Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin.

PubMed

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P; Elvin, Christopher M; Hill, Anita J; Choudhury, Namita R; Dutta, Naba K

2015-06-04

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin

NASA Astrophysics Data System (ADS)

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P.; Elvin, Christopher M.; Hill, Anita J.; Choudhury, Namita R.; Dutta, Naba K.

2015-06-01

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

Cell cycle regulation by the intrinsically disordered proteins p21 and p27.

PubMed

Yoon, Mi-Kyung; Mitrea, Diana M; Ou, Li; Kriwacki, Richard W

2012-10-01

Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)-cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27's regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs.

Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

PubMed

Varadi, Mihaly; Zsolyomi, Fruzsina; Guharoy, Mainak; Tompa, Peter

2015-01-01

Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.

Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013).

PubMed

Uversky, Vladimir N

2013-01-01

The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for "intrinsically disordered protein OR natively unfolded protein" returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a "Digested Disorder" project, which will encompass a series of reader's digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest covers papers published during the period of January, February and March of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013).

PubMed

DeForte, Shelly; Reddy, Krishna D; Uversky, Vladimir N

2013-01-01

The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a series of reader's digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

Isotope scattering and phonon thermal conductivity in light atom compounds: LiH and LiF

DOE PAGES

Lindsay, Lucas R.

2016-11-08

Engineered isotope variation is a pathway toward modulating lattice thermal conductivity (κ) of a material through changes in phonon-isotope scattering. The effects of isotope variation on intrinsic thermal resistance is little explored, as varying isotopes have relatively small differences in mass and thus do not affect bulk phonon dispersions. However, for light elements isotope mass variation can be relatively large (e.g., hydrogen and deuterium). Using a first principles Peierls-Boltzmann transport equation approach the effects of isotope variance on lattice thermal transport in ultra-low-mass compound materials LiH and LiF are characterized. The isotope mass variance modifies the intrinsic thermal resistance viamore » modulation of acoustic and optic phonon frequencies, while phonon-isotope scattering from mass disorder plays only a minor role. This leads to some unusual cases where values of isotopically pure systems ( 6LiH, 7Li 2H and 6LiF) are lower than the values from their counterparts with naturally occurring isotopes and phonon-isotope scattering. However, these differences are relatively small. The effects of temperature-driven lattice expansion on phonon dispersions and calculated κ are also discussed. This work provides insight into lattice thermal conductivity modulation with mass variation and the interplay of intrinsic phonon-phonon and phonon-isotope scattering in interesting light atom systems.« less

Alice in Wonderland Syndrome, Burning Mouth Syndrome, Cold Stimulus Headache, and HaNDL: Narrative Review.

PubMed

Valença, Marcelo M; de Oliveira, Daniella A; Martins, Hugo André de L

2015-10-01

Unusual headache syndromes are not as infrequent in clinical practice as was generally believed. About three fourths of the classified headache disorders found in the ICHD-II can be considered rare. The aim of this narrative review was to perform a literature review of the pathophysiology, clinical presentation, diagnostic criteria, and treatment of the following unusual headache disorders: Alice in Wonderland syndrome, burning mouth syndrome, cold stimulus headache, and the syndrome of transient headache and neurologic deficits with cerebrospinal fluid lymphocytosis. A literature review was performed using PubMed for each of the abovementioned headache disorders. The unusual headache syndromes as a distinct group of disorders are not as infrequent in clinical practice as was generally believed. Some of them, albeit considered as unusual, may occur with relative frequency, such as cold stimulus headache and burning mouth syndrome. © 2015 American Headache Society.

What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered.

PubMed

Dunker, A Keith; Babu, M Madan; Barbar, Elisar; Blackledge, Martin; Bondos, Sarah E; Dosztányi, Zsuzsanna; Dyson, H Jane; Forman-Kay, Julie; Fuxreiter, Monika; Gsponer, Jörg; Han, Kyou-Hoon; Jones, David T; Longhi, Sonia; Metallo, Steven J; Nishikawa, Ken; Nussinov, Ruth; Obradovic, Zoran; Pappu, Rohit V; Rost, Burkhard; Selenko, Philipp; Subramaniam, Vinod; Sussman, Joel L; Tompa, Peter; Uversky, Vladimir N

2013-01-01

"What's in a name? That which we call a rose By any other name would smell as sweet." From "Romeo and Juliet", William Shakespeare (1594) This article opens a series of publications on disambiguation of the basic terms used in the field of intrinsically disordered proteins. We start from the beginning, namely from the explanation of what the expression "intrinsically disordered protein" actually means and why this particular term has been chosen as the common denominator for this class of proteins characterized by broad structural, dynamic and functional characteristics.

Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree.

PubMed

DeForte, Shelly; Uversky, Vladimir N

2016-03-01

Missing regions in X-ray crystal structures in the Protein Data Bank (PDB) have played a foundational role in the study of intrinsically disordered protein regions (IDPRs), especially in the development of in silico predictors of intrinsic disorder. However, a missing region is only a weak indication of intrinsic disorder, and this uncertainty is compounded by the presence of ambiguous regions, where more than one structure of the same protein sequence "disagrees" in terms of the presence or absence of missing residues. The question is this: are these ambiguous regions intrinsically disordered, or are they the result of static disorder that arises from experimental conditions, ensembles of structures, or domain wobbling? A novel way of looking at ambiguous regions in terms of the pattern between multiple PDB structures has been demonstrated. It was found that the propensity for intrinsic disorder increases as the level of ambiguity decreases. However, it is also shown that ambiguity is more likely to occur as the protein region is placed within different environmental conditions, and even the most ambiguous regions as a set display compositional bias that suggests flexibility. The results suggested that ambiguity is a natural result for many IDPRs crystallized under different conditions and that static disorder and wobbling domains are relatively rare. Instead, it is more likely that ambiguity arises because many of these regions were conditionally or partially disordered. © 2016 The Protein Society.

Functions of intrinsic disorder in transmembrane proteins.

PubMed

Kjaergaard, Magnus; Kragelund, Birthe B

2017-09-01

Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine receptors. The functions of the disordered regions are many and varied. We will discuss selected examples including: (1) Organization of receptors, kinases, phosphatases and second messenger sources into signaling complexes. (2) Modulation of the membrane-embedded domain function by ball-and-chain like mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding protein disorder.

The alphabet of intrinsic disorder

PubMed Central

Theillet, Francois-Xavier; Kalmar, Lajos; Tompa, Peter; Han, Kyou-Hoon; Selenko, Philipp; Dunker, A. Keith; Daughdrill, Gary W.; Uversky, Vladimir N

2013-01-01

A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting. PMID:28516008

Modulating the Intrinsic Disorder in the Cytoplasmic Domain Alters the Biological Activity of the N-Methyl-d-aspartate-sensitive Glutamate Receptor*

PubMed Central

Choi, Ucheor B.; Kazi, Rashek; Stenzoski, Natalie; Wollmuth, Lonnie P.; Uversky, Vladimir N.; Bowen, Mark E.

2013-01-01

The NMDA-sensitive glutamate receptor is a ligand-gated ion channel that mediates excitatory synaptic transmission in the nervous system. Extracellular zinc allosterically regulates the NMDA receptor by binding to the extracellular N-terminal domain, which inhibits channel gating. Phosphorylation of the intrinsically disordered intracellular C-terminal domain alleviates inhibition by extracellular zinc. The mechanism for this functional effect is largely unknown. Proline is a hallmark of intrinsic disorder, so we used proline mutagenesis to modulate disorder in the cytoplasmic domain. Proline depletion selectively uncoupled zinc inhibition with little effect on receptor biogenesis, surface trafficking, or ligand-activated gating. Proline depletion also reduced the affinity for a PDZ domain involved in synaptic trafficking and affected small molecule binding. To understand the origin of these phenomena, we used single molecule fluorescence and ensemble biophysical methods to characterize the structural effects of proline mutagenesis. Proline depletion did not eliminate intrinsic disorder, but the underlying conformational dynamics were changed. Thus, we altered the form of intrinsic disorder, which appears sufficient to affect the biological activity. These findings suggest that conformational dynamics within the intrinsically disordered cytoplasmic domain are important for the allosteric regulation of NMDA receptor gating. PMID:23782697

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions

PubMed Central

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Uversky, Vladimir N.; Obradovic, Zoran

2008-01-01

Identifying relationships between function, amino acid sequence and protein structure represents a major challenge. In this study we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical approach, outlines the major findings and provides illustrative examples of biological processes and functions positively and negatively correlated with intrinsic disorder. PMID:17391014

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

PubMed

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Uversky, Vladimir N; Obradovic, Zoran

2007-05-01

Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical approach, outlines the major findings, and provides illustrative examples of biological processes and functions positively and negatively correlated with intrinsic disorder.

Hidden Structural Codes in Protein Intrinsic Disorder.

PubMed

Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

2017-10-17

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

Hydrogen-Exchange Mass Spectrometry for the Study of Intrinsic Disorder in Proteins

PubMed Central

Balasubramaniam, Deepa; Komives, Elizabeth A.

2012-01-01

Amide hydrogen/deuterium exchange detected by mass spectrometry (HXMS) is seeing wider use for the identification of intrinsically disordered parts of proteins. In this review, we discuss examples of how discovery of intrinsically disordered regions and their removal can aid in structure determination, biopharmaceutical quality control, the characterization of how posttranslational modifications affect weak structuring of disordered regions, the study of coupled folding and binding, and the characterization of amyloid formation. PMID:23099262

Functionality of intrinsic disorder in tumor necrosis factor-α and its receptors.

PubMed

Uversky, Vladimir N; El-Baky, Nawal Abd; El-Fakharany, Esmail M; Sabry, Amira; Mattar, Ehab H; Uversky, Alexey V; Redwan, Elrashdy M

2017-11-01

Tumor necrosis factor-α (TNF-α) is a pleiotropic inflammatory cytokine that exerts potent cytotoxic effects on solid tumor cells, while not affecting their normal counterparts. It is also known that TNF-α exerts many of its biological functions via interaction with specific receptors. To understand the potential roles of intrinsic disorder in the functioning of this important cytokine, we explored the peculiarities of intrinsic disorder distribution in human TNF-α and its homologs from various species, ranging from zebrafish to chimpanzee. We also studied the peculiarities of intrinsic disorder distribution in human TNF-α receptors, TNFR1 and TNFR2. Analysis revealed that cytoplasmic domains of TNF-α and its receptors are expected to be highly disordered. Furthermore, although the sequence identities of analyzed TNF-α homologs range from 99.57% (between human and chimpanzee proteins) to 22.33% (between frog and fish proteins), their intrinsic disorder profiles are characterized by a remarkable similarity. These observations indicate that the peculiarities of distribution of the intrinsic disorder propensity within the amino acid sequences are evolutionary conserved, and therefore could be of functional importance for this family of proteins. We also show that disordered and flexible regions of human TNF-α and its TNFR1 and TNFR2 receptors are crucial for some of their biological activities. © 2017 Federation of European Biochemical Societies.

Differential diagnosis of an unusual shoulder articular lesion in an ancient domestic dog (Canis lupus familiaris L., 1758).

PubMed

Lawler, D F; Rubin, D A; Evans, R H; Hildebolt, C F; Smith, K E; Widga, C; Martin, T J; Siegel, M; Sackman, J E; Smith, G K; Patel, T K

2013-12-01

A proximal humeral articular surface from an ancient domestic dog deliberate burial was examined during survey of small mammal bones from a prehistoric early Late Woodland archeological site. An unusual lesion on the caudolateral articular surface prompted micro-computed tomography to define detailed structure. Results indicate cortical or immature woven bone arising subchondrally, replacing normal trabeculae, extending through a breach in the cortical surface, and having sharp transition with surrounding normal bone. Organized bone within the lesion indicates that the dog lived for months-to-years following insult. Differential diagnoses initially included: sharp penetrating trauma; intrinsic or extrinsic blunt fracturing force; osteochondrosis or complication of an osteochondral lesion; unusual osteoarthritis; and neoplasia. Computed tomography ruled out normal or unusual osteoarthritis, and neoplasia. The nature and small size of the lesion, relatively small size of the dog, and lack of evidence for complicating infection, suggest against sharp penetrating trauma as a sole cause. The most plausible differential diagnoses include: uncommon fracture-producing force in a companion animal, and blunt intrinsic or extrinsic force causing fracture at a weak point, such as an early osteochondral lesion, that was obliterated by healing. Combined gross examination, micro-computed tomography, and archeological-anthropological influences facilitated refinement of differential diagnosis. Copyright © 2013 Elsevier Inc. All rights reserved.

Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013).

PubMed

Reddy, Krishna D; DeForte, Shelly; Uversky, Vladimir N

2014-01-01

The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

PubMed Central

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

2008-01-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

PubMed

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2007-05-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.

Functional Anthology of Intrinsic Disorder. III. Ligands, Postranslational Modifications and Diseases Associated with Intrinsically Disordered Proteins

PubMed Central

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

2008-01-01

Currently, the understanding of the relationships between function, amino acid sequence and protein structure continues to represent one of the major challenges of the modern protein science. As much as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bioinformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200,000 proteins from Swiss-Prot database, each annotated with at least one of the 875 functional keywords was described in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Using this tool, we have found that out of the 711 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). The second paper of the series was devoted to the presentation of 87 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions (Vucetic S., Xie H., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. II. Cellular components, domains, technical terms, developmental processes and coding sequence diversities correlated with long disordered regions. J. Proteome Res.). Protein structure and functionality can be modulated by various posttranslational modifications or/and as a result of binding of specific ligands. Numerous human diseases are associated with protein misfolding/misassembly/ misfunctioning. This work concludes the series of papers dedicated to the functional anthology of intrinsic disorder and describes ~80 Swiss-Prot functional keywords that are related to ligands, posttranslational modifications and diseases possessing strong positive or negative correlation with the predicted long disordered regions in proteins. PMID:17391016

Recombinant Intrinsically Disordered Proteins for NMR: Tips and Tricks.

PubMed

Calçada, Eduardo O; Korsak, Magdalena; Kozyreva, Tatiana

2015-01-01

The growing recognition of the several roles that intrinsically disordered proteins play in biology places an increasing importance on protein sample availability to allow the characterization of their structural and dynamic properties. The sample preparation is therefore the limiting step to allow any biophysical method being able to characterize the properties of an intrinsically disordered protein and to clarify the links between these properties and the associated biological functions. An increasing array of tools has been recruited to help prepare and characterize the structural and dynamic properties of disordered proteins. This chapter describes their sample preparation, covering the most common drawbacks/barriers usually found working in the laboratory bench. We want this chapter to be the bedside book of any scientist interested in preparing intrinsically disordered protein samples for further biophysical analysis.

Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.

PubMed

Wang, Chen; Uversky, Vladimir N; Kurgan, Lukasz

2016-05-01

Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions

PubMed Central

Hu, Gang; Wu, Zhonghua

2017-01-01

Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs. PMID:29257115

Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.

PubMed

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2007-05-01

Currently, the understanding of the relationships between function, amino acid sequence, and protein structure continues to represent one of the major challenges of the modern protein science. As many as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bionformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200 000 proteins from the Swiss-Prot database, each annotated with at least one of the 875 functional keywords, was described in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V.N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Using this tool, we have found that out of the 710 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (see above). The second paper of the series was devoted to the presentation of 87 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions (Vucetic, S.; Xie, H.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome Res. 2007, 5, 1899-1916). Protein structure and functionality can be modulated by various post-translational modifications or/and as a result of binding of specific ligands. Numerous human diseases are associated with protein misfolding/misassembly/misfunctioning. This work concludes the series of papers dedicated to the functional anthology of intrinsic disorder and describes approximately 80 Swiss-Prot functional keywords that are related to ligands, post-translational modifications, and diseases possessing strong positive or negative correlation with the predicted long disordered regions in proteins.

The Intrinsically X-Ray-weak Quasar PHL 1811. II. Optical and UV Spectra and Analysis

NASA Astrophysics Data System (ADS)

Leighly, Karen M.; Halpern, Jules P.; Jenkins, Edward B.; Casebeer, Darrin

2007-11-01

This is the second of two papers reporting observations and analysis of the unusually bright (mb=14.4), luminous (MB=-25.5), nearby (z=0.192) narrow-line quasar PHL 1811. The first paper reported that PHL 1811 is intrinsically X-ray-weak and presented a spectral energy distribution (SED). Here we present HST STIS optical and UV spectra, and ground-based optical spectra. The optical and UV line emission is very unusual. There is no evidence for forbidden or semiforbidden lines. The near-UV spectrum is dominated by very strong Fe II and Fe III, and unusual low-ionization lines such as Na I D and Ca II H and K are observed. High-ionization lines are very weak; C IV has an equivalent width of 6.6 Å, a factor of ~5 smaller than measured from quasar composite spectra. An unusual feature near 1200 Å can be deblended in terms of Lyα, N V, Si II, and C III* using the blueshifted C IV profile as a template. Photoionization modeling shows that the unusual line emission can be explained qualitatively by the unusually soft SED. Principally, a low gas temperature results in inefficient emission of collisionally excited lines, including the semiforbidden lines generally used as density diagnostics. The emission resembles that of high-density gas; in both cases this is a consequence of inefficient cooling. PHL 1811 is very unusual, but we note that quasar surveys may be biased against finding similar objects. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. These observations are associated with proposal 9181. Based on observations obtained at Kitt Peak National Observatory, a division of the National Optical Astronomy Observatories, which is operated by the Association of Universities for Research in Astronomy, Inc., under cooperative agreement with the National Science Foundation.

A Comprehensive Survey of the Roles of Highly Disordered Proteins in Type 2 Diabetes

PubMed Central

Du, Zhihua

2017-01-01

Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and players implicated in the manifestation and development of diabetes mellitus, proteins play several important roles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database has information on 34 human proteins experimentally shown to be related to the T2DM pathogenesis. It is known that many proteins associated with different human maladies are intrinsically disordered as a whole, or contain intrinsically disordered regions. The presented study shows that T2DM is not an exception to this rule, and many proteins known to be associated with pathogenesis of this malady are intrinsically disordered. The multiparametric bioinformatics analysis utilizing several computational tools for the intrinsic disorder characterization revealed that IRS1, IRS2, IRS4, MAFA, PDX1, ADIPO, PIK3R2, PIK3R5, SoCS1, and SoCS3 are expected to be highly disordered, whereas VDCC, SoCS2, SoCS4, JNK9, PRKCZ, PRKCE, insulin, GCK, JNK8, JNK10, PYK, INSR, TNF-α, MAPK3, and Kir6.2 are classified as moderately disordered proteins, and GLUT2, GLUT4, mTOR, SUR1, MAPK1, IKKA, PRKCD, PIK3CB, and PIK3CA are predicted as mostly ordered. More focused computational analyses and intensive literature mining were conducted for a set of highly disordered proteins related to T2DM. The resulting work represents a comprehensive survey describing the major biological functions of these proteins and functional roles of their intrinsically disordered regions, which are frequently engaged in protein–protein interactions, and contain sites of various posttranslational modifications (PTMs). It is also shown that intrinsic disorder-associated PTMs may play important roles in controlling the functions of these proteins. Consideration of the T2DM proteins from the perspective of intrinsic disorder provides useful information that can potentially lead to future experimental studies that may uncover latent and novel pathways associated with the disease. PMID:28934129

A Comprehensive Survey of the Roles of Highly Disordered Proteins in Type 2 Diabetes.

PubMed

Du, Zhihua; Uversky, Vladimir N

2017-09-21

Type 2 diabetes mellitus (T2DM) is a chronic and progressive disease that is strongly associated with hyperglycemia (high blood sugar) related to either insulin resistance or insufficient insulin production. Among the various molecular events and players implicated in the manifestation and development of diabetes mellitus, proteins play several important roles. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database has information on 34 human proteins experimentally shown to be related to the T2DM pathogenesis. It is known that many proteins associated with different human maladies are intrinsically disordered as a whole, or contain intrinsically disordered regions. The presented study shows that T2DM is not an exception to this rule, and many proteins known to be associated with pathogenesis of this malady are intrinsically disordered. The multiparametric bioinformatics analysis utilizing several computational tools for the intrinsic disorder characterization revealed that IRS1, IRS2, IRS4, MAFA, PDX1, ADIPO, PIK3R2, PIK3R5, SoCS1, and SoCS3 are expected to be highly disordered, whereas VDCC, SoCS2, SoCS4, JNK9, PRKCZ, PRKCE, insulin, GCK, JNK8, JNK10, PYK, INSR, TNF-α, MAPK3, and Kir6.2 are classified as moderately disordered proteins, and GLUT2, GLUT4, mTOR, SUR1, MAPK1, IKKA, PRKCD, PIK3CB, and PIK3CA are predicted as mostly ordered. More focused computational analyses and intensive literature mining were conducted for a set of highly disordered proteins related to T2DM. The resulting work represents a comprehensive survey describing the major biological functions of these proteins and functional roles of their intrinsically disordered regions, which are frequently engaged in protein-protein interactions, and contain sites of various posttranslational modifications (PTMs). It is also shown that intrinsic disorder-associated PTMs may play important roles in controlling the functions of these proteins. Consideration of the T2DM proteins from the perspective of intrinsic disorder provides useful information that can potentially lead to future experimental studies that may uncover latent and novel pathways associated with the disease.

Digested disorder

PubMed Central

Uversky, Vladimir N

2013-01-01

The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for “intrinsically disordered protein OR natively unfolded protein” returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a “Digested Disorder” project, which will encompass a series of reader’s digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest covers papers published during the period of January, February and March of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings. PMID:28516015

The alphabet of intrinsic disorder

PubMed Central

Uversky, Vladimir N

2013-01-01

The ability of a protein to fold into unique functional state or to stay intrinsically disordered is encoded in its amino acid sequence. Both ordered and intrinsically disordered proteins (IDPs) are natural polypeptides that use the same arsenal of 20 proteinogenic amino acid residues as their major building blocks. The exceptional structural plasticity of IDPs, their capability to exist as heterogeneous structural ensembles and their wide array of important disorder-based biological functions that complements functional repertoire of ordered proteins are all rooted within the peculiar differential usage of these building blocks by ordered proteins and IDPs. In fact, some residues (so-called disorder-promoting residues) are noticeably more common in IDPs than in sequences of ordered proteins, which, in their turn, are enriched in several order-promoting residues. Furthermore, residues can be arranged according to their “disorder promoting potencies,” which are evaluated based on the relative abundances of various amino acids in ordered and disordered proteins. This review continues a series of publications on the roles of different amino acids in defining the phenomenon of protein intrinsic disorder and concerns glutamic acid, which is the second most disorder-promoting residue. PMID:28516010

Global Conformational Selection and Local Induced Fit for the Recognition between Intrinsic Disordered p53 and CBP

PubMed Central

Yu, Qingfen; Ye, Wei; Wang, Wei; Chen, Hai-Feng

2013-01-01

The transactivation domain (TAD) of tumor suppressor p53 can bind with the nuclear coactivator binding domain (NCBD) of cyclic-AMP response element binding protein (CBP) and activate transcription. NMR experiments demonstrate that both apo-NCBD and TAD are intrinsic disordered and bound NCBD/TAD undergoes a transition to well folded. The recognition mechanism between intrinsic disordered proteins is still hotly debated. Molecular dynamics (MD) simulations in explicit solvent are used to study the recognition mechanism between intrinsic disordered TAD and NCBD. The average RMSD values between bound and corresponding apo states and Kolmogorov-Smirnov P test analysis indicate that TAD and NCBD may follow an induced fit mechanism. Quantitative analysis indicates there is also a global conformational selection. In summary, the recognition of TAD and NCBD might obey a local induced fit and global conformational selection. These conclusions are further supported by high-temperature unbinding kinetics and room temperature landscape analysis. These methods can be used to study the recognition mechanism of other intrinsic disordered proteins. PMID:23555731

Structural vs. intrinsic carriers: contrasting effects of cation chemistry and disorder on ionic conductivity in pyrochlores

DOE PAGES

Perriot, Romain; Uberuaga, Blas P.

