergoes marked changes during pregnancy in order to provide the necessary increase in blood flow to support growth and nutrition of the uterus, placenta, and developing fetus. Pregnancy-associated uterine vascular transformations are orchestrated by a complex array of endocrine and cellular mechanisms to bring about structural modifications at the maternal-fetal interface, which collectively lead to development of the uteroplacental circulation. Understanding intrinsic uterine vascular remodeling in pregnancy is essential for understanding the physiologic and pathophysiologic regulation of maternal uterine blood flow...
October 12, 2016: Reproductive Sciences
Alexander R Siegel, David E Wemmer
Bacterial sigma factors are subunits of RNA polymerase that direct the holoenzyme to specific sets of promoters in the genome, and are a central element of regulating transcription. Most polymerase holoenzymes open the promoter and initiate transcription rapidly after binding. However, polymerase containing members of the σ(54) family must be acted on by a transcriptional activator before DNA opening and initiation occur. A key domain in these transcriptional activators forms a hexameric AAA+ ATPase that acts through conformational changes brought on by ATP hydrolysis...
October 9, 2016: Journal of Molecular Biology
Antonino Natalello, Carlo Santambrogio, Rita Grandori
Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution...
October 11, 2016: Journal of the American Society for Mass Spectrometry
Jason C Lee, Lei Philip Wang, Joe Z Tsien
It is not uncommon for humans or animals to experience traumatic events in their lifetimes. However, the majority of individuals are resilient to long-term detrimental changes turning into anxiety and depression, such as post-traumatic stress disorder (PTSD). What underlying neural mechanism accounts for individual variability in stress resilience? Hyperactivity in fear circuits, such as the amygdalar system, is well-known to be the major pathophysiological basis for PTSD, much like a "stuck accelerator." Interestingly, increasing evidence demonstrates that dopamine (DA) - traditionally known for its role in motivation, reward prediction, and addiction - is also crucial in regulating fear learning and anxiety...
2016: Frontiers in Psychiatry
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