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Intrinsically disordered

Arjun Sethi, Valerie Voon, Hugo D Critchley, Mara Cercignani, Neil A Harrison
Computational models of reinforcement learning have helped dissect discrete components of reward-related function and characterize neurocognitive deficits in psychiatric illnesses. Stimulus novelty biases decision-making, even when unrelated to choice outcome, acting as if possessing intrinsic reward value to guide decisions toward uncertain options. Heightened novelty seeking is characteristic of attention deficit hyperactivity disorder, yet how this influences reward-related decision-making is computationally encoded, or is altered by stimulant medication, is currently uncertain...
March 13, 2018: Brain: a Journal of Neurology
S Sengottuvel, Pathan Fayaz Khan, N Mariyappa, Rajesh Patel, S Saipriya, K Gireesan
Cutaneous measurements of electrogastrogram (EGG) signals are heavily contaminated by artifacts due to cardiac activity, breathing, motion artifacts, and electrode drifts whose effective elimination remains an open problem. A common methodology is proposed by combining independent component analysis (ICA) and ensemble empirical mode decomposition (EEMD) to denoise gastric slow-wave signals in multichannel EGG data. Sixteen electrodes are fixed over the upper abdomen to measure the EGG signals under three gastric conditions, namely, preprandial, postprandial immediately, and postprandial 2 h after food for three healthy subjects and a subject with a gastric disorder...
March 1, 2018: SLAS Technology
Robert I Cukier
Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a ligand. Thus, the degree of conformational disorder of an IDP is of interest. We create a dichotomic Markov model that can explore entropic features of an IDP. The Markov condition introduces local (neighbor residues in a protein sequence) rotamer dependences that arise from van der Waals and other chemical constraints...
March 14, 2018: Journal of Chemical Physics
Gordon Parker, Amelia Paterson, Mia Romano, Isabelle Granville Smith
OBJECTIVES: To increase awareness of the sensory changes experienced during hypo/manic and depressive states by those with a bipolar disorder and determine if the prevalence of such features is similar across differing bipolar sub-types. METHODS: We interviewed 66 patients who acknowledged sensory changes during hypo/manic states. They were allocated to bipolar I, bipolar II and soft bipolar diagnostic categories and the prevalence of 10 differing sensory changes was quantified during hypo/manic and depressive phases...
March 1, 2018: Australasian Psychiatry: Bulletin of Royal Australian and New Zealand College of Psychiatrists
Hui Ye
Antimicrobial peptides are derived from the viral fusion domain of influenza virus hemagglutinin based on rational analysis of the intermolecular interaction between peptides and bacterial outer membrane. It is revealed that the isolated viral fusion domain is a negatively charged peptide HAfp1-23 that cannot effectively interact with the anionic membrane. Conversion of the native HAfp1-23 to a positively charged peptide HAfp1-23 _KK by E11K/D19K mutation can promote the peptide-membrane interaction substantially; this confers to the peptide a moderate antibacterial potency against antibiotic-resistant bacterial strains...
March 2018: Journal of Peptide Science: An Official Publication of the European Peptide Society
Yoshinori Hirano, Yu Amano, Shigenobu Yonemura, Toshio Hakoshima
Mechanotransduction by α-catenin facilitates the force-dependent development of adherens junctions (AJs) by recruiting vinculin to reinforce actin anchoring of AJs. The α-catenin mechanotransducing action is facilitated by its force-sensing device region that autoinhibits the vinculin-binding site 1 (VBS1). Here, we report the high-resolution structure of the force-sensing device region of α-catenin, which shows the autoinhibited form comprised of helix bundles E, F and G. The cryptic VBS1 is embedded into helix bundle E stabilized by direct interactions with the autoinhibitory region forming helix bundles F and G...
March 15, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Neerupma Bhardwaj, Kirtimaan Syal, Dipankar Chatterji
ppGpp, an alarmone for stringent response, plays an important role in the reprogramming of the transcription complex at the time of stress. In Escherichia coli, ppGpp mediates its action by binding to at least two different sites on RNA polymerase (RNAP). One of the sites to which ppGpp binds to RNAP is at the β'-ω interface; however, the underlying molecular mechanism and the physiological relevance of ppGpp binding to this site remain unclear. In this study, we have performed UV cross-linking experiments using32 P azido-labeled ppGpp to probe its association with RNAP in the absence and presence of ω, and observed weaker binding of ppGpp to the RNAP without ω...