2015-04-21

We use molecular dynamics simulations to investigate the role of cation disorder on oxygen diffusion in Gd 2Zr 2O 7 (GZO) and Gd 2Ti 2O 7 (GTO) pyrochlores, a class of complex oxides which contain a structural vacancy relative to the basic fluorite structure. The introduction of disorder has distinct effects depending on the chemistry of the material, increasing the mobility of structural carriers by up to four orders of magnitude in GZO. In contrast, in GTO, there is no mobility at zero or low disorder on the ns timescale, but higher disorder liberates the otherwise immobile carriers, allowing diffusionmore » with rates comparable to GZO for the fully disordered material. Here, we show that the cation disorder enhances the diffusivity by both increasing the concentration of mobile structural carriers and their individual mobility. The disorder also influences the diffusion in materials containing intrinsic carriers, such as additional vacancies VO or oxygen interstitials OI. And while in ordered GZO and GTO the contribution of the intrinsic carriers dominates the overall diffusion of oxygen, OI in GZO contributes along with structural carriers, and the total diffusion rate can be calculated by assuming simple additive contributions from the two sources. Although the disorder in the materials with intrinsic defects usually enhances the diffusivity as in the defect-free case, in low concentrations, cation antisites AB or BA, where A = Gd and B = Zr or Ti, can act as traps for fast intrinsic defects. The trapping results in a lowering of the diffusivity, and causes a non-monotonic behavior of the diffusivity with disorder. Conversely, in the case of slow intrinsic defects, the main effect of the disorder is to liberate the structural carriers, resulting in an increase of the diffusivity regardless of the defect trapping.« less

Electronegativity and intrinsic disorder of preeclampsia-related proteins.

PubMed

Polanco, Carlos; Castañón-González, Jorge Alberto; Uversky, Vladimir N; Buhse, Thomas; Samaniego Mendoza, José Lino; Calva, Juan J

2017-01-01

Preeclampsia, hemorrhage, and infection are the leading causes of maternal death in underdeveloped countries. Since several proteins associated with preeclampsia are known, we conducted a computational study which evaluated the commonness and potential functionality of intrinsic disorder of these proteins and also made an attempt to characterize their origin. The origin of the preeclampsia-related proteins was assessed with a supervised technique, a Polarity Index Method (PIM), which evaluates the electronegativity of proteins based solely on their sequence. The commonness of intrinsic disorder was evaluated using several disorder predictors from the PONDR family, the charge-hydropathy plot (CH-plot) and cumulative distribution function (CDF) analyses, and using the MobiDB web-based tool, whereas potential functionality of intrinsic disorder was studied with the D2P2 resource and ANCHOR predictor of disorder-based binding sites, and the STRING tool was used to build the interactivity networks of the preeclampsia-related proteins. Peculiarities of the PIM-derived polar profile of the group of preeclampsia-related proteins were then compared with profiles of a group of lipoproteins, antimicrobial peptides, angiogenesis-related proteins, and the intrinsically disordered proteins. Our results showed a high graphical correlation between preeclampsia proteins, lipoproteins, and the angiogenesis proteins. We also showed that many preeclampsia-related proteins contain numerous functional disordered regions. Therefore, these bioinformatics results led us to assume that the preeclampsia proteins are highly associated with the lipoproteins group, and that some preeclampsia-related proteins contain significant amounts of functional disorders.

Protein disorder in the human diseasome: unfoldomics of human genetic diseases

PubMed Central

Midic, Uros; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2009-01-01

Background Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685–8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases. Methods and findings We analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder. Conclusion These observations provide the basis for the construction of the human-genetic-disease-associated unfoldome. PMID:19594871

On the potential of using peculiarities of the protein intrinsic disorder distribution in mitochondrial cytochrome b to identify the source of animal meats

PubMed Central

Yacoub, Haitham A.; Sadek, Mahmoud A.; Uversky, Vladimir N.

2017-01-01

ABSTRACT This study was conducted to identify the source of animal meat based on the peculiarities of protein intrinsic disorder distribution in mitochondrial cytochrome b (mtCyt-b). The analysis revealed that animal and avian species can be discriminated based on the proportions of the two groups of residues, Leu+Ile, and Ser+Pro+Ala, in the amino acid sequences of their mtCyt-b. Although levels of the overall intrinsic disorder in mtCyt-b is not very high, the peculiarities of disorder distribution within the sequences of mtCyt-b from different species varies in a rather specific way. In fact, positions and intensities of disorder/flexibility “signals” in the corresponding disorder profiles are relatively unique for avian and animal species. Therefore, it is possible to devise a set of simple rules based on the peculiarities of disorder profiles of their mtCyt-b proteins to discriminate among species. This intrinsic disorder-based analysis represents a new technique that could be used to provide a promising solution for identification of the source of meats. PMID:28331777

The unfoldomics decade: an update on intrinsically disordered proteins.

PubMed

Dunker, A Keith; Oldfield, Christopher J; Meng, Jingwei; Romero, Pedro; Yang, Jack Y; Chen, Jessica Walton; Vacic, Vladimir; Obradovic, Zoran; Uversky, Vladimir N

2008-09-16

Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins. Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships. Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.

High-Throughput Characterization of Intrinsic Disorder in Proteins from the Protein Structure Initiative

PubMed Central

Johnson, Derrick E.; Xue, Bin; Sickmeier, Megan D.; Meng, Jingwei; Cortese, Marc S.; Oldfield, Christopher J.; Le Gall, Tanguy; Dunker, A. Keith; Uversky, Vladimir N.

2012-01-01

The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represent a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using Predictors of Natural Disordered Regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apo-myoglobin and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins. PMID:22651963

Abundance of intrinsic structural disorder in the histone H1 subtypes.

PubMed

Kowalski, Andrzej

2015-12-01

The intrinsically disordered proteins consist of partially structured regions linked to the unstructured stretches, which consequently form the transient and dynamic conformational ensembles. They undergo disorder to order transition upon binding their partners. Intrinsic disorder is attributed to histones H1, perceived as assemblers of chromatin structure and the regulators of DNA and proteins activity. In this work, the comparison of intrinsic disorder abundance in the histone H1 subtypes was performed both by the analysis of their amino acid composition and by the prediction of disordered stretches, as well as by identifying molecular recognition features (MoRFs) and ANCHOR protein binding regions (APBR) that are responsible for recognition and binding. Both human and model organisms-animals, plants, fungi and protists-have H1 histone subtypes with the properties typical of disordered state. They possess a significantly higher content of hydrophilic and charged amino acid residues, arranged in the long regions, covering over half of the whole amino acid residues in chain. Almost complete disorder corresponds to histone H1 terminal domains, including MoRFs and ANCHOR. Those motifs were also identified in a more ordered histone H1 globular domain. Compared to the control (globular and fibrous) proteins, H1 histones demonstrate the increased folding rate and a higher proportion of low-complexity segments. The results of this work indicate that intrinsic disorder is an inherent structural property of histone H1 subtypes and it is essential for establishing a protein conformation which defines functional outcomes affecting on DNA- and/or partner protein-dependent cell processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

WRN Mutation Update: Mutation Spectrum, Patient Registries, and Translational Prospects.

PubMed

Yokote, Koutaro; Chanprasert, Sirisak; Lee, Lin; Eirich, Katharina; Takemoto, Minoru; Watanabe, Aki; Koizumi, Naoko; Lessel, Davor; Mori, Takayasu; Hisama, Fuki M; Ladd, Paula D; Angle, Brad; Baris, Hagit; Cefle, Kivanc; Palanduz, Sukru; Ozturk, Sukru; Chateau, Antoinette; Deguchi, Kentaro; Easwar, T K M; Federico, Antonio; Fox, Amy; Grebe, Theresa A; Hay, Beverly; Nampoothiri, Sheela; Seiter, Karen; Streeten, Elizabeth; Piña-Aguilar, Raul E; Poke, Gemma; Poot, Martin; Posmyk, Renata; Martin, George M; Kubisch, Christian; Schindler, Detlev; Oshima, Junko

2017-01-01

Werner syndrome (WS) is a rare autosomal recessive disorder characterized by a constellation of adult onset phenotypes consistent with an acceleration of intrinsic biological aging. It is caused by pathogenic variants in the WRN gene, which encodes a multifunctional nuclear protein with exonuclease and helicase activities. WRN protein is thought to be involved in optimization of various aspects of DNA metabolism, including DNA repair, recombination, replication, and transcription. In this update, we summarize a total of 83 different WRN mutations, including eight previously unpublished mutations identified by the International Registry of Werner Syndrome (Seattle, WA) and the Japanese Werner Consortium (Chiba, Japan), as well as 75 mutations already reported in the literature. The Seattle International Registry recruits patients from all over the world to investigate genetic causes of a wide variety of progeroid syndromes in order to contribute to the knowledge of basic mechanisms of human aging. Given the unusually high prevalence of WS patients and heterozygous carriers in Japan, the major goal of the Japanese Consortium is to develop effective therapies and to establish management guidelines for WS patients in Japan and elsewhere. This review will also discuss potential translational approaches to this disorder, including those currently under investigation. © 2016 WILEY PERIODICALS, INC.

WRN Mutation Update: Mutation Spectrum, Patient Registries, and Translational Prospects

PubMed Central

Yokote, Koutaro; Chanprasert, Sirisak; Lee, Lin; Eirich, Katharina; Takemoto, Minoru; Watanabe, Aki; Koizumi, Naoko; Lessel, Davor; Mori, Takayasu; Hisama, Fuki M.; Ladd, Paula D.; Angle, Brad; Baris, Hagit; Cefle, Kivanc; Palanduz, Sukru; Ozturk, Sukru; Chateau, Antoinette; Deguchi, Kentaro; Easwar, T.K.M; Federico, Antonio; Fox, Amy; Grebe, Theresa A.; Hay, Beverly; Nampoothiri, Sheela; Seiter, Karen; Streeten, Elizabeth; Piña-Aguilar, Raul E.; Poke, Gemma; Poot, Martin; Posmyk, Renata; Martin, George M.; Kubisch, Christian; Schindler, Detlev; Oshima, Junko

2017-01-01

Werner syndrome (WS) is a rare autosomal recessive disorder characterized by a constellation of adult onset phenotypes consistent with an acceleration of intrinsic biological aging. It is caused by pathogenic variants in the WRN gene, which encodes a multifunctional nuclear protein with exonuclease and helicase activities. WRN protein is thought to be involved in optimization of various aspects of DNA metabolism, including DNA repair, recombination, replication, and transcription. In this update, we summarize a total of 83 different WRN mutations, including eight previously unpublished mutations identified by the International Registry of Werner Syndrome (Seattle, WA) and the Japanese Werner Consortium (Chiba, Japan), as well as 75 mutations already reported in the literature. The Seattle International Registry recruits patients from all over the world to investigate genetic causes of a wide variety of progeroid syndromes in order to contribute to the knowledge of basic mechanisms of human aging. Given the unusually high prevalence of WS patients and heterozygous carriers in Japan, the major goal of the Japanese Consortium is to develop effective therapies and to establish management guidelines for WS patients in Japan and elsewhere. This review will also discuss potential translational approaches to this disorder, including those currently under investigation. PMID:27667302

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perriot, Romain; Uberuaga, Blas P.

We use molecular dynamics simulations to investigate the role of cation disorder on oxygen diffusion in Gd 2Zr 2O 7 (GZO) and Gd 2Ti 2O 7 (GTO) pyrochlores, a class of complex oxides which contain a structural vacancy relative to the basic fluorite structure. The introduction of disorder has distinct effects depending on the chemistry of the material, increasing the mobility of structural carriers by up to four orders of magnitude in GZO. In contrast, in GTO, there is no mobility at zero or low disorder on the ns timescale, but higher disorder liberates the otherwise immobile carriers, allowing diffusionmore » with rates comparable to GZO for the fully disordered material. Here, we show that the cation disorder enhances the diffusivity by both increasing the concentration of mobile structural carriers and their individual mobility. The disorder also influences the diffusion in materials containing intrinsic carriers, such as additional vacancies VO or oxygen interstitials OI. And while in ordered GZO and GTO the contribution of the intrinsic carriers dominates the overall diffusion of oxygen, OI in GZO contributes along with structural carriers, and the total diffusion rate can be calculated by assuming simple additive contributions from the two sources. Although the disorder in the materials with intrinsic defects usually enhances the diffusivity as in the defect-free case, in low concentrations, cation antisites AB or BA, where A = Gd and B = Zr or Ti, can act as traps for fast intrinsic defects. The trapping results in a lowering of the diffusivity, and causes a non-monotonic behavior of the diffusivity with disorder. Conversely, in the case of slow intrinsic defects, the main effect of the disorder is to liberate the structural carriers, resulting in an increase of the diffusivity regardless of the defect trapping.« less

Understanding the Role of Intrinsic Disorder of Viral Proteins in the Oncogenicity of Different Types of HPV.

PubMed

Tamarozzi, Elvira Regina; Giuliatti, Silvana

2018-01-09

Intrinsic disorder is very important in the biological function of several proteins, and is directly linked to their foldability during interaction with their targets. There is a close relationship between the intrinsically disordered proteins and the process of carcinogenesis involving viral pathogens. Among these pathogens, we have highlighted the human papillomavirus (HPV) in this study. HPV is currently among the most common sexually transmitted infections, besides being the cause of several types of cancer. HPVs are divided into two groups, called high- and low-risk, based on their oncogenic potential. The high-risk HPV E6 protein has been the target of much research, in seeking treatments against HPV, due to its direct involvement in the process of cell cycle control. To understand the role of intrinsic disorder of the viral proteins in the oncogenic potential of different HPV types, the structural characteristics of intrinsically disordered regions of high and low-risk HPV E6 proteins were analyzed. In silico analyses of primary sequences, prediction of tertiary structures, and analyses of molecular dynamics allowed the observation of the behavior of such disordered regions in these proteins, thereby proving a direct relationship of structural variation with the degree of oncogenicity of HPVs. The results obtained may contribute to the development of new therapies, targeting the E6 oncoprotein, for the treatment of HPV-associated diseases.

Leuconostoc garlicum: an unusual pathogen in the era of vancomycin therapy.

PubMed

Kumar, Anil; Augustine, Deepthi; Mehta, Asmita; Dinesh, Kavitha R; Viswam, Darsana; Philip, Rosamma

2012-01-01

Leuconostoc garlicum, belonging to the family of Leuconostocaceae, is a catalase-negative, Gram-positive ovoid cocci, intrinsically resistant to vancomycin. Clinical infection by Leuconostoc garlicum is rare. We report a case of respiratory tract infection subsequent to vancomycin therapy.

The phenomenon of claimed memories of previous lives: possible interpretations and importance.

PubMed

Stevenson, I

2000-04-01

Several disorders or abnormalities observed in medicine and psychology are not explicable (or not fully explicable) by genetics and environmental influences, either alone or together. These include phobias and philias observed in early infancy, unusual play in childhood, homosexuality, gender identity disorder, a child's idea of having parents other than its own, differences in temperament manifested soon after birth, unusual birthmarks and their correspondence with wounds on a deceased person, unusual birth defects, and differences (physical and behavioral) between monozygotic twins. The hypothesis of previous lives can contribute to the further understanding of these phenomena. Copyright 2000 Harcourt Publishers Ltd.

Childhood and Current Autistic Features in Adolescents with Schizotypal Personality Disorder

PubMed Central

Esterberg, Michelle L.; Trotman, Hanan D.; Brasfield, Joy L.; Compton, Michael T.; Walker, Elaine F.

2008-01-01

The diagnostic boundaries between autistic- and schizophrenia-spectrum disorders have varied over the years, and some overlap in diagnostic criteria persists. The present study examined childhood and current signs of autistic disorder (AD) in adolescents with schizotypal personality disorder (SPD) or other personality disorders, as well as healthy controls. A structured interview was administered to rate participants’ current symptoms. Participants’ guardians were interviewed with the Autism Diagnostic Inventory-Revised (ADI-R), a clinical assessment of childhood and current autistic signs. Compared to both the other personality-disordered and healthy groups, adolescents with SPD were rated as having significantly more impairment on childhood and current social functioning, and having more unusual interests and behaviors. For the entire sample, impaired childhood social functioning and unusual interests and behaviors were associated with higher negative symptom scores. Current impairments in social functioning, unusual interests and behaviors, and communication were also linked with greater negative symptoms. However, neither childhood nor current autistic features significantly predicted later conversion to an Axis I psychotic disorder over the course of three years of follow-up. The findings indicate that past and current autistic signs are more common in adolescents with SPD, but neither current nor childhood autistic features are linked with conversion to psychosis. PMID:18554872

Increased Prevalence of Unusual Sensory Behaviors in Infants at Risk For, and Teens With, Autism Spectrum Disorder

ERIC Educational Resources Information Center

Van Etten, Hannah M.; Kaur, Maninderjit; Srinivasan, Sudha M.; Cohen, Shereen J.; Bhat, Anjana; Dobkins, Karen R.

2017-01-01

The current study investigated the prevalence and pattern of unusual sensory behaviors (USBs) in teens with Autism Spectrum Disorder (ASD) and infants (3-36 months) at risk for ASD. From two different sites (UCSD and UConn), caregivers of infants at high (n = 32) and low risk (n = 33) for ASD, and teenagers with (n = 12) and without ASD (n = 11),…

Genetic recombination is associated with intrinsic disorder in plant proteomes.

PubMed

Yruela, Inmaculada; Contreras-Moreira, Bruno

2013-11-09

Intrinsically disordered proteins, found in all living organisms, are essential for basic cellular functions and complement the function of ordered proteins. It has been shown that protein disorder is linked to the G + C content of the genome. Furthermore, recent investigations have suggested that the evolutionary dynamics of the plant nucleus adds disordered segments to open reading frames alike, and these segments are not necessarily conserved among orthologous genes. In the present work the distribution of intrinsically disordered proteins along the chromosomes of several representative plants was analyzed. The reported results support a non-random distribution of disordered proteins along the chromosomes of Arabidopsis thaliana and Oryza sativa, two model eudicot and monocot plant species, respectively. In fact, for most chromosomes positive correlations between the frequency of disordered segments of 30+ amino acids and both recombination rates and G + C content were observed. These analyses demonstrate that the presence of disordered segments among plant proteins is associated with the rates of genetic recombination of their encoding genes. Altogether, these findings suggest that high recombination rates, as well as chromosomal rearrangements, could induce disordered segments in proteins during evolution.

Digested disorder

PubMed Central

DeForte, Shelly; Reddy, Krishna D; Uversky, Vladimir N

2013-01-01

The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a “Digested Disorder” project and represent a series of reader’s digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings. PMID:28516028

Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains

PubMed Central

Williams, Robert W; Xue, Bin; Uversky, Vladimir N; Dunker, A Keith

2013-01-01

The Pfam database groups regions of proteins by how well hidden Markov models (HMMs) can be trained to recognize similarities among them. Conservation pressure is probably in play here. The Pfam seed training set includes sequence and structure information, being drawn largely from the PDB. A long standing hypothesis among intrinsically disordered protein (IDP) investigators has held that conservation pressures are also at play in the evolution of different kinds of intrinsic disorder, but we find that predicted intrinsic disorder (PID) is not always conserved across Pfam domains. Here we analyze distributions and clusters of PID regions in 193024 members of the version 23.0 Pfam seed database. To include the maximum information available for proteins that remain unfolded in solution, we employ the 10 linearly independent Kidera factors1–3 for the amino acids, combined with PONDR4 predictions of disorder tendency, to transform the sequences of these Pfam members into an 11 column matrix where the number of rows is the length of each Pfam region. Cluster analyses of the set of all regions, including those that are folded, show 6 groupings of domains. Cluster analyses of domains with mean VSL2b scores greater than 0.5 (half predicted disorder or more) show at least 3 separated groups. It is hypothesized that grouping sets into shorter sequences with more uniform length will reveal more information about intrinsic disorder and lead to more finely structured and perhaps more accurate predictions. HMMs could be trained to include this information. PMID:28516017

Disorder in milk proteins: caseins, intrinsically disordered colloids.

PubMed

Redwan, Elrashdy M; Xue, Bin; Almehdar, Hussein A; Uversky, Vladimir N

2015-01-01

This article opens a series of reviews on the abundance and roles of intrinsic disorder in milk proteins. The focus of this introductory article on caseins is symbolic, since caseins were among the first recognized functional unfolded proteins and since they are definitely the most disordered, the most abundant, and the most studied of all milk proteins. In eutherian milks, the casein family includes at least three and usually four major members (αs1-, αs2-, β-, and κ-caseins) that are unrelated in sequence. However, in some species, two different αS2-casein genes are active, and therefore the total number of caseins can be as high as five. These proteins have found a number of uses in food industry. The functional repertoire of caseins ranges from nutritional function to involvement in the improving and/or maintaining cardiovascular health, to crucial contribution to the milk capacity to transport calcium phosphate, to serve as molecular chaperones, and to protect the mother's mammary gland against amyloidoses and ectopic calcification. An intricate feature of caseins is their ability to assemble to colloidal protein particles, casein micelles, serving to sequester and transport amorphous calcium phosphate. These and many other functions of caseins are obviously dependent on their intrinsically disordered nature and are controlled by various posttranslational modifications. Since various aspects of casein structure and function are rather well studied and since several recent reviews emphasized the functional roles of caseins' intrinsic disorder, the major goal of this article is to show how intrinsic disorder is encoded in the amino acid sequences of these proteins.

The fragmented self: imbalance between intrinsic and extrinsic self-networks in psychotic disorders.

PubMed

Ebisch, Sjoerd J H; Aleman, André

2016-08-01

Self-disturbances are among the core features of schizophrenia and related psychotic disorders. The basic structure of the self could depend on the balance between intrinsic and extrinsic self-processing. We discuss studies on self-related processing in psychotic disorders that provide converging evidence for disrupted communication between neural networks subserving the so-called intrinsic self and extrinsic self. This disruption might be mainly caused by impaired integrity of key brain hubs. The intrinsic self has been associated with cortical midline structures involved in self-referential processing, autobiographical memory, and emotional evaluation. Additionally, we highlight central aspects of the extrinsic self in its interaction with the environment using sensorimotor networks, including self-experience in sensation and actions. A deficient relationship between these self-aspects because of disrupted between-network interactions offers a framework to explain core clinical features of psychotic disorders. In particular, we show how relative isolation and reduced modularity of networks subserving intrinsic and extrinsic self-processing might trigger the emergence of hallucinations and delusions, and why patients with psychosis typically have difficulties with self-other relationships and do not recognise mental problems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dopamine in the medial amygdala network mediates human bonding.

PubMed

Atzil, Shir; Touroutoglou, Alexandra; Rudy, Tali; Salcedo, Stephanie; Feldman, Ruth; Hooker, Jacob M; Dickerson, Bradford C; Catana, Ciprian; Barrett, Lisa Feldman

2017-02-28

Research in humans and nonhuman animals indicates that social affiliation, and particularly maternal bonding, depends on reward circuitry. Although numerous mechanistic studies in rodents demonstrated that maternal bonding depends on striatal dopamine transmission, the neurochemistry supporting maternal behavior in humans has not been described so far. In this study, we tested the role of central dopamine in human bonding. We applied a combined functional MRI-PET scanner to simultaneously probe mothers' dopamine responses to their infants and the connectivity between the nucleus accumbens (NAcc), the amygdala, and the medial prefrontal cortex (mPFC), which form an intrinsic network (referred to as the "medial amygdala network") that supports social functioning. We also measured the mothers' behavioral synchrony with their infants and plasma oxytocin. The results of this study suggest that synchronous maternal behavior is associated with increased dopamine responses to the mother's infant and stronger intrinsic connectivity within the medial amygdala network. Moreover, stronger network connectivity is associated with increased dopamine responses within the network and decreased plasma oxytocin. Together, these data indicate that dopamine is involved in human bonding. Compared with other mammals, humans have an unusually complex social life. The complexity of human bonding cannot be fully captured in nonhuman animal models, particularly in pathological bonding, such as that in autistic spectrum disorder or postpartum depression. Thus, investigations of the neurochemistry of social bonding in humans, for which this study provides initial evidence, are warranted.

Network organization is globally atypical in autism: A graph theory study of intrinsic functional connectivity.

PubMed

Keown, Christopher L; Datko, Michael C; Chen, Colleen P; Maximo, José Omar; Jahedi, Afrooz; Müller, Ralph-Axel

2017-01-01

Despite abundant evidence of brain network anomalies in autism spectrum disorder (ASD), findings have varied from broad functional underconnectivity to broad overconnectivity. Rather than pursuing overly simplifying general hypotheses ('under' vs. 'over'), we tested the hypothesis of atypical network distribution in ASD (i.e., participation of unusual loci in distributed functional networks). We used a selective high-quality data subset from the ABIDE datashare (including 111 ASD and 174 typically developing [TD] participants) and several graph theory metrics. Resting state functional MRI data were preprocessed and analyzed for detection of low-frequency intrinsic signal correlations. Groups were tightly matched for available demographics and head motion. As hypothesized, the Rand Index (reflecting how similar network organization was to a normative set of networks) was significantly lower in ASD than TD participants. This was accounted for by globally reduced cohesion and density, but increased dispersion of networks. While differences in hub architecture did not survive correction, rich club connectivity (among the hubs) was increased in the ASD group. Our findings support the model of reduced network integration (connectivity with networks) and differentiation (or segregation; based on connectivity outside network boundaries) in ASD. While the findings applied at the global level, they were not equally robust across all networks and in one case (greater cohesion within ventral attention network in ASD) even reversed.

Digested disorder

PubMed Central

Reddy, Krishna D; DeForte, Shelly; Uversky, Vladimir N

2014-01-01

The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a “Digested Disorder” project and represent a new issue of reader’s digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings. PMID:28232877

Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast.

PubMed

Popelka, Hana; Uversky, Vladimir N; Klionsky, Daniel J

2014-06-01

The mechanism of autophagy relies on complex cell signaling and regulatory processes. Each cell contains many proteins that lack a rigid 3-dimensional structure under physiological conditions. These dynamic proteins, called intrinsically disordered proteins (IDPs) and protein regions (IDPRs), are predominantly involved in cell signaling and regulation. Yet, very little is known about their presence among proteins of the core autophagy machinery. In this work, we characterized the autophagy protein Atg3 from yeast and human along with 2 variants to show that Atg3 is an IDPRs-containing protein and that disorder/order predicted for these proteins from their amino acid sequence corresponds to their experimental characteristics. Based on this consensus, we applied the same prediction methods to all known Atg proteins from Saccharomyces cerevisiae. The data presented here provide an insight into the structural dynamics of each Atg protein. They also show that intrinsic disorder at various levels has to be taken into consideration for about half of the Atg proteins. This work should become a useful tool that will facilitate and encourage exploration of protein intrinsic disorder in autophagy.

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

PubMed

Awile, Omar; Krisko, Anita; Sbalzarini, Ivo F; Zagrovic, Bojan

2010-07-15

The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity.

Human long intrinsically disordered protein regions are frequent targets of positive selection.

PubMed

Afanasyeva, Arina; Bockwoldt, Mathias; Cooney, Christopher R; Heiland, Ines; Gossmann, Toni I

2018-06-01

Intrinsically disordered regions occur frequently in proteins and are characterized by a lack of a well-defined three-dimensional structure. Although these regions do not show a higher order of structural organization, they are known to be functionally important. Disordered regions are rapidly evolving, largely attributed to relaxed purifying selection and an increased role of genetic drift. It has also been suggested that positive selection might contribute to their rapid diversification. However, for our own species, it is currently unknown whether positive selection has played a role during the evolution of these protein regions. Here, we address this question by investigating the evolutionary pattern of more than 6600 human proteins with intrinsically disordered regions and their ordered counterparts. Our comparative approach with data from more than 90 mammalian genomes uses a priori knowledge of disordered protein regions, and we show that this increases the power to detect positive selection by an order of magnitude. We can confirm that human intrinsically disordered regions evolve more rapidly, not only within humans but also across the entire mammalian phylogeny. They have, however, experienced substantial evolutionary constraint, hinting at their fundamental functional importance. We find compelling evidence that disordered protein regions are frequent targets of positive selection and estimate that the relative rate of adaptive substitutions differs fourfold between disordered and ordered protein regions in humans. Our results suggest that disordered protein regions are important targets of genetic innovation and that the contribution of positive selection in these regions is more pronounced than in other protein parts. © 2018 Afanasyeva et al.; Published by Cold Spring Harbor Laboratory Press.

An unusual cause of stridor in a neonate.

PubMed

Fah, K K; Tan, H K

1994-01-01

We report an unusual case of unilateral vocal fold palsy due to intracranial haemorrhage in a neonate with undiagnosed haemophilia A. Bleeding disorders in neonates are briefly discussed and the importance of a systemic investigation of stridor in children is emphasized.

Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range.

PubMed

Milles, Sigrid; Koehler, Christine; Gambin, Yann; Deniz, Ashok A; Lemke, Edward A

2012-10-01

Single molecule observation of fluorescence resonance energy transfer can be used to provide insight into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsically disordered proteins.

Intramolecular Three-Colour Single Pair FRET of Intrinsically Disordered Proteins with Increased Dynamic Range

PubMed Central

Milles, Sigrid; Koehler, Christine; Gambin, Yann

2012-01-01

Single molecule observation of fluorescence resonance energy transfer can be used to provide insights into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsically disordered proteins. PMID:22739670

Genes encoding intrinsic disorder in Eukaryota have high GC content

PubMed Central

Peng, Zhenling; Uversky, Vladimir N.

2016-01-01

ABSTRACT We analyze a correlation between the GC content in genes of 12 eukaryotic species and the level of intrinsic disorder in their corresponding proteins. Comprehensive computational analysis has revealed that the disordered regions in eukaryotes are encoded by the GC-enriched gene regions and that this enrichment is correlated with the amount of disorder and is present across proteins and species characterized by varying amounts of disorder. The GC enrichment is a result of higher rate of amino acid coded by GC-rich codons in the disordered regions. Individual amino acids have the same GC-content profile between different species. Eukaryotic proteins with the disordered regions encoded by the GC-enriched gene segments carry out important biological functions including interactions with RNAs, DNAs, nucleotides, binding of calcium and metal ions, are involved in transcription, transport, cell division and certain signaling pathways, and are localized primarily in nucleus, cytosol and cytoplasm. We also investigate a possible relationship between GC content, intrinsic disorder and protein evolution. Analysis of a devised “age” of amino acids, their disorder-promoting capacity and the GC-enrichment of their codons suggests that the early amino acids are mostly disorder-promoting and their codons are GC-rich while most of late amino acids are mostly order-promoting. PMID:28232902

Is schizoaffective disorder a distinct categorical diagnosis? A critical review of the literature

PubMed Central

Abrams, Daniel J; Rojas, Donald C; Arciniegas, David B

2008-01-01

Considerable debate surrounds the inclusion of schizoaffective disorder in psychiatric nosology. Schizoaffective disorder may be a variant of schizophrenia in which mood symptoms are unusually prominent but not unusual in type. This condition may instead reflect a severe form of either major depressive or bipolar disorder in which episode-related psychotic symptoms fail to remit completely between mood episodes. Alternatively, schizoaffective disorder may reflect the co-occurrence of two relatively common psychiatric illnesses, schizophrenia and a mood disorder (major depressive or bipolar disorder). Each of these formulations of schizoaffective disorder presents nosological challenges because the signs and symptoms of this condition cross conventional categorical diagnostic boundaries between psychotic disorders and mood disorders. The study, evaluation, and treatment of persons presently diagnosed with schizoaffective may be more usefully informed by a dimensional approach. It is in this context that this article reviews and contrasts the categorical and dimensional approaches to its description, neurobiology, and treatment. Based on this review, an argument for the study and treatment of this condition using a dimensional approach is offered. PMID:19337453

Learning to learn – intrinsic plasticity as a metaplasticity mechanism for memory formation

PubMed Central

Sehgal, Megha; Song, Chenghui; Ehlers, Vanessa L.; Moyer, James R.

2013-01-01

“Use it or lose it” is a popular adage often associated with use-dependent enhancement of cognitive abilities. Much research has focused on understanding exactly how the brain changes as a function of experience. Such experience-dependent plasticity involves both structural and functional alterations that contribute to adaptive behaviors, such as learning and memory, as well as maladaptive behaviors, including anxiety disorders, phobias, and posttraumatic stress disorder. With the advancing age of our population, understanding how use-dependent plasticity changes across the lifespan may also help to promote healthy brain aging. A common misconception is that such experience-dependent plasticity (e.g., associative learning) is synonymous with synaptic plasticity. Other forms of plasticity also play a critical role in shaping adaptive changes within the nervous system, including intrinsic plasticity – a change in the intrinsic excitability of a neuron. Intrinsic plasticity can result from a change in the number, distribution or activity of various ion channels located throughout the neuron. Here, we review evidence that intrinsic plasticity is an important and evolutionarily conserved neural correlate of learning. Intrinsic plasticity acts as a metaplasticity mechanism by lowering the threshold for synaptic changes. Thus, learning-related intrinsic changes can facilitate future synaptic plasticity and learning. Such intrinsic changes can impact the allocation of a memory trace within a brain structure, and when compromised, can contribute to cognitive decline during the aging process. This unique role of intrinsic excitability can provide insight into how memories are formed and, more interestingly, how neurons that participate in a memory trace are selected. Most importantly, modulation of intrinsic excitability can allow for regulation of learning ability – this can prevent or provide treatment for cognitive decline not only in patients with clinical disorders but also in the aging population. PMID:23871744

Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions.

PubMed

Gruet, Antoine; Dosnon, Marion; Blocquel, David; Brunel, Joanna; Gerlier, Denis; Das, Rahul K; Bonetti, Daniela; Gianni, Stefano; Fuxreiter, Monika; Longhi, Sonia; Bignon, Christophe

2016-02-01

Despite the partial disorder-to-order transition that intrinsically disordered proteins often undergo upon binding to their partners, a considerable amount of residual disorder may be retained in the bound form, resulting in a fuzzy complex. Fuzzy regions flanking molecular recognition elements may enable partner fishing through non-specific, transient contacts, thereby facilitating binding, but may also disfavor binding through various mechanisms. So far, few computational or experimental studies have addressed the effect of fuzzy appendages on partner recognition by intrinsically disordered proteins. In order to shed light onto this issue, we used the interaction between the intrinsically disordered C-terminal domain of the measles virus (MeV) nucleoprotein (NTAIL ) and the X domain (XD) of the viral phosphoprotein as model system. After binding to XD, the N-terminal region of NTAIL remains conspicuously disordered, with α-helical folding taking place only within a short molecular recognition element. To study the effect of the N-terminal fuzzy region on NTAIL /XD binding, we generated N-terminal truncation variants of NTAIL , and assessed their binding abilities towards XD. The results revealed that binding increases with shortening of the N-terminal fuzzy region, with this also being observed with hsp70 (another MeV NTAIL binding partner), and for the homologous NTAIL /XD pairs from the Nipah and Hendra viruses. Finally, similar results were obtained when the MeV NTAIL fuzzy region was replaced with a highly dissimilar artificial disordered sequence, supporting a sequence-independent inhibitory effect of the fuzzy region. © 2015 Federation of European Biochemical Societies.

Bipolar Disorder.

ERIC Educational Resources Information Center

Spearing, Melissa

Bipolar disorder, a brain disorder that causes unusual shifts in a person's mood, affects approximately one percent of the population. It commonly occurs in late adolescence and is often unrecognized. The diagnosis of bipolar disorder is made on the basis of symptoms, course of illness, and when possible, family history. Thoughts of suicide are…

Structural disorder within sendai virus nucleoprotein and phosphoprotein: insight into the structural basis of molecular recognition.

PubMed

Jensen, Malene Ringkjøbing; Bernadó, Pau; Houben, Klaartje; Blanchard, Laurence; Marion, Dominque; Ruigrok, Rob W H; Blackledge, Martin

2010-08-01

Intrinsically disordered regions of significant length are present throughout eukaryotic genomes, and are particularly prevalent in viral proteins. Due to their inherent flexibility, these proteins inhabit a conformational landscape that is too complex to be described by classical structural biology. The elucidation of the role that conformational flexibility plays in molecular function will redefine our understanding of the molecular basis of biological function, and the development of appropriate technology to achieve this aim remains one of the major challenges for the future of structural biology. NMR is the technique of choice for studying intrinsically disordered proteins, providing information about structure, flexibility and interactions at atomic resolution even in completely disordered proteins. In particular residual dipolar couplings (RDCs) are sensitive and powerful tools for determining local and long-range structural behaviour in flexible proteins. Here we describe recent applications of the use of RDCs to quantitatively describe the level of local structure in intrinsically disordered proteins involved in replication and transcription in Sendai virus.

The role of intrinsic disorder and dynamics in the assembly and function of the type II secretion system.

PubMed

Gu, Shuang; Shevchik, Vladimir E; Shaw, Rosie; Pickersgill, Richard W; Garnett, James A

2017-10-01

Many Gram-negative commensal and pathogenic bacteria use a type II secretion system (T2SS) to transport proteins out of the cell. These exported proteins or substrates play a major role in toxin delivery, maintaining biofilms, replication in the host and subversion of host immune responses to infection. We review the current structural and functional work on this system and argue that intrinsically disordered regions and protein dynamics are central for assembly, exo-protein recognition, and secretion competence of the T2SS. The central role of intrinsic disorder-order transitions in these processes may be a particular feature of type II secretion. Copyright © 2017 Elsevier B.V. All rights reserved.

Consequences of inducing intrinsic disorder in a high-affinity protein-protein interaction.

PubMed

Papadakos, Grigorios; Sharma, Amit; Lancaster, Lorna E; Bowen, Rebecca; Kaminska, Renata; Leech, Andrew P; Walker, Daniel; Redfield, Christina; Kleanthous, Colin

2015-04-29

The kinetic and thermodynamic consequences of intrinsic disorder in protein-protein recognition are controversial. We address this by inducing one partner of the high-affinity colicin E3 rRNase domain-Im3 complex (K(d) ≈ 10(-12) M) to become an intrinsically disordered protein (IDP). Through a variety of biophysical measurements, we show that a single alanine mutation at Tyr507 within the hydrophobic core of the isolated colicin E3 rRNase domain causes the enzyme to become an IDP (E3 rRNase(IDP)). E3 rRNase(IDP) binds stoichiometrically to Im3 and forms a structure that is essentially identical to the wild-type complex. However, binding of E3 rRNase(IDP) to Im3 is 4 orders of magnitude weaker than that of the folded rRNase, with thermodynamic parameters reflecting the disorder-to-order transition on forming the complex. Critically, pre-steady-state kinetic analysis of the E3 rRNase(IDP)-Im3 complex demonstrates that the decrease in affinity is mostly accounted for by a drop in the electrostatically steered association rate. Our study shows that, notwithstanding the advantages intrinsic disorder brings to biological systems, this can come at severe kinetic and thermodynamic cost.

A nationwide, cross-sectional survey on unusual sleep postures and sleep-disordered breathing-related symptoms in people with Down syndrome.

PubMed

Kuroda, H; Sawatari, H; Ando, S; Ohkusa, T; Rahmawati, A; Ono, J; Nishizaka, M; Hashiguchi, N; Matsuoka, F; Chishaki, A

2017-07-01

People with Down syndrome (DS) often have sleep-disordered breathing (SDB). Unusual sleep postures, such as leaning forward and sitting, are observed in people with DS. This study aimed to clarify the prevalence of unusual sleep postures and their relationships with SDB-related symptoms (SDB-RSs), such as snoring, witnessed apnoea, nocturnal awakening and excessive daytime sleepiness. A questionnaire, including demographic characteristics and the presence of unusual sleep postures, as well as SDB-RSs, was completed by 1149 parents of people with DS from Japan. Unusual sleep postures were recorded in 483 (42.0%) people with DS. These participants were significantly younger and had a history of low muscle tone more frequently than people without unusual sleep postures. In all ages, the leaning forward posture was more frequent than sitting. People with DS with unusual sleep postures suffered from SDB-RSs. Those who slept in the sitting posture had more frequent SDB-RSs than did those who slept with the leaning forward posture. Snoring, witnessed apnoea and nocturnal awakening were observed in 73.6, 27.2 and 58.2% of participants, respectively. Snoring increased with aging. Witnessed apnoea was more common in males and in those with hypothyroidism than in females and in those without hypothyroidism. Our study shows that there is a close relationship between unusual sleep postures and SDB-RSs. We recommend that all people with DS with unusual sleep postures should be checked for the presence of SDB. © 2017 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

PubMed Central

Tomasso, Maria E.; Tarver, Micheal J.; Devarajan, Deepa; Whitten, Steven T.

2016-01-01

The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PP II) structure. While intrinsic PP II propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (R h) can be predicted from experimental PP II propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that R h and chain propensity for PP II structure are linked via a simple power-law scaling relationship, which was tested using the experimental R h of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on R h were found to be generally weak when compared to PP II effects on R h. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PP II structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides. PMID:26727467

Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins.

PubMed

Uversky, Vladimir N

2015-03-01

Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins or regions that do not have unique 3D structures under functional conditions. Therefore, from the viewpoint of their lack of stable 3D structure, IDPs/IDPRs are inherently unstable. As much as structure and function of normal ordered globular proteins are determined by their amino acid sequences, the lack of unique 3D structure in IDPs/IDPRs and their disorder-based functionality are also encoded in the amino acid sequences. Because of their specific sequence features and distinctive conformational behavior, these intrinsically unstable proteins or regions have several applications in biotechnology. This review introduces some of the most characteristic features of IDPs/IDPRs (such as peculiarities of amino acid sequences of these proteins and regions, their major structural features, and peculiar responses to changes in their environment) and describes how these features can be used in the biotechnology, for example for the proteome-wide analysis of the abundance of extended IDPs, for recombinant protein isolation and purification, as polypeptide nanoparticles for drug delivery, as solubilization tools, and as thermally sensitive carriers of active peptides and proteins. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unusual Thermoelectric Behavior Indicating a Hopping to Bandlike Transport Transition in Pentacene

NASA Astrophysics Data System (ADS)

Germs, W. Chr.; Guo, K.; Janssen, R. A. J.; Kemerink, M.

2012-07-01

An unusual increase in the Seebeck coefficient with increasing charge carrier density is observed in pentacene thin film transistors. This behavior is interpreted as being due to a transition from hopping transport in static localized states to bandlike transport, occurring at temperatures below ˜250K. Such a transition can be expected for organic materials in which both static energetic disorder and dynamic positional disorder are important. While clearly visible in the temperature and density dependent Seebeck coefficient, the transition hardly shows up in the charge carrier mobility.

Clinical Practice Guideline for the Treatment of Intrinsic Circadian Rhythm Sleep-Wake Disorders: Advanced Sleep-Wake Phase Disorder (ASWPD), Delayed Sleep-Wake Phase Disorder (DSWPD), Non-24-Hour Sleep-Wake Rhythm Disorder (N24SWD), and Irregular Sleep-Wake Rhythm Disorder (ISWRD). An Update for 2015

PubMed Central

Auger, R. Robert; Burgess, Helen J.; Emens, Jonathan S.; Deriy, Ludmila V.; Thomas, Sherene M.; Sharkey, Katherine M.

2015-01-01

A systematic literature review and meta-analyses (where appropriate) were performed and the GRADE approach was used to update the previous American Academy of Sleep Medicine Practice Parameters on the treatment of intrinsic circadian rhythm sleep-wake disorders. Available data allowed for positive endorsement (at a second-tier degree of confidence) of strategically timed melatonin (for the treatment of DSWPD, blind adults with N24SWD, and children/ adolescents with ISWRD and comorbid neurological disorders), and light therapy with or without accompanying behavioral interventions (adults with ASWPD, children/adolescents with DSWPD, and elderly with dementia). Recommendations against the use of melatonin and discrete sleep-promoting medications are provided for demented elderly patients, at a second- and first-tier degree of confidence, respectively. No recommendations were provided for remaining treatments/ populations, due to either insufficient or absent data. Areas where further research is needed are discussed. Citation: Auger RR, Burgess HJ, Emens JS, Deriy LV, Thomas SM, Sharkey KM. Clinical practice guideline for the treatment of intrinsic circadian rhythm sleep-wake disorders: advanced sleep-wake phase disorder (ASWPD), delayed sleep-wake phase disorder (DSWPD), non-24-hour sleep-wake rhythm disorder (N24SWD), and irregular sleep-wake rhythm disorder (ISWRD). An update for 2015. J Clin Sleep Med 2015;11(10):1199–1236. PMID:26414986

Eating Disorders among College Women.

ERIC Educational Resources Information Center

Basow, Susan A.; Schneck, Renae

In the past 10 years, eating disorders among adolescent females have become of increasing concern. To assess the prevalence of eating disorders, unusual eating-related behaviors and attitudes, and psychological states among college women, 677 women, from three private northeastern United States colleges, completed a questionnaire assessing…

Dopamine in the medial amygdala network mediates human bonding

PubMed Central

Touroutoglou, Alexandra; Rudy, Tali; Salcedo, Stephanie; Feldman, Ruth; Hooker, Jacob M.; Dickerson, Bradford C.; Catana, Ciprian; Barrett, Lisa Feldman

2017-01-01

Research in humans and nonhuman animals indicates that social affiliation, and particularly maternal bonding, depends on reward circuitry. Although numerous mechanistic studies in rodents demonstrated that maternal bonding depends on striatal dopamine transmission, the neurochemistry supporting maternal behavior in humans has not been described so far. In this study, we tested the role of central dopamine in human bonding. We applied a combined functional MRI-PET scanner to simultaneously probe mothers’ dopamine responses to their infants and the connectivity between the nucleus accumbens (NAcc), the amygdala, and the medial prefrontal cortex (mPFC), which form an intrinsic network (referred to as the “medial amygdala network”) that supports social functioning. We also measured the mothers’ behavioral synchrony with their infants and plasma oxytocin. The results of this study suggest that synchronous maternal behavior is associated with increased dopamine responses to the mother’s infant and stronger intrinsic connectivity within the medial amygdala network. Moreover, stronger network connectivity is associated with increased dopamine responses within the network and decreased plasma oxytocin. Together, these data indicate that dopamine is involved in human bonding. Compared with other mammals, humans have an unusually complex social life. The complexity of human bonding cannot be fully captured in nonhuman animal models, particularly in pathological bonding, such as that in autistic spectrum disorder or postpartum depression. Thus, investigations of the neurochemistry of social bonding in humans, for which this study provides initial evidence, are warranted. PMID:28193868

N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins.