March 15, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Dorothea L Floris, Meng-Chuan Lai, Tanmay Nath, Michael P Milham, Adriana Di Martino
Background: The male predominance in the prevalence of autism spectrum disorder (ASD) has motivated research on sex differentiation in ASD. Multiple sources of evidence have suggested a neurophenotypic convergence of ASD-related characteristics and typical sex differences. Two existing, albeit competing, models provide predictions on such neurophenotypic convergence. These two models are testable with neuroimaging. Specifically, the Extreme Male Brain (EMB) model predicts that ASD is associated with enhanced brain maleness in both males and females with ASD (i...
2018: Molecular Autism
Changqing Lu, Lihua Dong, Hui Zhou, Qianmei Li, Guojiao Huang, Shu Jun Bai, Linchuan Liao
Oligodendrocytes are the myelin-producing cells of the central nervous system (CNS). A variety of brain disorders from "classical" demyelinating diseases, such as multiple sclerosis, stroke, schizophrenia, depression, Down syndrome and autism, are shown myelination defects. Oligodendrocyte myelination is regulated by a complex interplay of intrinsic, epigenetic and extrinsic factors. Gpr17 (G protein-coupled receptor 17) is a G protein-coupled receptor, and has been identified to be a regulator for oligodendrocyte development...
March 14, 2018: Scientific Reports
Suijuan Zhong, Shu Zhang, Xiaoying Fan, Qian Wu, Liying Yan, Ji Dong, Haofeng Zhang, Long Li, Le Sun, Na Pan, Xiaohui Xu, Fuchou Tang, Jun Zhang, Jie Qiao, Xiaoqun Wang
The mammalian prefrontal cortex comprises a set of highly specialized brain areas containing billions of cells and serves as the centre of the highest-order cognitive functions, such as memory, cognitive ability, decision-making and social behaviour. Although neural circuits are formed in the late stages of human embryonic development and even after birth, diverse classes of functional cells are generated and migrate to the appropriate locations earlier in development. Dysfunction of the prefrontal cortex contributes to cognitive deficits and the majority of neurodevelopmental disorders; there is therefore a need for detailed knowledge of the development of the prefrontal cortex...
March 14, 2018: Nature
Anthony Banks, Sanbo Qin, Kevin L Weiss, Christopher B Stanley, Huan-Xiang Zhou
Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering...
March 13, 2018: Biophysical Journal
Sneha Munshi, Soundhararajan Gopi, Sandhyaa Subramanian, Luis A Campos, Athi N Naganathan
The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature...
March 10, 2018: Nucleic Acids Research
Yanhua Ouyang, Likun Zhao, Zhuqing Zhang
Intrinsically disordered regions (IDRs) or proteins (IDPs), which play crucial biological functions in essential biological processes of life, do not have well-defined secondary or tertiary structures when isolated in solution. The highly dynamic properties and conformational heterogeneity of IDPs make them challenging to study with traditional experimental techniques. As a powerful complementary tool for experiments, all-atom molecular dynamics simulation can obtain detailed conformational information on IDPs, but the limitation of force field accuracy is a challenge for reproducing IDP conformers...
March 14, 2018: Physical Chemistry Chemical Physics: PCCP
Zhiyi Liu, Dimitra Pouli, Carlo A Alonzo, Antonio Varone, Sevasti Karaliota, Kyle P Quinn, Karl Münger, Katia P Karalis, Irene Georgakoudi
Monitoring subcellular functional and structural changes associated with metabolism is essential for understanding healthy tissue development and the progression of numerous diseases, including cancer, diabetes, and cardiovascular and neurodegenerative disorders. Unfortunately, established methods for this purpose either are destructive or require the use of exogenous agents. Recent work has highlighted the potential of endogenous two-photon excited fluorescence (TPEF) as a method to monitor subtle metabolic changes; however, mechanistic understanding of the connections between the detected optical signal and the underlying metabolic pathways has been lacking...