PubMed

Das, Rahul K; Crick, Scott L; Pappu, Rohit V

2012-02-17

Basic region leucine zippers (bZIPs) are modular transcription factors that play key roles in eukaryotic gene regulation. The basic regions of bZIPs (bZIP-bRs) are necessary and sufficient for DNA binding and specificity. Bioinformatic predictions and spectroscopic studies suggest that unbound monomeric bZIP-bRs are uniformly disordered as isolated domains. Here, we test this assumption through a comparative characterization of conformational ensembles for 15 different bZIP-bRs using a combination of atomistic simulations and circular dichroism measurements. We find that bZIP-bRs have quantifiable preferences for α-helical conformations in their unbound monomeric forms. This helicity varies from one bZIP-bR to another despite a significant sequence similarity of the DNA binding motifs (DBMs). Our analysis reveals that intramolecular interactions between DBMs and eight-residue segments directly N-terminal to DBMs are the primary modulators of bZIP-bR helicities. We test the accuracy of this inference by designing chimeras of bZIP-bRs to have either increased or decreased overall helicities. Our results yield quantitative insights regarding the relationship between sequence and the degree of intrinsic disorder within bZIP-bRs, and might have general implications for other intrinsically disordered proteins. Understanding how natural sequence variations lead to modulation of disorder is likely to be important for understanding the evolution of specificity in molecular recognition through intrinsically disordered regions (IDRs). Copyright © 2011 Elsevier Ltd. All rights reserved.

How disordered is my protein and what is its disorder for? A guide through the “dark side” of the protein universe

PubMed Central

Lieutaud, Philippe; Uversky, Alexey V.; Uversky, Vladimir N.; Longhi, Sonia

2016-01-01

ABSTRACT In the last 2 decades it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins lack a stable 3D structure, are ubiquitous and fulfill essential biological functions. Their conformational heterogeneity is encoded in their amino acid sequences, thereby allowing intrinsically disordered proteins or regions to be recognized based on properties of these sequences. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray crystallization. This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved in induced folding. It also provides a set of detailed instructions that should be followed to perform computational analysis of disorder. PMID:28232901

Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin.

PubMed

Bhattacharya, Arpan; Bhowmik, Soumitra; Singh, Amit K; Kodgire, Prashant; Das, Apurba K; Mukherjee, Tushar Kanti

2017-10-10

The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.

Out and Down: Incarceration and Psychiatric Disorders

ERIC Educational Resources Information Center

Schnittker, Jason; Massoglia, Michael; Uggen, Christopher

2012-01-01

Psychiatric disorders are unusually prevalent among current and former inmates, but it is not known what this relationship reflects. A putative causal relationship is contaminated by assorted influences, including childhood disadvantage, the early onset of most disorders, and the criminalization of substance use. Using the National Comorbidity…

Altered striatal intrinsic functional connectivity in pediatric anxiety

PubMed Central

Dorfman, Julia; Benson, Brenda; Farber, Madeline; Pine, Daniel; Ernst, Monique

2016-01-01

Anxiety disorders are among the most common psychiatric disorders of adolescence. Behavioral and task-based imaging studies implicate altered reward system function, including striatal dysfunction, in adolescent anxiety. However, no study has yet examined alterations of the striatal intrinsic functional connectivity in adolescent anxiety disorders. The current study examines striatal intrinsic functional connectivity (iFC), using six bilateral striatal seeds, among 35 adolescents with anxiety disorders and 36 healthy comparisons. Anxiety is associated with abnormally low iFC within the striatum (e.g., between nucleus accumbens and caudate nucleus), and between the striatum and prefrontal regions, including subgenual anterior cingulate cortex, posterior insula and supplementary motor area. The current findings extend prior behavioral and task-based imaging research, and provide novel data implicating decreased striatal iFC in adolescent anxiety. Alterations of striatal neurocircuitry identified in this study may contribute to the perturbations in the processing of motivational, emotional, interoceptive, and motor information seen in pediatric anxiety disorders. This pattern of the striatal iFC perturbations can guide future research on specific mechanisms underlying anxiety. PMID:27004799

Multifarious Roles of Intrinsic Disorder in Proteins Illustrate Its Broad Impact on Plant Biology

PubMed Central

Sun, Xiaolin; Rikkerink, Erik H.A.; Jones, William T.; Uversky, Vladimir N.

2013-01-01

Intrinsically disordered proteins (IDPs) are highly abundant in eukaryotic proteomes. Plant IDPs play critical roles in plant biology and often act as integrators of signals from multiple plant regulatory and environmental inputs. Binding promiscuity and plasticity allow IDPs to interact with multiple partners in protein interaction networks and provide important functional advantages in molecular recognition through transient protein–protein interactions. Short interaction-prone segments within IDPs, termed molecular recognition features, represent potential binding sites that can undergo disorder-to-order transition upon binding to their partners. In this review, we summarize the evidence for the importance of IDPs in plant biology and evaluate the functions associated with intrinsic disorder in five different types of plant protein families experimentally confirmed as IDPs. Functional studies of these proteins illustrate the broad impact of disorder on many areas of plant biology, including abiotic stress, transcriptional regulation, light perception, and development. Based on the roles of disorder in the protein–protein interactions, we propose various modes of action for plant IDPs that may provide insight for future experimental approaches aimed at understanding the molecular basis of protein function within important plant pathways. PMID:23362206

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires

NASA Astrophysics Data System (ADS)

Dufouleur, J.; Veyrat, L.; Dassonneville, B.; Xypakis, E.; Bardarson, J. H.; Nowka, C.; Hampel, S.; Schumann, J.; Eichler, B.; Schmidt, O. G.; Büchner, B.; Giraud, R.

2017-04-01

Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi2Te3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder.

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires

PubMed Central

Dufouleur, J.; Veyrat, L.; Dassonneville, B.; Xypakis, E.; Bardarson, J. H.; Nowka, C.; Hampel, S.; Schumann, J.; Eichler, B.; Schmidt, O. G.; Büchner, B.; Giraud, R.

2017-01-01

Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi2Te3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder. PMID:28374744

Weakly-coupled quasi-1D helical modes in disordered 3D topological insulator quantum wires.

PubMed

Dufouleur, J; Veyrat, L; Dassonneville, B; Xypakis, E; Bardarson, J H; Nowka, C; Hampel, S; Schumann, J; Eichler, B; Schmidt, O G; Büchner, B; Giraud, R

2017-04-04

Disorder remains a key limitation in the search for robust signatures of topological superconductivity in condensed matter. Whereas clean semiconducting quantum wires gave promising results discussed in terms of Majorana bound states, disorder makes the interpretation more complex. Quantum wires of 3D topological insulators offer a serious alternative due to their perfectly-transmitted mode. An important aspect to consider is the mixing of quasi-1D surface modes due to the strong degree of disorder typical for such materials. Here, we reveal that the energy broadening γ of such modes is much smaller than their energy spacing Δ, an unusual result for highly-disordered mesoscopic nanostructures. This is evidenced by non-universal conductance fluctuations in highly-doped and disordered Bi2Se3 and Bi 2 Te 3 nanowires. Theory shows that such a unique behavior is specific to spin-helical Dirac fermions with strong quantum confinement, which retain ballistic properties over an unusually large energy scale due to their spin texture. Our result confirms their potential to investigate topological superconductivity without ambiguity despite strong disorder.

Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins.

PubMed

Dzuricky, Michael; Roberts, Stefan; Chilkoti, Ashutosh

2018-05-01

A flurry of research in recent years has revealed the molecular origins of many membraneless organelles to be the liquid phase separation of intrinsically disordered proteins (IDPs). Consequently, protein disorder has emerged as an important driver of intracellular compartmentalization by providing specialized microenvironments chemically distinct from the surrounding medium. Though the importance of protein disorder and its relationship to intracellular phase behavior are clear, a detailed understanding of how such phase behavior can be predicted and controlled remains elusive. While research in IDPs has largely focused on the implications of structural disorder on cellular function and disease, another field, that of artificial protein polymers, has focused on the de novo design of protein polymers with controllable material properties. A subset of these polymers, specifically those derived from structural proteins such as elastin and resilin, are also disordered sequences that undergo liquid-liquid phase separation. This phase separation has been used in a variety of biomedical applications, and researchers studying these polymers have developed methods to precisely characterize and tune their phase behavior. Despite their disparate origins, both fields are complementary as they study the phase behavior of intrinsically disordered polypeptides. This Perspective hopes to stimulate collaborative efforts by highlighting the similarities between these two fields and by providing examples of how such collaboration could be mutually beneficial.

Emergence and evolution of an interaction between intrinsically disordered proteins

PubMed Central

Hultqvist, Greta; Åberg, Emma; Camilloni, Carlo; Sundell, Gustav N; Andersson, Eva; Dogan, Jakob; Chi, Celestine N; Vendruscolo, Michele; Jemth, Per

2017-01-01

Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450–600 million years ago, while NCBD was present in the protostome/deuterostome ancestor. The most ancient CID/NCBD formed a relatively weak complex (Kd∼5 µM). At the time of the first vertebrate-specific whole genome duplication, the affinity had increased (Kd∼200 nM) and was maintained in further speciation. Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations. DOI: http://dx.doi.org/10.7554/eLife.16059.001 PMID:28398197

MELAS Syndrome and Kidney Disease Without Fanconi Syndrome or Proteinuria: A Case Report.

PubMed

Rudnicki, Michael; Mayr, Johannes A; Zschocke, Johannes; Antretter, Herwig; Regele, Heinz; Feichtinger, René G; Windpessl, Martin; Mayer, Gert; Pölzl, Gerhard

2016-12-01

Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS syndrome) represents one of the most frequent mitochondrial disorders. The majority of MELAS cases are caused by m.3243A>G mutation in the mitochondrial MT-TL1 gene, which encodes the mitochondrial tRNA Leu(UUR) . Kidney involvement usually manifests as Fanconi syndrome or focal segmental glomerulosclerosis. We describe a patient with MELAS mutation, cardiomyopathy, and chronic kidney disease without Fanconi syndrome, proteinuria, or hematuria. While the patient was waitlisted for heart transplantation, her kidney function deteriorated from an estimated glomerular filtration rate of 33 to 20mL/min/1.73m 2 within several months. Kidney biopsy was performed to distinguish decreased kidney perfusion from intrinsic kidney pathology. Histologic examination of the biopsy specimen showed only a moderate degree of tubular atrophy and interstitial fibrosis, but quantitative analysis of the m.3243A>G mitochondrial DNA mutation revealed high heteroplasmy levels of 89% in the kidney. Functional assessment showed reduced activity of mitochondrial enzymes in kidney tissue, which was confirmed by immunohistology. In conclusion, we describe an unusual case of MELAS syndrome with chronic kidney disease without apparent proteinuria or tubular disorders associated with Fanconi syndrome, but widespread interstitial fibrosis and a high degree of heteroplasmy of the MELAS specific mutation and low mitochondrial activity in the kidney. Copyright © 2016 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Intrinsic connectivity networks within cerebellum and beyond in eating disorders.

PubMed

Amianto, F; D'Agata, F; Lavagnino, L; Caroppo, P; Abbate-Daga, G; Righi, D; Scarone, S; Bergui, M; Mortara, P; Fassino, S

2013-10-01

Cerebellum seems to have a role both in feeding behavior and emotion regulation; therefore, it is a region that warrants further neuroimaging studies in eating disorders, severe conditions that determine a significant impairment in the physical and psychological domain. The aim of this study was to examine the cerebellum intrinsic connectivity during functional magnetic resonance imaging resting state in anorexia nervosa (AN), bulimia nervosa (BN), and healthy controls (CN). Resting state brain activity was decomposed into intrinsic connectivity networks (ICNs) using group spatial independent component analysis on the resting blood oxygenation level dependent time courses of 12 AN, 12 BN, and 10 CN. We extracted the cerebellar ICN and compared it between groups. Intrinsic connectivity within the cerebellar network showed some common alterations in eating disordered compared to healthy subjects (e.g., a greater connectivity with insulae, vermis, and paravermis and a lesser connectivity with parietal lobe); AN and BN patients were characterized by some peculiar alterations in connectivity patterns (e.g., greater connectivity with the insulae in AN compared to BN, greater connectivity with anterior cingulate cortex in BN compared to AN). Our data are consistent with the presence of different alterations in the cerebellar network in AN and BN patients that could be related to psychopathologic dimensions of eating disorders.

Unusual social behavior in HPC-1/syntaxin1A knockout mice is caused by disruption of the oxytocinergic neural system.

PubMed

Fujiwara, Tomonori; Sanada, Masumi; Kofuji, Takefumi; Akagawa, Kimio

2016-07-01

HPC-1/syntaxin1A (STX1A), a neuronal soluble N-ethylmaleimide-sensitive fusion attachment protein receptor, contributes to neural function in the CNS by regulating transmitter release. Recent studies reported that STX1A is associated with human neuropsychological disorders, such as autism spectrum disorder and attention deficit hyperactivity disorder. Previously, we showed that STX1A null mutant mice (STX1A KO) exhibit neuropsychological abnormalities, such as fear memory deficits, attenuation of latent inhibition, and unusual social behavior. These observations suggested that STX1A may be involved in the neuropsychological basis of these abnormalities. Here, to study the neural basis of social behavior, we analyzed the profile of unusual social behavior in STX1A KO with a social novelty preference test, which is a useful method for quantification of social behavior. Interestingly, the unusual social behavior in STX1A KO was partially rescued by intracerebroventricular administration of oxytocin (OXT). In vivo microdialysis studies revealed that the extracellular OXT concentration in the CNS of STX1A KO was significantly lower compared with wild-type mice. Furthermore, dopamine-induced OXT release was reduced in STX1A KO. These results suggested that STX1A plays an important role in social behavior through regulation of the OXTergic neural system. Dopamine (DA) release is reduced in CNS of syntaxin1A null mutant mice (STX1A KO). Unusual social behavior was observed in STX1A KO. We found that oxytocin (OXT) release, which was stimulated by DA, was reduced and was rescued the unusual social behavior in STX1A KO was rescued by OXT. These results indicated that STX1A plays an important role in promoting social behavior through regulation of DA-induced OXT release in amygdala. © 2016 International Society for Neurochemistry.

Reasons for Quitting Smoking Prior to a Self-Quit Attempt among Smokers with and without Posttraumatic Stress Disorder or Other Anxiety/Mood Psychopathology

PubMed Central

Marshall, Erin C.; Vujanovic, Anka A.; Kutz, Amanda; Gibson, Laura; Leyro, Teresa; Zvolensky, Michael J.

2009-01-01

The present investigation examined intrinsic and extrinsic reasons for quitting among daily cigarette smokers with posttraumatic stress disorder (PTSD) as compared to clinical daily smokers with other anxiety and mood disorders (AM) and daily smokers with no current axis I psychopathology (C) prior to a self-guided quit attempt. It was hypothesized that (1) the PTSD group would report greater intrinsic (i.e., self-control and health concerns) reasons for quitting smoking, and (2) among those with PTSD, anxiety sensitivity (fear of anxiety; AS) would predict greater intrinsic reasons for quitting smoking. Participants were 143 (58.7% female; Mage = 29.66 years, SD = 11.88) daily cigarette smokers. Partially consistent with prediction, the PTSD group reported significantly greater self-control intrinsic reasons for quitting, but not health concern intrinsic reasons, than the C group (p <.01). The PTSD group also reported greater immediate reinforcement extrinsic reasons for quitting than the C group (p <.05). The PTSD and AM groups did not significantly differ on any reasons for quitting. Also partially consistent with hypotheses, higher levels of anxiety sensitivity in daily smokers with axis I psychopathology (both PTSD and AM groups) significantly predicted greater self-control intrinsic reasons for quitting. AS did not significantly predict immediate reinforcement extrinsic reasons for quitting. The current findings suggest that individuals with PTSD and other psychopathology may have unique motivations for quitting smoking that could be usefully explored within smoking cessation treatment programs. PMID:19444735

Reasons for quitting smoking prior to a self-quit attempt among smokers with and without posttraumatic stress disorder or other anxiety/mood psychopathology.

PubMed

Marshall, Erin C; Vujanovic, Anka A; Kutz, Amanda; Gibson, Laura; Leyro, Teresa; Zvolensky, Michael J

2009-01-01

The present investigation examined intrinsic and extrinsic reasons for quitting among daily cigarette smokers with posttraumatic stress disorder (PTSD) as compared to clinical daily smokers with other anxiety and mood disorders (AM) and daily smokers with no current Axis I psychopathology (C) prior to a self-guided quit attempt. It was hypothesized that (1) the PTSD group would report greater intrinsic (ie, self-control and health concerns) reasons for quitting smoking, and (2) among those with PTSD, anxiety sensitivity (fear of anxiety; AS) would predict greater intrinsic reasons for quitting smoking. Participants were 143 (58.7% female; M(age) = 29.66 years, SD = 11.88) daily cigarette smokers. Partially consistent with prediction, the PTSD group reported significantly greater self-control intrinsic reasons for quitting, but not health concern intrinsic reasons, than the C group (p < .01). The PTSD group also reported greater immediate reinforcement extrinsic reasons for quitting than the C group (p < .05). The PTSD and AM groups did not significantly differ on any reasons for quitting. Also partially consistent with hypotheses, higher levels of anxiety sensitivity in daily smokers with Axis I psychopathology (both PTSD and AM groups) significantly predicted greater self-control intrinsic reasons for quitting. AS did not significantly predict immediate reinforcement extrinsic reasons for quitting. The current findings suggest that individuals with PTSD and other psychopathology may have unique motivations for quitting smoking that could be usefully explored within smoking cessation treatment programs.

Motivation and Contingency Management Treatments for Substance Use Disorders.

PubMed

Walter, Kimberly N; Petry, Nancy M

2016-01-01

Contingency management (CM) is a highly efficacious psychosocial treatment for substance use disorders based on the principles of behavioral analysis. CM involves delivering a tangible positive reinforcer following objective evidence of submission of a drug-negative urine sample. Although CM interventions primarily involve applying extrinsic rewards, a patient's intrinsic motivation to change substance use behavior may also be impacted by CM. This chapter provides an introduction to CM interventions for substance use disorders and examines the impact of CM on intrinsic motivation . It also addresses applications of this intervention to other conditions and patient populations.

Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses

PubMed Central

Hébrard, Eugénie; Bessin, Yannick; Michon, Thierry; Longhi, Sonia; Uversky, Vladimir N; Delalande, François; Van Dorsselaer, Alain; Romero, Pedro; Walter, Jocelyne; Declerk, Nathalie; Fargette, Denis

2009-01-01

Background VPgs are viral proteins linked to the 5' end of some viral genomes. Interactions between several VPgs and eukaryotic translation initiation factors eIF4Es are critical for plant infection. However, VPgs are not restricted to phytoviruses, being also involved in genome replication and protein translation of several animal viruses. To date, structural data are still limited to small picornaviral VPgs. Recently three phytoviral VPgs were shown to be natively unfolded proteins. Results In this paper, we report the bacterial expression, purification and biochemical characterization of two phytoviral VPgs, namely the VPgs of Rice yellow mottle virus (RYMV, genus Sobemovirus) and Lettuce mosaic virus (LMV, genus Potyvirus). Using far-UV circular dichroism and size exclusion chromatography, we show that RYMV and LMV VPgs are predominantly or partly unstructured in solution, respectively. Using several disorder predictors, we show that both proteins are predicted to possess disordered regions. We next extend theses results to 14 VPgs representative of the viral diversity. Disordered regions were predicted in all VPg sequences whatever the genus and the family. Conclusion Based on these results, we propose that intrinsic disorder is a common feature of VPgs. The functional role of intrinsic disorder is discussed in light of the biological roles of VPgs. PMID:19220875

Ensemble models of proteins and protein domains based on distance distribution restraints.

PubMed

Jeschke, Gunnar

2016-04-01

Conformational ensembles of intrinsically disordered peptide chains are not fully determined by experimental observations. Uncertainty due to lack of experimental restraints and due to intrinsic disorder can be distinguished if distance distributions restraints are available. Such restraints can be obtained from pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy applied to pairs of spin labels. Here, we introduce a Monte Carlo approach for generating conformational ensembles that are consistent with a set of distance distribution restraints, backbone dihedral angle statistics in known protein structures, and optionally, secondary structure propensities or membrane immersion depths. The approach is tested with simulated restraints for a terminal and an internal loop and for a protein with 69 residues by using sets of sparse restraints for underlying well-defined conformations and for published ensembles of a premolten globule-like and a coil-like intrinsically disordered protein. © 2016 Wiley Periodicals, Inc.

Does water stress promote the proteome-wide adjustment of intrinsically disordered proteins in plants?

PubMed

Zamora-Briseño, Jesús Alejandro; Reyes-Hernández, Sandi Julissa; Zapata, Luis Carlos Rodríguez

2018-06-02

Plant response to water stress involves the activation of mechanisms expected to help them cope with water scarcity. Among these mechanisms, proteome-wide adjustment is well known. This includes actions to save energy, protect cellular and molecular components, and maintain vital functions of the cell. Intrinsically disordered proteins, which are proteins without a rigid three-dimensional structure, are seen as emerging multifunctional cellular components of proteomes. They are highly abundant in eukaryotic proteomes, and numerous functions for these proteins have been proposed. Here, we discuss several reasons why the collection of intrinsically disordered proteins in a proteome (disordome) could be subjected to an active regulation during conditions of water scarcity in plants. We also discuss the potential misinterpretations of disordome content estimations made so far due to bias-prone data and the need for reliable analysis based on experimental data in order to acknowledge the plasticity nature of the disordome.

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins*

PubMed Central

2016-01-01

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. PMID:26851286

Expression, fermentation and purification of a predicted intrinsically disordered region of the transcription factor, NFAT5.

PubMed

DuMond, Jenna F; He, Yi; Burg, Maurice B; Ferraris, Joan D

2015-11-01

Hypertonicity stimulates Nuclear Factor of Activated T-cells 5 (NFAT5) nuclear localization and transactivating activity. Many transcription factors are known to contain intrinsically disordered regions (IDRs) which become more structured with local environmental changes such as osmolality, temperature and tonicity. The transactivating domain of NFAT5 is predicted to be intrinsically disordered under normal tonicity, and under high NaCl, the activity of this domain is increased. To study the binding of co-regulatory proteins at IDRs a cDNA construct expressing the NFAT5 TAD was created and transformed into Escherichia coli cells. Transformed E. coli cells were mass produced by fermentation and extracted by cell lysis to release the NFAT5 TAD. The NFAT5 TAD was subsequently purified using a His-tag column, cation exchange chromatography as well as hydrophobic interaction chromatography and then characterized by mass spectrometry (MS). Published by Elsevier Inc.

Field-Free Nucleation of Antivortices and Giant Vortices in Nonsuperconducting Materials

NASA Astrophysics Data System (ADS)

Amundsen, Morten; Ouassou, Jabir Ali; Linder, Jacob

2018-05-01

Giant vortices with higher phase winding than 2 π are usually energetically unfavorable, but geometric symmetry constraints on a superconductor in a magnetic field are known to stabilize such objects. Here, we show via microscopic calculations that giant vortices can appear in intrinsically nonsuperconducting materials, even without any applied magnetic field. The enabling mechanism is the proximity effect to a host superconductor where a current flows, and we also demonstrate that antivortices can appear in this setup. Our results open the possibility to study electrically controllable topological defects in unusual environments, which do not have to be exposed to magnetic fields or intrinsically superconducting, but instead display other types of order.

Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

NASA Astrophysics Data System (ADS)

D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

2015-03-01

Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

Restless 'rest': intrinsic sensory hyperactivity and disinhibition in post-traumatic stress disorder.

PubMed

Clancy, Kevin; Ding, Mingzhou; Bernat, Edward; Schmidt, Norman B; Li, Wen

2017-07-01

Post-traumatic stress disorder is characterized by exaggerated threat response, and theoretical accounts to date have focused on impaired threat processing and dysregulated prefrontal-cortex-amygdala circuitry. Nevertheless, evidence is accruing for broad, threat-neutral sensory hyperactivity in post-traumatic stress disorder. As low-level, sensory processing impacts higher-order operations, such sensory anomalies can contribute to widespread dysfunctions, presenting an additional aetiological mechanism for post-traumatic stress disorder. To elucidate a sensory pathology of post-traumatic stress disorder, we examined intrinsic visual cortical activity (based on posterior alpha oscillations) and bottom-up sensory-driven causal connectivity (Granger causality in the alpha band) during a resting state (eyes open) and a passive, serial picture viewing state. Compared to patients with generalized anxiety disorder (n = 24) and healthy control subjects (n = 20), patients with post-traumatic stress disorder (n = 25) demonstrated intrinsic sensory hyperactivity (suppressed posterior alpha power, source-localized to the visual cortex-cuneus and precuneus) and bottom-up inhibition deficits (reduced posterior→frontal Granger causality). As sensory input increased from resting to passive picture viewing, patients with post-traumatic stress disorder failed to demonstrate alpha adaptation, highlighting a rigid, set mode of sensory hyperactivity. Interestingly, patients with post-traumatic stress disorder also showed heightened frontal processing (augmented frontal gamma power, source-localized to the superior frontal gyrus and dorsal cingulate cortex), accompanied by attenuated top-down inhibition (reduced frontal→posterior causality). Importantly, not only did suppressed alpha power and bottom-up causality correlate with heightened frontal gamma power, they also correlated with increased severity of sensory and executive dysfunctions (i.e. hypervigilance and impulse control deficits, respectively). Therefore, sensory aberrations help construct a vicious cycle in post-traumatic stress disorder that is in action even at rest, implicating dysregulated triangular sensory-prefrontal-cortex-amygdala circuitry: intrinsic sensory hyperactivity and disinhibition give rise to frontal overload and disrupt executive control, fuelling and perpetuating post-traumatic stress disorder symptoms. Absent in generalized anxiety disorder, these aberrations highlight a unique sensory pathology of post-traumatic stress disorder (ruling out effects merely reflecting anxious hyperarousal), motivating new interventions targeting sensory processing and the sensory brain in these patients. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase

PubMed Central

Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie D.

2010-01-01

Summary Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations utilizing experimental NMR and small-angle x-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. PMID:20399186

Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB

NASA Astrophysics Data System (ADS)

Liu, Hao; Guo, Xiang; Han, Jingcheng; Luo, Ray; Chen, Hai-Feng

2018-06-01

Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

PubMed Central

Meng, Fanchi; Na, Insung; Kurgan, Lukasz; Uversky, Vladimir N.

2015-01-01

The cell nucleus contains a number of membrane-less organelles or intra-nuclear compartments. These compartments are dynamic structures representing liquid-droplet phases which are only slightly denser than the bulk intra-nuclear fluid. They possess different functions, have diverse morphologies, and are typically composed of RNA (or, in some cases, DNA) and proteins. We analyzed 3005 mouse proteins localized in specific intra-nuclear organelles, such as nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinuclear compartment and compared them with ~29,863 non-nuclear proteins from mouse proteome. Our analysis revealed that intrinsic disorder is enriched in the majority of intra-nuclear compartments, except for the nuclear pore and lamina. These compartments are depleted in proteins that lack disordered domains and enriched in proteins that have multiple disordered domains. Moonlighting proteins found in multiple intra-nuclear compartments are more likely to have multiple disordered domains. Protein-protein interaction networks in the intra-nuclear compartments are denser and include more hubs compared to the non-nuclear proteins. Hubs in the intra-nuclear compartments (except for the nuclear pore) are enriched in disorder compared with non-nuclear hubs and non-nuclear proteins. Therefore, our work provides support to the idea of the functional importance of intrinsic disorder in the cell nucleus and shows that many proteins associated with sub-nuclear organelles in nuclei of mouse cells are enriched in disorder. This high level of disorder in the mouse nuclear proteins defines their ability to serve as very promiscuous binders, possessing both large quantities of potential disorder-based interaction sites and the ability of a single such site to be involved in a large number of interactions. PMID:26712748

Grave's Disease and Primary Biliary Cirrhosis-An Unusual and Challenging Association.

PubMed

Shetty, Shiran; Rajasekaran, Senthilkumar; Venkatakrishnan, Leela

2014-03-01

Jaundice in Grave's diseases is uncommon, but when it does occur, complication of thyrotoxicosis (heart failure/infection) or intrinsic liver disease should be considered. Grave's disease can cause asymptomatic elevation of liver enzymes, jaundice and rarely acute liver failure. It is associated with other autoimmune diseases like autoimmune hepatitis, or primary biliary cirrhosis. The cause of jaundice in Grave's disease is multifactorial.

Grave's Disease and Primary Biliary Cirrhosis—An Unusual and Challenging Association

PubMed Central

Shetty, Shiran; Rajasekaran, Senthilkumar; Venkatakrishnan, Leela

2013-01-01

Jaundice in Grave's diseases is uncommon, but when it does occur, complication of thyrotoxicosis (heart failure/infection) or intrinsic liver disease should be considered. Grave's disease can cause asymptomatic elevation of liver enzymes, jaundice and rarely acute liver failure. It is associated with other autoimmune diseases like autoimmune hepatitis, or primary biliary cirrhosis. The cause of jaundice in Grave's disease is multifactorial. PMID:25755537

Pernicious anemia and juvenile-onset diabetes mellitus in an adolescent: a case report.

PubMed

Yu, L C; Warrier, R P; Ducos, R S

1989-02-01

We report a case of a 15-year-old black boy who developed juvenile-onset pernicious anemia in association with insulin-dependent diabetes mellitus. He had both intrinsic factor and parietal cell antibodies in addition to anti-islet cell surface antibodies. The existence of pernicious anemia and diabetes mellitus in such a young child makes this an unusual case.

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins

PubMed Central

Perez, Romel B.; Tischer, Alexander; Auton, Matthew; Whitten, Steven T.

2014-01-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins, mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline and alanine to glycine substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (Rh) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the glycine substitutions decreased polyproline II (PPII) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in Rh were not associated with folding. The experiments showed that changes in local PPII structure cause changes in Rh that are variable and that depend on the intrinsic chain propensities of proline and alanine residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed proline and alanine effects on the structures of intrinsically disordered proteins. PMID:25244701

Behavioural Phenotype in Borjeson-Forssman-Lehmann Syndrome

ERIC Educational Resources Information Center

de Winter, C. F.; van Dijk, F.; Stolker, J. J.; Hennekam, R. C. M.

2009-01-01

Background: Borjeson-Forssman-Lehmann syndrome (BFLs) is an X-linked inherited disorder characterised by unusual facial features, abnormal fat distribution and intellectual disability. As many genetically determined disorders are characterised not only by physical features but also by specific behaviour, we studied whether a specific behavioural…

Folding of a salivary intrinsically disordered protein upon binding to tannins.

PubMed

Canon, Francis; Ballivian, Renaud; Chirot, Fabien; Antoine, Rodolphe; Sarni-Manchado, Pascale; Lemoine, Jérôme; Dugourd, Philippe

2011-05-25

We used ion mobility spectrometry to explore conformational adaptability of intrinsically disordered proteins bound to their targets in complex mixtures. We investigated the interactions between a human salivary proline-rich protein IB5 and a model of wine and tea tannin: epigallocatechin gallate (EgCG). Collisional cross sections of naked IB5 and IB5 complexed with N = 1-15 tannins were recorded. The data demonstrate that IB5 undergoes an unfolded to folded structural transition upon binding with EgCG.

Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer

PubMed Central

Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

2016-01-01

Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease. PMID:27453073

Collagenous gastritis: an unusual association with profound weight loss.

PubMed

Wang, Hanlin L; Shah, Amit G; Yerian, Lisa M; Cohen, Russell D; Hart, John

2004-02-01

Collagenous gastritis is a distinctive disorder characterized by thickening of the subepithelial collagen layer in the gastric mucosa. Although this entity was recognized in 1989, its etiology, pathogenesis, and clinicopathologic features remain poorly understood because of its rarity. An unusual case of collagenous gastritis was observed in a 37-year-old man who presented with profound weight loss, a feature that has not previously been emphasized.

Optic phonons and anisotropic thermal conductivity in hexagonal Ge 2Sb 2Te 5

DOE PAGES

Mukhopadhyay, Saikat; Lindsay, Lucas R.; Singh, David

2016-11-16

The lattice thermal conductivity ($κ$) of hexagonal Ge 2Sb 2Tesub>5 (h-GST) is studied via direct first-principles calculations. We find significant intrinsic anisotropy of ( $κ$ a/$κ$ c~2) of $κ$ in bulk h-GST along different transport directions. The dominant contribution to$κ$ is from optic phonons, ~75%. This is extremely unusual as the acoustic phonon modes carry most of the heat in typical semiconductors and insulators with small unit cells. Very recently, Lee et. al. observed anisotropic in GST thin films and attributed this to thermal resistance of amorphous regions near grain boundaries. However, our results suggest an additional strong intrinsic anisotropymore » for the pure hexagonal phase. This derives from bonding anisotropy along different crystal directions, specifically from weak interlayer coupling, which gives anisotropic phonon dispersions. The phonon spectrum of h-GST has very dispersive optic branches with higher group velocities along the a-axis as compared to flat optic bands along the c-axis. The importance of optic mode contributions for the thermal conductivity in low-$κ$ h-GST is unusual, and development of fundamental physical understanding of these contributions may be critical to better understanding of thermal conduction in other complex layered materials.« less

Faculty and Government Roles in Campus Unrest

ERIC Educational Resources Information Center

Baxter, William F.

1969-01-01

This letter from a faculty member at Stanford University to the U.S. Assistant Attorney General "offers unusual perceptions of faculty opportunities for helpfulness in student disorders, and persuasive arguments for government to leave the essential responsibility for the problem of disorder to campus authorities. (Editor/WM)

Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins.

PubMed

Uversky, Vladimir N

2016-03-25

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Wide-line NMR and DSC studies on intrinsically disordered p53 transactivation domain and its helically pre-structured segment

PubMed Central

Tompa, Peter; Han, Kyou-Hoon; Bokor, Mónika; Kamasa, Pawel; Tantos, Ágnes; Fritz, Beáta; Kim, Do-Hyoung; Lee, Chewook; Verebélyi, Tamás; Tompa, Kálmán

2016-01-01

Wide-line 1H NMR intensity and differential scanning calorimetry measurements were carried out on the intrinsically disordered 73-residue full transactivation domain (TAD) of the p53 tumor suppressor protein and two peptides: one a wild type p53 TAD peptide with a helix pre-structuring property, and a mutant peptide with a disabled helix-forming propensity. Measurements were carried out in order to characterize their water and ion binding characteristics. By quantifying the number of hydrate water molecules, we provide a microscopic description for the interactions of water with a wild-type p53 TAD and two p53 TAD peptides. The results provide direct evidence that intrinsically disordered proteins (IDPs) and a less structured peptide not only have a higher hydration capacity than globular proteins, but are also able to bind a larger amount of charged solute ions. [BMB Reports 2016; 49(9): 497-501] PMID:27418282

Folding propensity of intrinsically disordered proteins by osmotic stress

DOE PAGES

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; ...

2016-10-11

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). 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. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Folding propensity of intrinsically disordered proteins by osmotic stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

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). 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. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Sequence Complexity of Amyloidogenic Regions in Intrinsically Disordered Human Proteins

PubMed Central

Das, Swagata; Pal, Uttam; Das, Supriya; Bagga, Khyati; Roy, Anupam; Mrigwani, Arpita; Maiti, Nakul C.

2014-01-01

An amyloidogenic region (AR) in a protein sequence plays a significant role in protein aggregation and amyloid formation. We have investigated the sequence complexity of AR that is present in intrinsically disordered human proteins. More than 80% human proteins in the disordered protein databases (DisProt+IDEAL) contained one or more ARs. With decrease of protein disorder, AR content in the protein sequence was decreased. A probability density distribution analysis and discrete analysis of AR sequences showed that ∼8% residue in a protein sequence was in AR and the region was in average 8 residues long. The residues in the AR were high in sequence complexity and it seldom overlapped with low complexity regions (LCR), which was largely abundant in disorder proteins. The sequences in the AR showed mixed conformational adaptability towards α-helix, β-sheet/strand and coil conformations. PMID:24594841

Juvenile xanthogranuloma: an unusual cause of intratesticular mass in childhood.

PubMed

Weiss, Vivian L; Brock, John W; Cajaiba, Mariana M

2014-05-01

Juvenile xanthogranuloma (JXG) is a common histiocytic disorder of infancy and early childhood, most frequently presenting with cutaneous lesions. Whereas involvement of several visceral sites is well documented, only 4 cases of primary testicular JXG have been reported. Although this benign disorder typically presents with a favorable clinical outcome, the unusual presentation as an intratesticular lesion can lead to diagnostic challenges. In this study, we present the case of a 6-month-old male child with an incidentally discovered testicular mass that was diagnosed as a JXG and briefly review the existing literature in an attempt to bring awareness to this uncommon presentation. Copyright © 2014 Elsevier Inc. All rights reserved.

Autism in Early Childhood: An Unusual Developmental Course—Three Case Reports

PubMed Central

Cohen-Ophir, Michal; Castel-Deutsh, Tsophia; Tirosh, Emanuel

2012-01-01

Autistic spectrum disorder (ASD) is typically characterized by either an emerging and gradual course or developmental regression in early childhood. The versatile clinical course is progressively acknowledged in recent years. Children with developmental disorders in general are referred to the Child Development Center for a multidisciplinary assessment, investigation, treatment and followup. We report three infants with an initial diagnosis of developmental delays, recovery of normal development following intervention in a multidisciplinary center, and subsequent regression into classic autism following their discharge from the program. An extensive medical workup was noncontributory. This unusual presentation, to our knowledge not reported previously, should be recognized by professionals involved in child development and psychiatry. PMID:22937419

The assessment of schizotypy by the O-LIFE (Oxford-Liverpool Inventory for Feelings and Experiences) in patients with schizophrenia and affective disorders.

PubMed

Dembińska-Krajewska, Daria; Rybakowski, Janusz

2016-12-23

The aim of the study was to assess schizotypy by using the Oxford-Liverpool Inventory of Feelings and Experiences (O-LIFE), in the groups of patients with schizophrenia, bipolar disorder (BD) and unipolar (recurrent) depression (UD). An important element of the study was to compare - in terms of similarity - the results obtained in schizophrenia and BD, and - in terms of differences - the results obtained in BD and UD. The study involved 58 patients with schizophrenia (35 men, 23 women, mean age = 34.0, SD = 9.8), 52 patients with BD (22 men, 30 women, mean age = 40.3, SD = 13.6) and 57 UD patients (24 men, 33 women, mean age = 50.2, SD = 11.9), treated in the Department of Adult Psychiatry, Poznan University of Medical Sciences. For the assessment of schizotypy, the full version of the O-LIFE questionnaire (104 questions) was used, including such dimensions as: unusual experiences, cognitive disorganization, introvertive anhedonia and impulsive nonconformity. The biggest differences between diagnostic groups were found in the dimensions of unusual experiences and impulsive nonconformity. Similarities between schizophrenia and BD were found for unusual experiences, cognitive disorganization and introvertive anhedonia. Differences between BD and UD were obtained for unusual experiences and impulsive nonconformity. The assessment of schizotypy in three diagnostic groups (it was the first study in patients with UD), allowed to address contemporary pathogenic and clinical concepts pertaining to similarities between schizophrenia and BD as well as to differences between two types of affective disorders.

Abnormalities of Intrinsic Functional Connectivity in Autism Spectrum Disorders

PubMed Central

Monk, Christopher S.; Peltier, Scott J.; Wiggins, Jillian Lee; Weng, Shih-Jen; Carrasco, Melisa; Risi, Susan; Lord, Catherine

2009-01-01

Autism spectrum disorders (ASD) impact social functioning and communication, and individuals with these disorders often have restrictive and repetitive behaviors. Accumulating data indicate that ASD is associated with alterations of neural circuitry. Functional MRI (FMRI) studies have focused on connectivity in the context of psychological tasks. However, even in the absence of a task, the brain exhibits a high degree of functional connectivity, known as intrinsic or resting connectivity. Notably, the default network, which includes the posterior cingulate cortex, retro-splenial, lateral parietal cortex/angular gyrus, medial prefrontal cortex, superior frontal gyrus, temporal lobe, and parahippocampal gyrus, is strongly active when there is no task. Altered intrinsic connectivity within the default network may underlie offline processing that may actuate ASD impairments. Using FMRI, we sought to evaluate intrinsic connectivity within the default network in ASD. Relative to controls, the ASD group showed weaker connectivity between the posterior cingulate cortex and superior frontal gyrus and stronger connectivity between the posterior cingulate cortex and both the right temporal lobe and right parahippocampal gyrus. Moreover, poorer social functioning in the ASD group was correlated with weaker connectivity between the posterior cingulate cortex and the superior frontal gyrus. In addition, more severe restricted and repetitive behaviors in ASD were correlated with stronger connectivity between the posterior cingulate cortex and right parahippocampal gyrus. These findings indicate that ASD subjects show altered intrinsic connectivity within the default network, and connectivity between these structures is associated with specific ASD symptoms. PMID:19409498

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

PubMed Central

Marsh, Joseph A.; Forman-Kay, Julie D.

2010-01-01

Abstract Intrinsically disordered proteins (IDPs), which lack folded structure and are disordered under nondenaturing conditions, have been shown to perform important functions in a large number of cellular processes. These proteins have interesting structural properties that deviate from the random-coil-like behavior exhibited by chemically denatured proteins. In particular, IDPs are often observed to exhibit significant compaction. In this study, we have analyzed the hydrodynamic radii of a number of IDPs to investigate the sequence determinants of this compaction. Net charge and proline content are observed to be strongly correlated with increased hydrodynamic radii, suggesting that these are the dominant contributors to compaction. Hydrophobicity and secondary structure, on the other hand, appear to have negligible effects on compaction, which implies that the determinants of structure in folded and intrinsically disordered proteins are profoundly different. Finally, we observe that polyhistidine tags seem to increase IDP compaction, which suggests that these tags have significant perturbing effects and thus should be removed before any structural characterizations of IDPs. Using the relationships observed in this analysis, we have developed a sequence-based predictor of hydrodynamic radius for IDPs that shows substantial improvement over a simple model based upon chain length alone. PMID:20483348

Internal friction in an intrinsically disordered protein—Comparing Rouse-like models with experiments

NASA Astrophysics Data System (ADS)

Soranno, Andrea; Zosel, Franziska; Hofmann, Hagen

2018-03-01

Internal friction is frequently found in protein dynamics. Its molecular origin however is difficult to conceptualize. Even unfolded and intrinsically disordered polypeptide chains exhibit signs of internal friction despite their enormous solvent accessibility. Here, we compare four polymer theories of internal friction with experimental results on the intrinsically disordered protein ACTR (activator of thyroid hormone receptor). Using nanosecond fluorescence correlation spectroscopy combined with single-molecule Förster resonance energy transfer (smFRET), we determine the time scales of the diffusive chain dynamics of ACTR at different solvent viscosities and varying degrees of compaction. Despite pronounced differences between the theories, we find that all models can capture the experimental viscosity-dependence of the chain relaxation time. In contrast, the observed slowdown upon chain collapse of ACTR is not captured by any of the theories and a mechanistic link between chain dimension and internal friction is still missing, implying that the current theories are incomplete. In addition, a discrepancy between early results on homopolymer solutions and recent single-molecule experiments on unfolded and disordered proteins suggests that internal friction is likely to be a composite phenomenon caused by a variety of processes.

NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model

PubMed Central

Heisel, Kurt A.; Krishnan, V. V.

2014-01-01

The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex (NPC) is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on 13Cα, 1Hα, and 1HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). PMID:24037535

Internal friction in an intrinsically disordered protein-Comparing Rouse-like models with experiments.

PubMed

Soranno, Andrea; Zosel, Franziska; Hofmann, Hagen

2018-03-28

Internal friction is frequently found in protein dynamics. Its molecular origin however is difficult to conceptualize. Even unfolded and intrinsically disordered polypeptide chains exhibit signs of internal friction despite their enormous solvent accessibility. Here, we compare four polymer theories of internal friction with experimental results on the intrinsically disordered protein ACTR (activator of thyroid hormone receptor). Using nanosecond fluorescence correlation spectroscopy combined with single-molecule Förster resonance energy transfer (smFRET), we determine the time scales of the diffusive chain dynamics of ACTR at different solvent viscosities and varying degrees of compaction. Despite pronounced differences between the theories, we find that all models can capture the experimental viscosity-dependence of the chain relaxation time. In contrast, the observed slowdown upon chain collapse of ACTR is not captured by any of the theories and a mechanistic link between chain dimension and internal friction is still missing, implying that the current theories are incomplete. In addition, a discrepancy between early results on homopolymer solutions and recent single-molecule experiments on unfolded and disordered proteins suggests that internal friction is likely to be a composite phenomenon caused by a variety of processes.

Three reasons protein disorder analysis makes more sense in the light of collagen

PubMed Central

Oates, Matt E.; Tompa, Peter; Gough, Julian

2016-01-01

Abstract We have identified that the collagen helix has the potential to be disruptive to analyses of intrinsically disordered proteins. The collagen helix is an extended fibrous structure that is both promiscuous and repetitive. Whilst its sequence is predicted to be disordered, this type of protein structure is not typically considered as intrinsic disorder. Here, we show that collagen‐encoding proteins skew the distribution of exon lengths in genes. We find that previous results, demonstrating that exons encoding disordered regions are more likely to be symmetric, are due to the abundance of the collagen helix. Other related results, showing increased levels of alternative splicing in disorder‐encoding exons, still hold after considering collagen‐containing proteins. Aside from analyses of exons, we find that the set of proteins that contain collagen significantly alters the amino acid composition of regions predicted as disordered. We conclude that research in this area should be conducted in the light of the collagen helix. PMID:26941008

Sensory Processing in Adults with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Crane, Laura; Goddard, Lorna; Pring, Linda

2009-01-01

Unusual sensory processing has been widely reported in autism spectrum disorders (ASDs); however, the majority of research in this area has focused on children. The present study assessed sensory processing in adults with ASD using the Adult/Adolescent Sensory Profile (AASP), a 60-item self-report questionnaire assessing levels of sensory…

Living and Working with a Central Auditory Processing Disorder (CAPD).

ERIC Educational Resources Information Center

Paton, Judith W.

This paper describes adult symptoms of Central Auditory Processing Disorder and provides strategies for dealing with this disability. Symptoms include talking or turning on the television louder than normal, interpreting words too literally, needing remarks repeated, having difficulty sounding out words, ignoring people, being unusually sensitive…

Patients Reporting Ritual Abuse in Childhood: A Clinical Syndrome. Report of 37 Cases.

ERIC Educational Resources Information Center

Young, Walter C.; And Others

1991-01-01

Thirty-seven adult dissociative disorder patients who reported ritual abuse in childhood by satanic cults are described. A clinical syndrome is presented that includes dissociative states with satanic overtones, posttraumatic stress disorder, survivor guilt, unusual fears, and substance abuse. Questions concerning reliability, credibility, and…

Trichosporon inkin and Trichosporon mucoides as unusual causes of white piedra of scalp hair.

PubMed

Tendolkar, Uma; Shinde, Alka; Baveja, Sujata; Dhurat, Rachita; Phiske, Meghana

2014-01-01

White piedra of scalp hair is considered a rare entity. We report three cases of this disorder all of whom presented with nodules on the hair. Potassium hydroxide preparations of the hair revealed clustered arthrospores and mature, easily detachable nodules. Cultures grew Trichosporon inkin in 2 patients and Trichosporon mucoides in one patient. Both these fungi are unusual causes of white piedra.

NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

PubMed Central

Konrat, Robert

2014-01-01

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

Understanding disordered and unfolded proteins using single-molecule FRET and polymer theory.

PubMed

Hofmann, Hagen

2016-11-17

Understanding protein folding and the functional properties of intrinsically disordered proteins (IDPs) requires detailed knowledge of the forces that act in polypeptide chains. These forces determine the dimensions and dynamics of unfolded and disordered proteins and have been suggested to impact processes such as the coupled binding and folding of IDPs, or the rate of protein folding reactions. Much of the progress in understanding the physical and chemical properties of unfolded and intrinsically disordered polypeptide chains has been made possible by the recent developments in single-molecule fluorescence techniques. However, the interpretation of the experimental results requires concepts from polymer physics in order to be understood. Here, I review some of the theories used to describe the dimensions of unfolded polypeptide chains under varying solvent conditions together with their more recent application to experimental data.

The Intrinsically Disordered Regions of the Drosophila melanogaster Hox Protein Ultrabithorax Select Interacting Proteins Based on Partner Topology

PubMed Central

Hsiao, Hao-Ching; Gonzalez, Kim L.; Catanese, Daniel J.; Jordy, Kristopher E.; Matthews, Kathleen S.; Bondos, Sarah E.

2014-01-01

Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and α-α superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues. PMID:25286318

Characteristics of challenging behaviours in adults with autistic disorder, PDD-NOS, and intellectual disability.

PubMed

Matson, Johnny L; Rivet, Tessa T

2008-12-01

Challenging behaviours are frequently a problem for people with autism spectrum disorders (ASD) and intellectual disability (ID). A better understanding of which individuals display which behaviours, at what rates, and the relationship of these behaviours to comorbid psychopathology would have important implications. A group of 161 adults with ASD (autistic disorder or Pervasive Developmental Disorder--Not Otherwise Specified [PDD-NOS]) and 159 matched controls with ID only residing in two large residential facilities in Southeastern United States, were studied using the Autism Spectrum Disorders--Behavior Problems for Adults (ASD-BPA). In all four categories of challenging behaviour measured by the ASD-BPA (Aggression/Destruction, Stereotypy, Self-Injurious Behavior, and Disruptive Behavior), frequency of challenging behaviours increased with severity of autistic symptoms. The greatest group differences were found for Stereotypy (repeated/unusual vocalisations/body movements and unusual object play), Self-Injurious Behavior (harming self and mouthing/swallowing objects), Aggression/Destruction (banging on objects), and Disruptive Behavior (elopement). Challenging behaviours in people with ASD and ID are barriers to effective education, training, and social development, and often persist throughout adulthood. Thus, programs designed to remediate such behaviours should continue across the life-span of these individuals.

Ensemble characterization of an intrinsically disordered FG-Nup peptide and its F>A mutant in DMSO-d6.

PubMed

Reid, Korey M; Sunanda, Punnepalli; Raghothama, S; Krishnan, V V

2017-11-01

Intrinsically disordered proteins (IDP) lack a well-defined 3D-structure under physiological conditions, yet, the inherent disorder represented by an ensemble of conformation plays a critical role in many cellular and regulatory processes. Nucleoporins, or Nups, are the proteins found in the nuclear pore complex (NPC). The central pore of the NPC is occupied by Nups, which have phenylalanine-glycine domain repeats and are intrinsically disordered, and therefore are termed FG-Nups. These FG-domain repeats exhibit differing cohesiveness character and differ from least (FG) to most (GLFG) cohesive. The designed FG-Nup is a 25 AA model peptide containing a noncohesive FG-motif flanked by two cohesive GLFG-motifs (WT peptide). Complete NMR-based ensemble characterization of this peptide along with a control peptide with an F>A substitution (MU peptide) are discussed. Ensemble characterization of the NMR-determined models suggests that both the peptides do not have consistent secondary structures and continue to be disordered. Nonetheless, the role of cohesive elements mediated by the GLFG motifs is evident in the WT ensemble of structures that are more compact than the MU peptide. The approach presented here allows an alternate way to investigate the specific roles of distinct amino acid motifs that translate into the long-range organization of the ensemble of structures and in general on the nature of IDPs. © 2017 Wiley Periodicals, Inc.

Synchrony and neural coding in cerebellar circuits

PubMed Central

Person, Abigail L.; Raman, Indira M.

2012-01-01

The cerebellum regulates complex movements and is also implicated in cognitive tasks, and cerebellar dysfunction is consequently associated not only with movement disorders, but also with conditions like autism and dyslexia. How information is encoded by specific cerebellar firing patterns remains debated, however. A central question is how the cerebellar cortex transmits its integrated output to the cerebellar nuclei via GABAergic synapses from Purkinje neurons. Possible answers come from accumulating evidence that subsets of Purkinje cells synchronize their firing during behaviors that require the cerebellum. Consistent with models predicting that coherent activity of inhibitory networks has the capacity to dictate firing patterns of target neurons, recent experimental work supports the idea that inhibitory synchrony may regulate the response of cerebellar nuclear cells to Purkinje inputs, owing to the interplay between unusually fast inhibitory synaptic responses and high rates of intrinsic activity. Data from multiple laboratories lead to a working hypothesis that synchronous inhibitory input from Purkinje cells can set the timing and rate of action potentials produced by cerebellar nuclear cells, thereby relaying information out of the cerebellum. If so, then changing spatiotemporal patterns of Purkinje activity would allow different subsets of inhibitory neurons to control cerebellar output at different times. Here we explore the evidence for and against the idea that a synchrony code defines, at least in part, the input–output function between the cerebellar cortex and nuclei. We consider the literature on the existence of simple spike synchrony, convergence of Purkinje neurons onto nuclear neurons, and intrinsic properties of nuclear neurons that contribute to responses to inhibition. Finally, we discuss factors that may disrupt or modulate a synchrony code and describe the potential contributions of inhibitory synchrony to other motor circuits. PMID:23248585

Intrinsic Functional Connectivity of Amygdala-Based Networks in Adolescent Generalized Anxiety Disorder

ERIC Educational Resources Information Center

Roy, Amy K.; Fudge, Julie L.; Kelly, Clare; Perry, Justin S. A.; Daniele, Teresa; Carlisi, Christina; Benson, Brenda; Castellanos, F. Xavier; Milham, Michael P.; Pine, Daniel S.; Ernst, Monique

2013-01-01

Objective: Generalized anxiety disorder (GAD) typically begins during adolescence and can persist into adulthood. The pathophysiological mechanisms underlying this disorder remain unclear. Recent evidence from resting state functional magnetic resonance imaging (R-fMRI) studies in adults suggests disruptions in amygdala-based circuitry; the…

Chemical-Induced Erythrocytosis in Wistar Rats: Assessment as a Model for Human Polycythemia.

DTIC Science & Technology

1985-05-01

polycythemic condition are unusual features that are more typically found in polycythemia vera, an autonomous myeloproliferative disorder in man that results...polycythemia vera, an autonomous myeloproliferative disorder in man that results from clonal neoplasia of bone marrow stem cells. However, the data described...5 and stroma cell lines [55]. These diseases are commonly termed ’ myeloproliferative disorders’, or better, ’myelodysplastic disease’ which emphasizes

Using electropalatography (EPG) to diagnose and treat articulation disorders associated with mild cerebral palsy: a case study.

PubMed

Gibbon, Fiona E; Wood, Sara E

2003-01-01

Some children with mild cerebral palsy have articulation disorders that are resistant to conventional speech therapy techniques. This preliminary study investigated the use of electropalatography (EPG) to diagnose and treat a long-standing articulation disorder that had not responded to conventional speech therapy techniques in an 8-year-old boy (D) with a congenital left hemiplegia. The targets for EPG therapy were speech errors affecting velar targets /k, g, eta/, which were consistently fronted to alveolar placement [t, d, n]. After 15 sessions of EPG therapy over a 4-month period, D's ability to produce velars improved significantly. The EPG data revealed two features of diagnostic importance. The first was an unusually asymmetrical pattern of tongue-palate contact and the second was unusually long stop closure durations. These features are interpreted as a subtle form of impaired speech motor control that could be related to a mild residual neurological deficit. The results suggest that EPG is of potential benefit for diagnosing and treating articulation disorders in individuals with mild cerebral palsy.

Unfoldomics of human diseases: linking protein intrinsic disorder with diseases

PubMed Central

Uversky, Vladimir N; Oldfield, Christopher J; Midic, Uros; Xie, Hongbo; Xue, Bin; Vucetic, Slobodan; Iakoucheva, Lilia M; Obradovic, Zoran; Dunker, A Keith

2009-01-01

Background Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and IDRs is leading to an entire field aimed at their systematic structural characterization and at determination of their mechanisms of action. Bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. These activities complement the functions of structured proteins. IDPs and IDRs were shown to participate in both one-to-many and many-to-one signaling. Alternative splicing and posttranslational modifications are frequently used to tune the IDP functionality. Several individual IDPs were shown to be associated with human diseases, such as cancer, cardiovascular disease, amyloidoses, diabetes, neurodegenerative diseases, and others. This raises questions regarding the involvement of IDPs and IDRs in various diseases. Results IDPs and IDRs were shown to be highly abundant in proteins associated with various human maladies. As the number of IDPs related to various diseases was found to be very large, the concepts of the disease-related unfoldome and unfoldomics were introduced. Novel bioinformatics tools were proposed to populate and characterize the disease-associated unfoldome. Structural characterization of the members of the disease-related unfoldome requires specialized experimental approaches. IDPs possess a number of unique structural and functional features that determine their broad involvement into the pathogenesis of various diseases. Conclusion Proteins associated with various human diseases are enriched in intrinsic disorder. These disease-associated IDPs and IDRs are real, abundant, diversified, vital, and dynamic. These proteins and regions comprise the disease-related unfoldome, which covers a significant part of the human proteome. Profound association between intrinsic disorder and various human diseases is determined by a set of unique structural and functional characteristics of IDPs and IDRs. Unfoldomics of human diseases utilizes unrivaled bioinformatics and experimental techniques, paves the road for better understanding of human diseases, their pathogenesis and molecular mechanisms, and helps develop new strategies for the analysis of disease-related proteins. PMID:19594884

Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein.

PubMed

Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

2017-10-21

Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.

Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein

NASA Astrophysics Data System (ADS)

Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

2017-10-01

Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.

Ingestion Reiterada de Cuerpos Extranos. Forma Inusual de Presentacion del Sindrome de Munchausen por Poderes (Reiterated Ingestion of Foreign Bodies. Unusual Form of Presentation of Munchausen Syndrome by Proxy).

ERIC Educational Resources Information Center

Terreros, I. Gomez de; And Others

1996-01-01

An unusual case of Munchausen syndrome by proxy is reported. A mother with a psychiatric record of behavior disorders and family dysfunction perpetrated the ingestion of foreign bodies (for example, earrings, a screw, sewing needles) on a 10-month-old infant with a history of prematurity, repeated visits to emergency rooms, and nonjustified…

Anomalous frequency-dependent ionic conductivity of lesion-laden human-brain tissue

NASA Astrophysics Data System (ADS)

Emin, David; Akhtari, Massoud; Fallah, Aria; Vinters, Harry V.; Mathern, Gary W.

2017-10-01

We study the effect of lesions on our four-electrode measurements of the ionic conductivity of (˜1 cm3) samples of human brain excised from patients undergoing pediatric epilepsy surgery. For most (˜94%) samples, the low-frequency ionic conductivity rises upon increasing the applied frequency. We attributed this behavior to the long-range (˜0.4 mm) diffusion of solvated sodium cations before encountering intrinsic impenetrable blockages such as cell membranes, blood vessels, and cell walls. By contrast, the low-frequency ionic conductivity of some (˜6%) brain-tissue samples falls with increasing applied frequency. We attribute this unusual frequency-dependence to the electric-field induced liberation of sodium cations from traps introduced by the unusually severe pathology observed in samples from these patients. Thus, the anomalous frequency-dependence of the ionic conductivity indicates trap-producing brain lesions.

Multiple structure-intrinsic disorder interactions regulate and coordinate Hox protein function

NASA Astrophysics Data System (ADS)

Bondos, Sarah

During animal development, Hox transcription factors determine fate of developing tissues to generate diverse organs and appendages. Hox proteins are famous for their bizarre mutant phenotypes, such as replacing antennae with legs. Clearly, the functions of individual Hox proteins must be distinct and reliable in vivo, or the organism risks malformation or death. However, within the Hox protein family, the DNA-binding homeodomains are highly conserved and the amino acids that contact DNA are nearly invariant. These observations raise the question: How do different Hox proteins correctly identify their distinct target genes using a common DNA binding domain? One possible means to modulate DNA binding is through the influence of the non-homeodomain protein regions, which differ significantly among Hox proteins. However genetic approaches never detected intra-protein interactions, and early biochemical attempts were hindered because the special features of ``intrinsically disordered'' sequences were not appreciated. We propose the first-ever structural model of a Hox protein to explain how specific contacts between distant, intrinsically disordered regions of the protein and the homeodomain regulate DNA binding and coordinate this activity with other Hox molecular functions.

Defining intrinsic vs. extrinsic atopic dermatitis.

PubMed

Karimkhani, Chante; Silverberg, Jonathan I; Dellavalle, Robert P

2015-06-16

Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin condition characterized by eczematous lesions, i.e. ill-demarcated erythematous patches and plaques. AD is commonly associated with elevated immunoglobulin E (IgE) and atopic disorders, such as asthma, hay fever, and food allergies. Rackemann and Mallory were some of the first to distinguish between asthma based on the presence ("extrinsic") or absence ("intrinsic") of allergy. This distinction has subsequently been applied to AD based on the presence ("extrinsic") or absence ("intrinsic") of increased IgE and atopic disease. Although the distinction between intrinsic and extrinsic AD is widely used, it remains controversial.

Quantifying the effects of disorder on switching of perpendicular spin ice arrays

NASA Astrophysics Data System (ADS)

Kempinger, Susan; Fraleigh, Robert; Lammert, Paul; Crespi, Vincent; Samarth, Nitin; Zhang, Sheng; Schiffer, Peter

There is much contemporary interest in probing custom designed, frustrated systems such as artificial spin ice. To that end, we study arrays of lithographically patterned, single-domain Pt/Co multilayer islands. Due to the perpendicular anisotropy of these materials, we are able to use diffraction-limited magneto-optical Kerr effect microscopy to access the magnetic state in situ with an applied field. As we tune the interaction strength by adjusting the lattice spacing, we observe the switching field distribution broadening with increasing dipolar interactions. Using a simple mathematical analysis we extract the intrinsic disorder (the disorder that would be present without interactions) from these switching field distributions. We also characterize the intrinsic disorder by systematically removing neighbor effects from the switching field distribution. Understanding this disorder contribution as well as the interaction strength allows us to more accurately characterize the moment correlation. This project was funded by the US Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division under Grant No. DE- SC0010778

Computer Simulations of Intrinsically Disordered Proteins

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Chatterjee, Prathit; Ham, Sihyun

2017-05-01

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.

Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

PubMed

Jensen, Malene Ringkjøbing; Markwick, Phineus R L; Meier, Sebastian; Griesinger, Christian; Zweckstetter, Markus; Grzesiek, Stephan; Bernadó, Pau; Blackledge, Martin

2009-09-09

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

PubMed

Mercadante, Davide; Milles, Sigrid; Fuertes, Gustavo; Svergun, Dmitri I; Lemke, Edward A; Gräter, Frauke

2015-06-25

Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae.

PubMed

Ivanyi-Nagy, Roland; Lavergne, Jean-Pierre; Gabus, Caroline; Ficheux, Damien; Darlix, Jean-Luc

2008-02-01

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning-possibly mediated by intrinsically disordered protein segments-is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication.

RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae

PubMed Central

Ivanyi-Nagy, Roland; Lavergne, Jean-Pierre; Gabus, Caroline; Ficheux, Damien; Darlix, Jean-Luc

2008-01-01

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning—possibly mediated by intrinsically disordered protein segments—is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication. PMID:18033802

GABA(A) Receptor Alpha5 Subunit as a Candidate Gene for Autism and Bipolar Disorder: A Proposed Endophenotype with Parent-of-Origin and Gain-of-Function Features, with or without Oculocutaneous Albinism

ERIC Educational Resources Information Center

Delong, Robert

2007-01-01

Our earlier family history studies of individuals with autism found a high incidence of major affective disorder, especially bipolar disorder, and unusual talents or intellectual abilities among family members. We now describe a subgroup of such families, selected from a large clinical experience, illustrating specific features of major affective…

Lurasidone

MedlinePlus

Lurasidone is used to treat the symptoms of schizophrenia (a mental illness that causes disturbed or unusual ... often than prescribed by your doctor.Lurasidone controls schizophrenia and depression in people with bipolar disorder but ...

Chlorpromazine

MedlinePlus

Chlorpromazine is used to treat the symptoms of schizophrenia (a mental illness that causes disturbed or unusual ... chlorpromazine.If you are taking chlorpromazine to treat schizophrenia or another psychotic disorder, chlorpromazine may control your ...

Quetiapine

MedlinePlus

... tablets are used to treat the symptoms of schizophrenia (a mental illness that causes disturbed or unusual ... a treatment program to treat bipolar disorder and schizophrenia in children and teenagers. Quetiapine is in a ...

Unusual headaches in the elderly.

PubMed

Bamford, Cynthia C; Mays, MaryAnn; Tepper, Stewart J

2011-08-01

Prevalence of headache lowers with age, and headaches of elderly adults tend to be different than those of the younger population. Secondary headaches, such as headaches associated with vascular disease, head trauma, and neoplasm, are more common. Also, certain headache types tend to be geriatric disorders, such as primary cough headache, hypnic headache, typical aura without headache, exploding head syndrome, and giant cell arteritis. This review provides an overview of some of the major and unusual geriatric headaches, both primary and secondary.

Enduring Mental Health: Prevalence and Prediction

PubMed Central

2016-01-01

We review epidemiological evidence indicating that most people will develop a diagnosable mental disorder, suggesting that only a minority experience enduring mental health. This minority has received little empirical study, leaving the prevalence and predictors of enduring mental health unknown. We turn to the population-representative Dunedin cohort, followed from birth to midlife, to compare people never-diagnosed with mental disorder (N = 171; 17% prevalence) to those diagnosed at 1–2 study waves, the cohort mode (N = 409). Surprisingly, compared to this modal group, never-diagnosed Study members were not born into unusually well-to-do families, nor did their enduring mental health follow markedly sound physical health, or unusually high intelligence. Instead, they tended to have an advantageous temperament/personality style, and negligible family history of mental disorder. As adults, they report superior educational and occupational attainment, greater life satisfaction, and higher-quality relationships. Our findings draw attention to “enduring mental health” as a revealing psychological phenotype and suggest it deserves further study. PMID:27929304

Donor Stem Cell Transplant or Donor White Blood Cell Infusions in Treating Patients With Hematologic Cancer

ClinicalTrials.gov

2017-09-25

Chronic Myeloproliferative Disorders; Leukemia; Lymphoma; Multiple Myeloma and Plasma Cell Neoplasm; Myelodysplastic Syndromes; Myelodysplastic/Myeloproliferative Neoplasms; Unusual Cancers of Childhood

Olanzapine Injection

MedlinePlus

Olanzapine extended-release injection is used to treat schizophrenia (a mental illness that causes disturbed or unusual ... treat episodes of agitation in people who have schizophrenia or in people who have bipolar I disorder ( ...

Unusual early-onset Huntingtons disease.

PubMed

Vargas, Antonio P; Carod-Artal, Francisco J; Bomfim, Denise; Vázquez-Cabrera, Carolina; Dantas-Barbosa, Carmela

2003-06-01

Huntington's disease is an autosomal dominant progressive neurodegenerative disorder characterized by involuntary movements, cognitive decline, and behavioral disorders leading to functional disability. In contrast to patients with adult onset, in which chorea is the major motor abnormality, children often present with spasticity, rigidity, and significant intellectual decline associated with a more rapidly progressive course. An unusual early-onset Huntington's disease case of an 11-year-old boy with severe hypokinetic/rigid syndrome appearing at the age of 2.5 years is presented. Clinical diagnosis was confirmed by polymerase chain reaction study of the expanded IT-15 allele with a compatible size of 102 cytosine-adenosine-guanosine repeats L-Dopa mildly ameliorated rigidity, bradykinesia, and dystonia. We conclude that Huntington's disease should be included in the differential diagnoses of regressive syndromes of early childhood.

The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation

NASA Astrophysics Data System (ADS)

Shirai, Nobu C.; Kikuchi, Macoto

2016-02-01

α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of α-syn is induced not only by increases in α-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of α-syn and macromolecular crowding, we construct a lattice gas model of α-syn in contact with a crowding agent reservoir based on statistical mechanics. The main assumption is that α-syn can be expressed as coarse-grained particles with internal states coupled with effective volume; and disordered states are modeled by larger particles with larger internal entropy than other states. Thanks to the simplicity of the model, we can exactly calculate the number of conformations of crowding agents, and this enables us to prove that the original grand canonical ensemble with a crowding agent reservoir is mathematically equivalent to a canonical ensemble without crowding agents. In this expression, the effect of macromolecular crowding is absorbed in the internal entropy of disordered states; it is clearly shown that the crowding effect reduces the internal entropy. Based on Monte Carlo simulation, we provide scenarios of crowding-induced fibril formation. We also discuss the recent controversy over the existence of helically folded tetramers of α-syn, and suggest that macromolecular crowding is the key to resolving the controversy.

Multimodal Investigation of Network Level Effects Using Intrinsic Functional Connectivity, Anatomical Covariance, and Structure-to-Function Correlations in Unmedicated Major Depressive Disorder

PubMed Central

Scheinost, Dustin; Holmes, Sophie E; DellaGioia, Nicole; Schleifer, Charlie; Matuskey, David; Abdallah, Chadi G; Hampson, Michelle; Krystal, John H; Anticevic, Alan; Esterlis, Irina

2018-01-01

Converging evidence suggests that major depressive disorder (MDD) affects multiple large-scale brain networks. Analyses of the correlation or covariance of regional brain structure and function applied to structural and functional MRI data may provide insights into systems-level organization and structure-to-function correlations in the brain in MDD. This study applied tensor-based morphometry and intrinsic connectivity distribution to identify regions of altered volume and intrinsic functional connectivity in data from unmedicated individuals with MDD (n=17) and healthy comparison participants (HC, n=20). These regions were then used as seeds for exploratory anatomical covariance and connectivity analyses. Reduction in volume in the anterior cingulate cortex (ACC) and lower structural covariance between the ACC and the cerebellum were observed in the MDD group. Additionally, individuals with MDD had significantly lower whole-brain intrinsic functional connectivity in the medial prefrontal cortex (mPFC). This mPFC region showed altered connectivity to the ventral lateral PFC (vlPFC) and local circuitry in MDD. Global connectivity in the ACC was negatively correlated with reported depressive symptomatology. The mPFC–vlPFC connectivity was positively correlated with depressive symptoms. Finally, we observed increased structure-to-function correlation in the PFC/ACC in the MDD group. Although across all analysis methods and modalities alterations in the PFC/ACC were a common finding, each modality and method detected alterations in subregions belonging to distinct large-scale brain networks. These exploratory results support the hypothesis that MDD is a systems level disorder affecting multiple brain networks located in the PFC and provide new insights into the pathophysiology of this disorder. PMID:28944772

Multimodal Investigation of Network Level Effects Using Intrinsic Functional Connectivity, Anatomical Covariance, and Structure-to-Function Correlations in Unmedicated Major Depressive Disorder.