March 2018: Science Advances
Murali Aarthy, Deepak Kumar, Rajanish Giri, Sanjeev Kumar Singh
Human papillomavirus (HPV) has been the primary causative agent of cervical cancer, the most threatening cancer affecting millions of women worldwide. HPV, a small non enveloped DNA virus of high and low risk types contain intrinsically disordered region and it also plays significant role in the development of cervical cancer. HPV E7 contains an ordered Zinc finger motif that binds to pRB and alters its function. It utilizes both disordered N-terminal and structured C-terminal regions for cellular transformation...
March 10, 2018: Gene
Myungchul Song, Kyunghee Song, Sunghee Kim, Jinyoung Lee, Sueyun Hwang, Chingtack Han
Caenorhabditis elegans C09F5.1 is a nematode-specific gene that encodes a type II transmembrane protein containing the BRICHOS domain. The gene was isolated as a heat-sensitive mutant, but the function of the protein remained unclear. We examined the expression pattern and subcellular localization of C09F5.1 as well as its roles in thermotolerance and chaperone function. Expression of C09F5.1 under heat shock conditions was induced in a heat shock factor 1 (HSF-1)-dependent manner. However, under normal growth conditions, most cells types exposed to mechanical stimuli expressed C09F5...
March 13, 2018: Genes
Helle Wessel Andersson, Aslak Steinsbekk, Espen Walderhaug, Eli Otterholt, Trond Nordfjærn
Introduction: Dropout from inpatient treatment for substance use disorder (SUD) is an ongoing challenge. The aim of this study was to identify demographic, substance use, and psychological factors that predict dropout from postdetoxification inpatient SUD treatment. Materials and methods: A total of 454 patients from 5 inpatient SUD centers in Central Norway were consecutively included in this naturalistic, prospective cohort study. Results: A total of 132 patients (28%) did not complete the planned treatment stay (dropped out)...
2018: Substance Abuse: Research and Treatment
Patricia Santofimia-Castaño, Bruno Rizzuti, Olga Abián, Adrián Velázquez-Campoy, Juan L Iovanna, José L Neira
BACKGROUND: NUPR1 is a multifunctional intrinsically disordered protein (IDP) involved, among other functions, in chromatin remodelling, and development of pancreatic ductal adenocarcinoma (PDAC). It interacts with several biomolecules through hydrophobic patches around residues Ala33 and Thr68. The drug trifluoperazine (TFP), which hampers PDAC development in xenografted mice, also binds to those regions. Because of the large size of the hot-spot interface of NUPR1, small molecules could not be adequate to modulate its functions...
March 9, 2018: Biochimica et Biophysica Acta
Liying Li, J P McGinnis, Kausik Si
Prion-like proteins overlap with intrinsically disordered and low-complexity sequence families. These proteins are widespread, especially among mRNA-binding proteins. A salient feature of these proteins is the ability to form protein assemblies with distinct biophysical and functional properties. While prion-like proteins are involved in myriad of cellular processes, we propose potential roles for protein assemblies in regulated protein synthesis. Since proteins are the ultimate functional output of gene expression, when, where, and how much of a particular protein is made dictates the functional state of a cell...
March 9, 2018: Trends in Cell Biology
Xuewei Dong, Qin Qiao, Zhenyu Qian, Guanghong Wei
The amyloid deposits of human islet amyloid polypeptide (hIAPP) are found in type II diabetes patients. hIAPP monomer is intrinsically disordered in solution, whereas it can form amyloid fibrils both in vivo and in vitro. Extensive evidence suggests that hIAPP causes the disruption of cellular membrane, and further induces cytotoxicity and the death of islet β-cells in pancreas. The presence of membrane also accelerates the hIAPP fibril formation. hIAPP oligomers and protofibrils in the early stage of aggregation were reported to be the most cytotoxic, disrupting the membrane integrity and giving rise to the pathological process...
March 9, 2018: Biochimica et Biophysica Acta
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