PubMed

Scheinost, Dustin; Holmes, Sophie E; DellaGioia, Nicole; Schleifer, Charlie; Matuskey, David; Abdallah, Chadi G; Hampson, Michelle; Krystal, John H; Anticevic, Alan; Esterlis, Irina

2018-04-01

Converging evidence suggests that major depressive disorder (MDD) affects multiple large-scale brain networks. Analyses of the correlation or covariance of regional brain structure and function applied to structural and functional MRI data may provide insights into systems-level organization and structure-to-function correlations in the brain in MDD. This study applied tensor-based morphometry and intrinsic connectivity distribution to identify regions of altered volume and intrinsic functional connectivity in data from unmedicated individuals with MDD (n=17) and healthy comparison participants (HC, n=20). These regions were then used as seeds for exploratory anatomical covariance and connectivity analyses. Reduction in volume in the anterior cingulate cortex (ACC) and lower structural covariance between the ACC and the cerebellum were observed in the MDD group. Additionally, individuals with MDD had significantly lower whole-brain intrinsic functional connectivity in the medial prefrontal cortex (mPFC). This mPFC region showed altered connectivity to the ventral lateral PFC (vlPFC) and local circuitry in MDD. Global connectivity in the ACC was negatively correlated with reported depressive symptomatology. The mPFC-vlPFC connectivity was positively correlated with depressive symptoms. Finally, we observed increased structure-to-function correlation in the PFC/ACC in the MDD group. Although across all analysis methods and modalities alterations in the PFC/ACC were a common finding, each modality and method detected alterations in subregions belonging to distinct large-scale brain networks. These exploratory results support the hypothesis that MDD is a systems level disorder affecting multiple brain networks located in the PFC and provide new insights into the pathophysiology of this disorder.

[Asperger syndrome associated with macrosomia and sexual identity disorder].

PubMed

Fleta Zaragozano, J; Zapata Usábel, M; López Moreno, María J; Olivares López, J L

2005-10-01

Asperger Syndrome is a pervasive developmental disorder of unknown origin, characterized by pedantic language, lack of reciprocity in social interactions, unusual interests, motor clumsiness and normal or above average intelligence quotient, among other symptoms. Since 1994 it has been defined as a specific entity. We describe the case of a boy with this syndrome, with elevated body weight and height and sexual identity disorder. These alterations have not previously been described in the scientific literature on Asperger syndrome.

A rare case of lateral ovotesticular disorder with Klinefelter syndrome mosaicism 46, XX/47, XXY: An unusual presentation.

PubMed

Talreja, Shyam M; Banerjee, Indraneel; Yadav, Sher Singh; Tomar, Vinay

2015-01-01

Ovotesticular disorder of sex development (OT-DSD) is a rare disorder of sexual differentiation characterized by the presence of both ovarian and testicular tissues in the same individual. It's incidence ranges from 3% to 10% of all disorder of DSD's, and the most common presentation is 46, XX followed by 46, XX/46, XY mosaicism and 46, XY. Klinefelter syndrome (KS) mosaicism 46, XX/47, XXY is extremely rare, and its association with the ovotesticular disorder is even rarer. We report an unusual case of 16-year-old with male habitus who presented with complains of cyclic hematuria. On examination, he had bilateral gynecomastia, unilateral left cryptorchidism, absent facial hair, sparse axillary hair growth, and pubic hair distribution of feminine type. The right testis was of normal size located normally in hemiscrotum and was confirmed by radio imaging. Ultrasonography and magnetic resonance imaging revealed a cystic area behind posterior half of urinary bladder. Chromosomal analysis revealed 46, XX/47, XXY mosaicism of female karyotype and KS. Histopathological report of this left side excised specimen confirmed the structures to be ovary, uterus, and fallopian tube, thus confirming our diagnosis of the lateral ovotesticular disorder. Meticulous workup combined interdisciplinary approach will lead to early diagnosis and resolve timely sex reassignment issues and also prevent consequences arising due to gonadal insufficiency.

Myasthenia Gravis: Unusual Presentations and Diagnostic Pitfalls.

PubMed

Rodolico, Carmelo; Parisi, Daniela; Portaro, Simona; Biasini, Fiammetta; Sinicropi, Stefano; Ciranni, Annamaria; Toscano, Antonio; Messina, Sonia; Musumeci, Olimpia; Vita, Giuseppe; Girlanda, Paolo

2016-08-30

Myasthenia gravis (MG) is an autoimmune disorder presenting with fluctuating, fatigable muscle weakness. Initial symptoms classically involve ocular and proximal limb muscles. Rarely, MG may onset with unusual features, so it can be misdiagnosed with other neuromuscular diseases. To describe unusual and atypical presentations of MG in a large cohort of patients, considering and discussing diagnostic difficulties and pitfalls. We report on 21 out of 508 MG patients, coming to our department in the last 27 years and presenting with atypical or unusual features. The diagnosis was achieved performing a careful clinical examination, a proper neurophysiological assessment, the neostigmine test, the AChR and MuSK antibodies assay and chest CT-scan. Patients with atypical/unusual MG onset were the 4.4% of all MG patients population. We describe seven different clinical categories: asymmetric distal upper limbs weakness, foot drop, isolated triceps brachii weakness and foot drop, post exertional axial weakness with dropped head, acute facial dyplegia, limb-girdle MG and MG with sudden lower limbs weakness and recurrent falls. Atypical and unusual presentations may increase the risk to misdiagnose or delay MG diagnosis. Isolated limb-girdle presentation is the most frequent atypical form in our series.

Unusual scaling laws for plasmonic nanolasers beyond the diffraction limit.

PubMed

Wang, Suo; Wang, Xing-Yuan; Li, Bo; Chen, Hua-Zhou; Wang, Yi-Lun; Dai, Lun; Oulton, Rupert F; Ma, Ren-Min

2017-12-01

Plasmonic nanolasers are a new class of amplifiers that generate coherent light well below the diffraction barrier bringing fundamentally new capabilities to biochemical sensing, super-resolution imaging, and on-chip optical communication. However, a debate about whether metals can enhance the performance of lasers has persisted due to the unavoidable fact that metallic absorption intrinsically scales with field confinement. Here, we report plasmonic nanolasers with extremely low thresholds on the order of 10 kW cm -2 at room temperature, which are comparable to those found in modern laser diodes. More importantly, we find unusual scaling laws allowing plasmonic lasers to be more compact and faster with lower threshold and power consumption than photonic lasers when the cavity size approaches or surpasses the diffraction limit. This clarifies the long-standing debate over the viability of metal confinement and feedback strategies in laser technology and identifies situations where plasmonic lasers can have clear practical advantage.

[Unusual aspect of pernicious anemia during association of beta-thalassemia: a new case report and literature review].

PubMed

Diop, Madoky Magatte; Toure, P S; Leye, M Y; Leye, A; El Fadjri, S; Diop, M; Ka, M M; Diop, Oulimata D; Fall, S; Ndiaye, F S

2012-01-01

Pernicious anemia appears classically by macrocytosis. We report a case of a late discovered Biermer disease, on a 42-year-old young black woman. The reason was an unusual aspect of this disease in a context of betathalassemia. The patient presented chronic anemia which evolved during about ten year. Biology showed a normocytosis and signs of hemolysis according to beta-thalassemia. This was confirmed by an electrophoresis showing 9.1 % of fraction F some haemoglobin. Since this date, the patient was treated by folic acid alone with periodic transfusions of red blood cell. She presented eight years after the beginning of her disease, neurological deterioration. Diagnosis of pernicious anemia was finally established up on histological gastritis, low level of the blood rate of vitamin B12, macrocytosis, and presence of intrinsic anti-factor and parietal anti-cells antibodies.

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

PubMed Central

Vacic, Vladimir; Markwick, Phineus R. L.; Oldfield, Christopher J.; Zhao, Xiaoyue; Haynes, Chad; Uversky, Vladimir N.; Iakoucheva, Lilia M.

2012-01-01

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7–2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations. PMID:23055912

A multi-state coarse grained modeling approach for an intrinsically disordered peptide

NASA Astrophysics Data System (ADS)

Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

2017-09-01

Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

Characterising intra- and inter-intrinsic network synchrony in combat-related post-traumatic stress disorder.

PubMed

Dunkley, Benjamin T; Doesburg, Sam M; Jetly, Rakesh; Sedge, Paul A; Pang, Elizabeth W; Taylor, Margot J

2015-11-30

Soldiers with post-traumatic stress disorder (PTSD) exhibit elevated gamma-band synchrony in left fronto-temporal cortex, and connectivity measures in these regions correlate with comorbidities and PTSD severity, which suggests increased gamma synchrony is related to symptomology. However, little is known about the role of intrinsic, phase-synchronised networks in the disorder. Using magnetoencephalography (MEG), we characterised spectral connectivity in the default-mode, salience, visual, and attention networks during resting-state in a PTSD population and a trauma-exposed control group. Intrinsic network connectivity was examined in canonical frequency bands. We observed increased inter-network synchronisation in the PTSD group compared with controls in the gamma (30-80 Hz) and high-gamma range (80-150 Hz). Analyses of connectivity and symptomology revealed that PTSD severity was positively associated with beta synchrony in the ventral-attention-to-salience networks, and gamma synchrony within the salience network, but also negatively correlated with beta synchrony within the visual network. These novel results show that frequency-specific, network-level atypicalities may reflect trauma-related alterations of ongoing functional connectivity, and correlations of beta synchrony in attentional-to-salience and visual networks with PTSD severity suggest complicated network interactions mediate symptoms. These results contribute to accumulating evidence that PTSD is a complicated network-based disorder expressed as altered neural interactions. Crown Copyright © 2015. Published by Elsevier Ireland Ltd. All rights reserved.

Probing Structural Transitions in the Intrinsically Disordered C-Terminal Domain of the Measles Virus Nucleoprotein by Vibrational Spectroscopy of Cyanylated Cysteines

PubMed Central

Bischak, Connor G.; Longhi, Sonia; Snead, David M.; Costanzo, Stéphanie; Terrer, Elodie; Londergan, Casey H.

2010-01-01

Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) were cyanylated at cysteine and their infrared spectra in the C≡N stretching region were recorded both in the absence and in the presence of one of the physiological partners of NTAIL, namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within NTAIL, the C≡N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level. PMID:20816082

A multi-state coarse grained modeling approach for an intrinsically disordered peptide.

PubMed

Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

2017-09-07

Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα14 is disordered in dilute solutions; however, it strictly adopts the α-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

Longitudinal relaxation properties of 1HN and 1Hα determined by direct-detected 13C NMR experiments to study intrinsically disordered proteins (IDPs)

NASA Astrophysics Data System (ADS)

Hošek, Tomáš; Gil-Caballero, Sergi; Pierattelli, Roberta; Brutscher, Bernhard; Felli, Isabella C.

2015-05-01

Intrinsically disordered proteins (IDPs) are functional proteins containing large fragments characterized by high local mobility. Bioinformatic studies have suggested that a significant fraction (more than 30%) of eukaryotic proteins has disordered regions of more than 50 amino acids in length. Hence, NMR methods for the characterization of local compactness and solvent accessibility in such highly disordered proteins are of high importance. Among the available approaches, the HET-SOFAST/BEST experiments (Schanda et al., 2006, Rennella et al., 2014) provide semi-quantitative information by monitoring longitudinal 1H relaxation of amide protons under different initial conditions. However, when approaching physiological sample conditions, the potential of these amide 1H detected experiments is reduced due to rapid amide proton solvent exchange. 13C direct detection methods therefore provide a valuable alternative thanks to a higher chemical shift dispersion and their intrinsic insensitivity toward solvent exchange. Here we present two sets of 13C-detected experiments, which indirectly measure 1HN and 1Hα inversion recovery profiles. The experiments consist of an initial spin inversion-recovery block optimized for selective manipulation of different types of proton spins followed by a CON read-out scheme. The proposed experiments were tested on human α-synuclein and ubiquitin, two representative examples of unfolded and folded proteins.

Probing the intrinsic charge transport in indacenodithiophene-co-benzothiadiazole thin films

NASA Astrophysics Data System (ADS)

Wang, Wenhe; Tang, Wei; Zhao, Jiaqing; Bao, Bei; Xing, Hui; Guo, Xiaojun; Wang, Shun; Liu, Ying

2017-12-01

Indacenodithiophene-co-benzothiadiazole (IDTBT) belongs to a class of donor-acceptor polymers, exhibiting high electronic mobility and low energetic disorder. Applying vacuum as dielectric enables us to investigate the intrinsic charge transport properties in IDTBT. Vacuum-gap IDTBT field-effect transistors (FET) show high mobilites approaching 1 cm2V-1s-1. In addition, with increasing dielectric constant of the gate insulators, the mobilites of IDTBT transistors first increase and then decrease. The reason could be attributed to effect of both charge carrier accumulation and the presence of dipolar disorder at the semiconductor/insulator interface induced by polar insulator layer.

Brain State Differentiation and Behavioral Inflexibility in Autism†

PubMed Central

Uddin, Lucina Q.; Supekar, Kaustubh; Lynch, Charles J.; Cheng, Katherine M.; Odriozola, Paola; Barth, Maria E.; Phillips, Jennifer; Feinstein, Carl; Abrams, Daniel A.; Menon, Vinod

2015-01-01

Autism spectrum disorders (ASDs) are characterized by social impairments alongside cognitive and behavioral inflexibility. While social deficits in ASDs have extensively been characterized, the neurobiological basis of inflexibility and its relation to core clinical symptoms of the disorder are unknown. We acquired functional neuroimaging data from 2 cohorts, each consisting of 17 children with ASDs and 17 age- and IQ-matched typically developing (TD) children, during stimulus-evoked brain states involving performance of social attention and numerical problem solving tasks, as well as during intrinsic, resting brain states. Effective connectivity between key nodes of the salience network, default mode network, and central executive network was used to obtain indices of functional organization across evoked and intrinsic brain states. In both cohorts examined, a machine learning algorithm was able to discriminate intrinsic (resting) and evoked (task) functional brain network configurations more accurately in TD children than in children with ASD. Brain state discriminability was related to severity of restricted and repetitive behaviors, indicating that weak modulation of brain states may contribute to behavioral inflexibility in ASD. These findings provide novel evidence for a potential link between neurophysiological inflexibility and core symptoms of this complex neurodevelopmental disorder. PMID:25073720

The intermembrane space domain of Tim23 is intrinsically disordered with a distinct binding region for presequences

PubMed Central

de la Cruz, Laura; Bajaj, Rakhi; Becker, Stefan; Zweckstetter, Markus

2010-01-01

Proteins targeted to the mitochondrial matrix are translocated through the outer and the inner mitochondrial membranes by two protein complexes, the translocase of the outer membrane (TOM) and one of the translocases of the inner membrane (TIM23). The protein Tim23, the core component of TIM23, consists of an N-terminal, soluble domain in the intermembrane space (IMS) and a C-terminal domain that forms the import pore across the inner membrane. Before translocation proceeds, precursor proteins are recognized by the N-terminal domain of Tim23, Tim23N (residues 1–96). By using NMR spectroscopy, we show that Tim23N is a monomeric protein belonging to the family of intrinsically disordered proteins. Titrations of Tim23N with two presequences revealed a distinct binding region of Tim23N formed by residues 71–84. In a charge-hydropathy plot containing all soluble domains of TOM and TIM23, Tim23N was found to be the only domain with more than 40 residues in the IMS that is predicted to be intrinsically disordered, suggesting that Tim23N might function as hub in the mitochondrial import machinery protein network. PMID:20718036

The α-Helical Structure of Prodomains Promotes Translocation of Intrinsically Disordered Neuropeptide Hormones into the Endoplasmic Reticulum*

PubMed Central

Dirndorfer, Daniela; Seidel, Ralf P.; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F.; Tatzelt, Jörg

2013-01-01

Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation. PMID:23532840

The α-helical structure of prodomains promotes translocation of intrinsically disordered neuropeptide hormones into the endoplasmic reticulum.

PubMed

Dirndorfer, Daniela; Seidel, Ralf P; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F; Tatzelt, Jörg

2013-05-17

Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation.

Backbone conformational preferences of an intrinsically disordered protein in solution.

PubMed

Espinoza-Fonseca, L Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, José

2012-06-01

We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple binding partners. Based on this evidence, we propose that the backbone conformational preferences of KID provide a thermodynamic advantage for folding and binding without negatively affecting the kinetics of binding. We further discuss the relation of our results to previous studies to rationalize the functional implications of the conformational preferences of IDPs, such as the optimization of structural disorder in protein-protein interactions. This study illustrates the importance in obtaining atomistic information of intrinsically disordered proteins in real time to reveal functional features arising from their complex conformational space.

Temporal complexity in emission from Anderson localized lasers

NASA Astrophysics Data System (ADS)

Kumar, Randhir; Balasubrahmaniyam, M.; Alee, K. Shadak; Mujumdar, Sushil

2017-12-01

Anderson localization lasers exploit resonant cavities formed due to structural disorder. The inherent randomness in the structure of these cavities realizes a probability distribution in all cavity parameters such as quality factors, mode volumes, mode structures, and so on, implying resultant statistical fluctuations in the temporal behavior. Here we provide direct experimental measurements of temporal width distributions of Anderson localization lasing pulses in intrinsically and extrinsically disordered coupled-microresonator arrays. We first illustrate signature exponential decays in the spatial intensity distributions of the lasing modes that quantify their localized character, and then measure the temporal width distributions of the pulsed emission over several configurations. We observe a dependence of temporal widths on the disorder strength, wherein the widths show a single-peaked, left-skewed distribution in extrinsic disorder and a dual-peaked distribution in intrinsic disorder. We propose a model based on coupled rate equations for an emitter and an Anderson cavity with a random mode structure, which gives excellent quantitative and qualitative agreement with the experimental observations. The experimental and theoretical analyses bring to the fore the temporal complexity in Anderson-localization-based lasing systems.

Highly Disordered Proteins in Prostate Cancer.

PubMed

Uversky, Vladimir N; Na, Insung; Landau, Kevin S; Schenck, Ryan O

2017-01-01

Prostate cancer is one of the major threats to the man's health. There are several mechanisms of the prostate cancer development characterized by the involvement of various androgen-related and androgen-unrelated factors in prostate cancer pathogenesis and in the metastatic carcinogenesis of prostate. In all these processes, proteins play various important roles, and the KEGG database has information on 88 human proteins experimentally shown to be involved in prostate cancer. It is known that many proteins associated with different human maladies are intrinsically disordered (i.e., they do not have stable secondary and/or tertiary structure in their unbound states). The goal of this review is to consider several highly disordered proteins known to be associated with the prostate cancer pathogenesis in order to better understand the roles of disordered proteins in this disease. We also hope that consideration of the pathology-related proteins from the perspective of intrinsic disorder can potentially lead to future experimental studies of these proteins to find novel pathways associated with prostate cancer. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

From Disorder to Mis-Order: Structural Aspects of Pathogenic Oligomerization in Conformational Diseases.

PubMed

Yiu, Chin Pang Benny; Chen, Yu Wai

2017-01-01

Proteins implicated in neurological conformational diseases contain substantial amounts of "intrinsic disorder". These native monomeric functional states may transit into some oligomeric states that have high β-sheet contents and seed the formation of insoluble amyloid fibrils. The prevailing view is that these "toxic" oligomers should be targeted for drug development. Here, an overview of the diseases was presented, within the general framework of the oligomerization of intrinsically disordered proteins. These systems pose some specific challenges to structural studies: the toxic oligomers are transient, low in concentration, and often need to be studied in a heterogeneous environment. Nevertheless, there have been much exciting progress as a result of the creative use of experimental techniques, a selection of these were outlined. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Intrinsically disordered proteins--relation to general model expressing the active role of the water environment.

PubMed

Kalinowska, Barbara; Banach, Mateusz; Konieczny, Leszek; Marchewka, Damian; Roterman, Irena

2014-01-01

This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the "fuzzy oil drop" model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location conflicts with theoretical predictions. We show that the structural influence of the water environment determines the positions of disordered fragments, leading to the formation of a hydrophobic core overlaid by a hydrophilic mantle. This phenomenon is further described by studying selected proteins which are known to be unstable and contain intrinsically disordered fragments. Their properties are established quantitatively, explaining the causative relation between the protein's structure and function and facilitating further comparative analyses of various structural models. © 2014 Elsevier Inc. All rights reserved.

Genetic and Diagnostic Biomarker Development in ASD Toddlers Using Resting State Functional MRI

DTIC Science & Technology

2015-09-01

for public release; distribution unlimited Autism spectrum disorder (ASD); biomarker; early brain development; intrinsic functional brain networks...three large neuroimaging/neurobehavioral datasets to identify brain-imaging based biomarkers for Autism Spectrum Disorders (ASD). At Yale, we focus...neurobehavioral!datasets!in!order!to!identify! brainFimaging!based!biomarkers!for! Autism ! Spectrum ! Disorders !(ASD),!including!1)!BrainMap,! developed!and

Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads

PubMed Central

Baruah, Anupaul; Rani, Pooja; Biswas, Parbati

2015-01-01

This work quantitatively characterizes intrinsic disorder in proteins in terms of sequence composition and backbone conformational entropy. Analysis of the normalized relative composition of the amino acid triads highlights a distinct boundary between globular and disordered proteins. The conformational entropy is calculated from the dihedral angles of the middle amino acid in the amino acid triad for the conformational ensemble of the globular, partially and completely disordered proteins relative to the non-redundant database. Both Monte Carlo (MC) and Molecular Dynamics (MD) simulations are used to characterize the conformational ensemble of the representative proteins of each group. The results show that the globular proteins span approximately half of the allowed conformational states in the Ramachandran space, while the amino acid triads in disordered proteins sample the entire range of the allowed dihedral angle space following Flory’s isolated-pair hypothesis. Therefore, only the sequence information in terms of the relative amino acid triad composition may be sufficient to predict protein disorder and the backbone conformational entropy, even in the absence of well-defined structure. The predicted entropies are found to agree with those calculated using mutual information expansion and the histogram method. PMID:26138206

Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Launay, Hélène; Barré, Patrick; Puppo, Carine

2016-08-12

The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in themore » oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.« less

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

PubMed

Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

2016-03-14

The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models.

PubMed

Henriques, João; Skepö, Marie

2016-07-12

Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [ Henriques et al. J. Chem. Theory Comput. 2015 , 11 , 3420 - 3431 ], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.

Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

NASA Astrophysics Data System (ADS)

Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

2017-01-01

Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs.

Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

PubMed Central

Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

2017-01-01

Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs. PMID:28054562

Intrinsic motivation as a predictor of work outcome after vocational rehabilitation in schizophrenia.

PubMed

Saperstein, Alice M; Fiszdon, Joanna M; Bell, Morris D

2011-09-01

Intrinsic motivation is a construct commonly used in explaining goal-directed behavior. In people with schizophrenia, intrinsic motivation is usually subsumed as a feature of negative symptoms or underlying neurocognitive dysfunction. A growing literature reflects an interest in defining and measuring motivational impairment in schizophrenia and in delineating the specific role of intrinsic motivation as both an independent predictor and a mediator of psychosocial functioning. This cross-sectional study examined intrinsic motivation as a predictor of vocational outcomes for 145 individuals with schizophrenia and schizoaffective disorder participating in a 6-month work rehabilitation trial. Correlation and mediation analyses examined baseline intrinsic motivation and negative symptoms in relation to work hours and work performance. Data support a significant relationship between intrinsic motivation and negative symptoms and significant correlations with outcome variables, such that lower negative symptoms and greater intrinsic motivation were associated with better work functioning. Moreover, in this sample, intrinsic motivation fully mediated the relationships between negative symptoms, work productivity, and work performance. These results have significant implications on the design of work rehabilitation interventions for people with schizophrenia and support a role for targeting intrinsic motivation directly to influence vocational functioning. Future directions for research and intervention are discussed.

Brief Report: An Unusual Manifestation of Diagnostic Overshadowing of Pervasive Developmental Disorder--Not Otherwise Specified--A Five Year Longitudinal Case Study

ERIC Educational Resources Information Center

Meera, S. S.; Kaipa, Ramesh; Thomas, Jaslin; Shivashankar, N.

2013-01-01

Children with communication disorders present with a range of comorbid conditions. Occasionally one of the comorbid conditions manifests so strongly that the primary condition goes unnoticed by the clinician. This tendency to overlook comorbid health problems in the presence of a disability is referred to as diagnostic overshadowing. This is a…

Disorders of Behavioral and Emotional Regulation in the First Years of Life: Early Risks and Intervention in the Developing Parent-Infant Relationship

ERIC Educational Resources Information Center

Papousek, Mechthild, Ed.; Schieche, Michael, Ed.; Wurmser, Harald, Ed.

2007-01-01

For every five healthy babies and infants, there is at least one who brings unusual stresses for its parents with behaviors such as inconsolable crying, sleep disorders, refusal to eat, chronic moodiness, incessant demands for attention, fearful clinging, or tantrums. Available for the first time in English, this influential German collection…

[Patients with unusual requests for extractions 2. Mental incompetency and psycho-pathologic causes].

PubMed

Broers, D L M; Brands, W G; de Jongh, A; Willems, D L

2010-11-01

If there is no indication for tooth removal purely based on dental criteria, but the patient requests for removal due to fear of dental treatment, or because of a mental disorder such as posttraumatic stress disorder, a somatoform pain disorder or a disorder of body image perception, then the question is whether the patient is mentally competent to make this decision. In case of a tooth removal request on psychopathologic basis, a dentist has to refuse to carry out such treatment, but he should make an effort to help or guide the patient in some other way.

Nonlinear microwave response of an MgB2 thin film

NASA Astrophysics Data System (ADS)

Purnell, A. J.; Cohen, L. F.; Zhai, H. Y.; Christen, H. M.; Paranthaman, M. P.; Lowndes, D. H.; Hao, Ling; Gallop, J. C.

2004-04-01

MgB2 is a two-gap superconductor and as a result may manifest unusual physical properties. The performance of MgB2 films at microwave frequencies has so far been rather poor compared to that of Nb alloys and this may result from intrinsic behaviour related to the double-gap structure or extrinsic properties due to non-optimized thin films. Here we give a detailed report on the microwave magnetic field dependent surface impedance of an MgB2 thin film, using a parallel plate resonator, as a function of temperature. We discuss whether the framework used to analyse nonlinear behaviour for other superconductors, both low and high Tc, but single-gap, has any validity for MgB2 and whether the films are limited by intrinsic or extrinsic behaviour. The key result is the observation of junction-type switching effects at high microwave power.

Intrinsic Chemiluminescence Generation during Advanced Oxidation of Persistent Halogenated Aromatic Carcinogens.

PubMed

Mao, Li; Liu, Yu-Xiang; Huang, Chun-Hua; Gao, Hui-Ying; Kalyanaraman, Balaraman; Zhu, Ben-Zhan

2015-07-07

The ubiquitous distribution coupled with their carcinogenicity has raised public concerns on the potential risks to both human health and the ecosystem posed by the halogenated aromatic compounds (XAr). Recently, advanced oxidation processes (AOPs) have been increasingly favored as an "environmentally-green" technology for the remediation of such recalcitrant and highly toxic XAr. Here, we show that AOPs-mediated degradation of the priority pollutant pentachlorophenol and all other XAr produces an intrinsic chemiluminescence that directly depends on the generation of the extremely reactive hydroxyl radicals. We propose that the hydroxyl radical-dependent formation of quinoid intermediates and electronically excited carbonyl species is responsible for this unusual chemiluminescence production. A rapid, sensitive, simple, and effective chemiluminescence method was developed to quantify trace amounts of XAr and monitor their real-time degradation kinetics. These findings may have broad biological and environmental implications for future research on this important class of halogenated persistent organic pollutants.

Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease

MedlinePlus

... the CDC Bovine Spongiform Encephalopathy (BSE), or Mad Cow Disease Note: Javascript is disabled or is not ... spongiform encephalopathy) is a progressive neurological disorder of cattle that results from infection by an unusual transmissible ...

A boy with developmental delay, malformations, and evidence of a connective tissue disorder: possibly a new type of cutis laxa.

PubMed

Armstrong, Linlea; Jimenez, Carmencita; Hunter, Alasdair G W

2003-05-15

We report a 7.5-year-old boy with loose translucent skin, aortic dilatation, hyperextensible veins, recurrent respiratory problems, pectus excavatum, arthralgias, lax joints, mild epiphyseal dysplasia, and umbilical and inguinal hernias. He also has developmental delay, progressive bilateral sensorineural hearing loss, an unusual facial appearance, terminal digit hypoplasia with unusual radiographic changes in some of the phalanges, glandular hypospadias, shawl scrotum, and undescended testes. Biochemical investigations, including electrophoresis of Types 1 and 3 procollagens and collagens, and quantification of serum copper and ceruloplasmin, are normal. Relative to age-matched control patients the electron micrographs of the boy's dermis show elastin fibers to be decreased in number, and abnormal in appearance, with a low matrix to microfibril ratio. The organ distribution of abnormalities and the nature of the findings suggest a connective tissue disorder. We contrast and compare this boy's phenotype to those of the classic connective tissue disorders. We conclude that he has cutis laxa with features that distinguish him from previously described types of cutis laxa. Copyright 2003 Wiley-Liss, Inc.

Eating disorders during pregnancy.

PubMed

Cardwell, Michael S

2013-04-01

Eating disorders during pregnancy, once thought to be rare, occur in a significant number of women. The incidences of the major eating disorders-anorexia nervosa and bulimia nervosa-are increasing because of cultural pressures on the drive for thinness. Because the age range for these major eating disorders overlaps with the age range for reproductive function, it is not unusual for a clinician to encounter a pregnant patient with a major eating disorder. Eating disorders attributable to the pregnant state include pregnancy sickness, pica, and ptyalism. The diagnostic criteria, etiology, nutritional behavioral influences, evolutionary psychological considerations where elucidated, and treatment of these disorders will be presented. Obstetricians and gynecologists, family physicians After completing this CME activity, physicians should be better able to review how the major eating disorders impact pregnancy, to diagnose eating disorders during pregnancy using the diagnostic criteria, and to treat eating disorders during pregnancy.

Intrinsic gray-matter connectivity of the brain in adults with autism spectrum disorder

PubMed Central

Ecker, Christine; Ronan, Lisa; Feng, Yue; Daly, Eileen; Murphy, Clodagh; Ginestet, Cedric E.; Brammer, Michael; Fletcher, Paul C.; Bullmore, Edward T.; Suckling, John; Baron-Cohen, Simon; Williams, Steve; Loth, Eva; Murphy, Declan G. M.; Bailey, A. J.; Baron-Cohen, S.; Bolton, P. F.; Bullmore, E. T.; Carrington, S.; Chakrabarti, B.; Daly, E. M.; Deoni, S. C.; Ecker, C.; Happe, F.; Henty, J.; Jezzard, P.; Johnston, P.; Jones, D. K.; Lai, M. C.; Lombardo, M. V.; Madden, A.; Mullins, D.; Murphy, C. M.; Murphy, D. G.; Pasco, G.; Sadek, S.; Spain, D.; Steward, R.; Suckling, J.; Wheelwright, S.; Williams, S. C.

2013-01-01

Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions that are accompanied by atypical brain connectivity. So far, in vivo evidence for atypical structural brain connectivity in ASD has mainly been based on neuroimaging studies of cortical white matter. However, genetic studies suggest that abnormal connectivity in ASD may also affect neural connections within the cortical gray matter. Such intrinsic gray-matter connections are inherently more difficult to describe in vivo but may be inferred from a variety of surface-based geometric features that can be measured using magnetic resonance imaging. Here, we present a neuroimaging study that examines the intrinsic cortico-cortical connectivity of the brain in ASD using measures of “cortical separation distances” to assess the global and local intrinsic “wiring costs” of the cortex (i.e., estimated length of horizontal connections required to wire the cortex within the cortical sheet). In a sample of 68 adults with ASD and matched controls, we observed significantly reduced intrinsic wiring costs of cortex in ASD, both globally and locally. Differences in global and local wiring cost were predominantly observed in fronto-temporal regions and also significantly predicted the severity of social and repetitive symptoms (respectively). Our study confirms that atypical cortico-cortical “connectivity” in ASD is not restricted to the development of white-matter connections but may also affect the intrinsic gray-matter architecture (and connectivity) within the cortical sheet. Thus, the atypical connectivity of the brain in ASD is complex, affecting both gray and white matter, and forms part of the core neural substrates underlying autistic symptoms. PMID:23878213

Intrinsic gray-matter connectivity of the brain in adults with autism spectrum disorder.

PubMed

Ecker, Christine; Ronan, Lisa; Feng, Yue; Daly, Eileen; Murphy, Clodagh; Ginestet, Cedric E; Brammer, Michael; Fletcher, Paul C; Bullmore, Edward T; Suckling, John; Baron-Cohen, Simon; Williams, Steve; Loth, Eva; Murphy, Declan G M

2013-08-06

Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions that are accompanied by atypical brain connectivity. So far, in vivo evidence for atypical structural brain connectivity in ASD has mainly been based on neuroimaging studies of cortical white matter. However, genetic studies suggest that abnormal connectivity in ASD may also affect neural connections within the cortical gray matter. Such intrinsic gray-matter connections are inherently more difficult to describe in vivo but may be inferred from a variety of surface-based geometric features that can be measured using magnetic resonance imaging. Here, we present a neuroimaging study that examines the intrinsic cortico-cortical connectivity of the brain in ASD using measures of "cortical separation distances" to assess the global and local intrinsic "wiring costs" of the cortex (i.e., estimated length of horizontal connections required to wire the cortex within the cortical sheet). In a sample of 68 adults with ASD and matched controls, we observed significantly reduced intrinsic wiring costs of cortex in ASD, both globally and locally. Differences in global and local wiring cost were predominantly observed in fronto-temporal regions and also significantly predicted the severity of social and repetitive symptoms (respectively). Our study confirms that atypical cortico-cortical "connectivity" in ASD is not restricted to the development of white-matter connections but may also affect the intrinsic gray-matter architecture (and connectivity) within the cortical sheet. Thus, the atypical connectivity of the brain in ASD is complex, affecting both gray and white matter, and forms part of the core neural substrates underlying autistic symptoms.

Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity.

PubMed

Lai, Julian; Koh, Chuan Hock; Tjota, Monika; Pieuchot, Laurent; Raman, Vignesh; Chandrababu, Karthik Balakrishna; Yang, Daiwen; Wong, Limsoon; Jedd, Gregory

2012-09-25

Like animals and plants, multicellular fungi possess cell-to-cell channels (septal pores) that allow intercellular communication and transport. Here, using a combination of MS of Woronin body-associated proteins and a bioinformatics approach that identifies related proteins based on composition and character, we identify 17 septal pore-associated (SPA) proteins that localize to the septal pore in rings and pore-centered foci. SPA proteins are not homologous at the primary sequence level but share overall physical properties with intrinsically disordered proteins. Some SPA proteins form aggregates at the septal pore, and in vitro assembly assays suggest aggregation through a nonamyloidal mechanism involving mainly α-helical and disordered structures. SPA loss-of-function phenotypes include excessive septation, septal pore degeneration, and uncontrolled Woronin body activation. Together, our data identify the septal pore as a complex subcellular compartment and focal point for the assembly of unstructured proteins controlling diverse aspects of intercellular connectivity.

Neural Systems Approaches to Understanding Major Depressive Disorder: An Intrinsic Functional Organization Perspective

PubMed Central

Hamilton, J. Paul; Chen, Michael C.; Gotlib, Ian H.

2012-01-01

Recent research detailing the intrinsic functional organization of the brain provides a unique and useful framework to gain a better understanding of the neural bases of Major Depressive Disorder (MDD). In this review, we first present a brief history of neuroimaging research that has increased our understanding of the functional macro-architecture of the brain. From this macro-architectural perspective, we examine the extant body of functional neuroimaging research assessing MDD with a specific emphasis on the contributions of default-mode, executive, and salience networks in this debilitating disorder. Next, we describe recent investigations conducted in our laboratory in which we explicitly adopt a neural-systems perspective in examining the relations among these networks in MDD. Finally, we offer directions for future research that we believe will facilitate the development of more detailed and integrative models of neural dysfunction in depression. PMID:23477309

Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.

PubMed

Schuler, Benjamin; Soranno, Andrea; Hofmann, Hagen; Nettels, Daniel

2016-07-05

The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.

Unusual headache syndromes.

PubMed

Queiroz, Luiz P

2013-01-01

Some headache syndromes have few cases reported in the literature. Their clinical characteristics, pathogenesis, and treatment may have not been completely defined. They may not actually be uncommon but rather under-recognized and/or underreported. A literature review of unusual headache syndromes, searching PubMed and ISI Web of Knowledge, was performed. After deciding which disorders to study, relevant publications in scientific journals, including original articles, reviews, meeting abstracts, and letters or correspondences to the editors were searched. This paper reviewed the clinical characteristics, the pathogenesis, the diagnosis, and the treatment of five interesting and unusual headache syndromes: exploding head syndrome, red ear syndrome, neck-tongue syndrome, nummular headache, and cardiac cephalgia. Recognizing some unusual headaches, either primary or secondary, may be a challenge for many non-headache specialist physicians. It is important to study them because the correct diagnosis may result in specific treatments that may improve the quality of life of these patients, and this can even be life saving. © 2013 American Headache Society.

Dynamics, Conformational Entropy, and Frustration in Protein-Protein Interactions Involving an Intrinsically Disordered Protein Domain.

PubMed

Lindström, Ida; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of subnanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using nuclear magnetic resonance side chain and backbone relaxation, stopped-flow kinetics, isothermal titration calorimetry, and computational studies, we have characterized the interaction between the globular TAZ1 domain of the CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2). We show that the TAZ1/TAD-STAT2 complex retains considerable subnanosecond motions, with TAD-STAT2 undergoing only a partial disorder-to-order transition. We report here the first experimental determination of the conformational entropy change for both binding partners in an IDP binding interaction and find that the total change even exceeds in magnitude the binding enthalpy and is comparable to the contribution from the hydrophobic effect, demonstrating its importance in the binding energetics. Furthermore, we show that the conformational entropy change for TAZ1 is also instrumental in maintaining a biologically meaningful binding affinity. Strikingly, a spatial clustering of very high amplitude motions and a cluster of more rigid sites in the complex exist, which through computational studies we found to overlap with regions that experience energetic frustration and are less frustrated, respectively. Thus, the residual dynamics in the bound state could be necessary for faster dissociation, which is important for proteins that interact with multiple binding partners.

Generalised lymphangiectasia: pulmonary presentation in an adult.

PubMed Central

White, J. E.; Veale, D.; Fishwick, D.; Mitchell, L.; Corris, P. A.

1996-01-01

A 25 year old man presented with dyspnoea and was found to have generalised, but predominantly pulmonary, lymphangiectasis without gastrointestinal symptoms. This is an unusual presentation of a disorder previously diagnosed only in childhood. Images PMID:8882089

Tourette Syndrome

MedlinePlus

If you have Tourette syndrome, you make unusual movements or sounds, called tics. You have little or no control over them. Common tics are throat- ... spin, or, rarely, blurt out swear words. Tourette syndrome is a disorder of the nervous system. It ...

Increased Prevalence of Unusual Sensory Behaviors in Infants at Risk for, and Teens with, Autism Spectrum Disorder.

PubMed

Van Etten, Hannah M; Kaur, Maninderjit; Srinivasan, Sudha M; Cohen, Shereen J; Bhat, Anjana; Dobkins, Karen R

2017-11-01

The current study investigated the prevalence and pattern of unusual sensory behaviors (USBs) in teens with Autism Spectrum Disorder (ASD) and infants (3-36 months) at risk for ASD. From two different sites (UCSD and UConn), caregivers of infants at high (n = 32) and low risk (n = 33) for ASD, and teenagers with (n = 12) and without ASD (n = 11), completed age-appropriate Sensory Profile questionnaires (Infant/Toddler Sensory Profile; Dunn 2002; Adolescent/Adult Sensory Profile; Brown and Dunn 2002). The results show that high-risk infants and teenagers with ASD exhibit higher-than-typical prevalence of USBs. Results of our distribution analyses investigating the direction of sensory atypicalities (greater-than-typical vs. less-than-typical) revealed a fair degree of consistency amongst teens, however, USB patterns were more varied in high-risk infants.

Intrinsic and Extrinsic Origins of the Polar Kerr Effect in a Chiral p-WAVE Superconductor

NASA Astrophysics Data System (ADS)

Goryo, Jun

Recently, the measurement of the polar Kerr effect (PKE) in the quasi two-dimensional superconductor Sr2RuO4, which is motivated to observe the chirality of px + ipy-wave pairing, has been reported. We clarify that the PKE has intrinsic and extrinsic (disorder-induced) origins. The extrinsic contribution would be dominant in the PKE experiment.

Distal trisomy 10q syndrome, report of a patient with duplicated q24.31 – qter, autism spectrum disorder and unusual features

PubMed Central

Al-Sarraj, Yasser; Al-Khair, Hakam Abu; Taha, Rowaida Ziad; Khattab, Namat; El Sayed, Zakaria H; Elhusein, Bushra; El-Shanti, Hatem

2014-01-01

Key Clinical Message We report on a patient with distal trisomy 10q syndrome presenting with a few previously undescribed physical features, as well as, autism spectrum disorder (ASD). We recommend that patients with distal trisomy 10q syndrome should have a behavioral evaluation for ASD for the early institution of therapy. PMID:25614812

Familial endocrine myxolentiginosis.

PubMed

Panossian, D H; Marais, G E; Marais, H J

1995-11-01

We present an unusual case of a left atrial myxoma as a feature of a familial mesoectodermal disorder and review the literature. The new term "familial endocrine myxolentiginosis" is proposed, which is descriptive of the major clinical components of the syndrome. Myriad features of this disorder include (1) cardiac myxomas; (2) cutaneous myxomas; (3) multiple lentigines or blue nevi, particularly of the head and neck; (4) bilateral primary pigmented nodular adrenocortical hyperplasia; (5) unusual testicular tumors; (6) pituitary tumors; (7) myxoid fibroadenomas of the breast; (8) myxomatous disorder of the stroma of the breast; (9) ductal adenoma of the breast; and (10) psammomatous melanotic schwannoma. A tentative diagnosis is suggested by identifying two features and a definitive diagnosis is made by three or more features. The clinical and pathologic features of cardiac myxoma in familial endocrine myxolentiginosis are identical to those of familial cardiac myxoma: age < 40 years, atypical locations, multicentric origins, and recurrent presentations. A Venn diagram classification for cardiac myxomas is proposed. We include photographic, echocardiographic, biopsy, and adrenal computerized tomography documentation in our patient. Recognition of this disorder is important because of its clinical, surgical, and genetic implications. The availability of transesophageal echocardiographic technology should allow early diagnosis of this underdiagnosed entity. Clinicians should consider this entity in the differential diagnosis of their patients with any one of these manifestations.

Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

PubMed

Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

2018-01-24

Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

Converging on the function of intrinsically disordered nucleoporins in the nuclear pore complex.

PubMed

Peleg, Orit; Lim, Roderick Y H

2010-07-01

Several biological mechanisms involve proteins or proteinaceous components that are intrinsically disordered. A case in point pertains to the nuclear pore complex (NPC), which regulates molecular transport between the nucleus and the cytoplasm. NPC functionality is dependent on unfolded domains rich in Phe-Gly (FG) repeats (i.e., FG-domains) that collectively act to promote or hinder cargo translocation. To a large extent, our understanding of FG-domain behavior is limited to in vitro investigations given the difficulty to resolve them directly in the NPC. Nevertheless, recent findings indicate a collective convergence towards rationalizing FG-domain function. This review aims to glean further insight into this fascinating problem by taking an objective look at the boundary conditions and contextual details underpinning FG-domain behavior in the NPC. Here, we treat the FG-domains as being commensurate with polymeric chains to address ambiguities such as for instance, how FG-domains tethered to the central channel of the NPC would behave differently as compared with their free-floating counterparts in solution. By bringing such fundamental questions to the fore, this review seeks to illuminate the importance of how such parameters can hold influence over the structure-function relation of intrinsically disordered proteins in the NPC and beyond.

[The case of an adult man with savant syndrome in the course of autism spectrum disorder].

PubMed

Sipowicz, Kasper; Pietras, Tadeusz

2017-07-21

The paper reports on a case of 57-year man with autism spectrum disorder and epilepsy with an unusual feature of calendar calculation. Namely, this is the case of savant syndrome, which appears rarely in the course of various neuropsychiatric disorders. Commorbidity of epilepsy and autism particularly predispose to the aforementioned syndrome. In the presented case, apart from the calendar calculation, the man has high language abilities. As previous studies suggest, the extraordinary abilities among persons with savant syndrome works similarly to the language module in healthy persons. Savant syndrome may appear in any patient with neuropsychiatric disorders, particularly in those suffering from autism spectrum disorder with comorbid epilepsy.

Molecular recognition features (MoRFs) in three domains of life.

PubMed

Yan, Jing; Dunker, A Keith; Uversky, Vladimir N; Kurgan, Lukasz

2016-03-01

Intrinsically disordered proteins and protein regions offer numerous advantages in the context of protein-protein interactions when compared to the structured proteins and domains. These advantages include ability to interact with multiple partners, to fold into different conformations when bound to different partners, and to undergo disorder-to-order transitions concomitant with their functional activity. Molecular recognition features (MoRFs) are widespread elements located in disordered regions that undergo disorder-to-order transition upon binding to their protein partners. We characterize abundance, composition, and functions of MoRFs and their association with the disordered regions across 868 species spread across Eukaryota, Bacteria and Archaea. We found that although disorder is substantially elevated in Eukaryota, MoRFs have similar abundance and amino acid composition across the three domains of life. The abundance of MoRFs is highly correlated with the amount of intrinsic disorder in Bacteria and Archaea but only modestly correlated in Eukaryota. Proteins with MoRFs have significantly more disorder and MoRFs are present in many disordered regions, with Eukaryota having more MoRF-free disordered regions. MoRF-containing proteins are enriched in the ribosome, nucleus, nucleolus and microtubule and are involved in translation, protein transport, protein folding, and interactions with DNAs. Our insights into the nature and function of MoRFs enhance our understanding of the mechanisms underlying the disorder-to-order transition and protein-protein recognition and interactions. The fMoRFpred method that we used to annotate MoRFs is available at http://biomine.ece.ualberta.ca/fMoRFpred/.

Questionnaires that screen for multiple sleep disorders.

PubMed

Klingman, Karen J; Jungquist, Carla R; Perlis, Michael L

2017-04-01

The goal of this review was to identify, describe, and evaluate the existing multiple sleep disorders screening questionnaires for their comprehensiveness, brevity, and psychometric quality. A systematic review was conducted using Medline/PubMed, cumulative index to nursing & allied health literature, health and psychosocial instruments and the "grey literature". Search terms were "sleep disorders, screening, questionnaires, and psychometrics". The scope of the search was limited to English language articles for adult age groups from 1989 through 2015. Of the n = 2812 articles identified, most were assessment or treatment guideline reviews, topical reviews, and/or empirical articles. Seven of the articles described multiple sleep disorders screening instruments. Of the identified instruments, two questionnaires (the Holland sleep Disorders questionnaire and sleep-50) were evaluated as comprehensive and one questionnaire (the global sleep assessment questionnaire [GSAQ]) was judged to be both comprehensive and efficient. The GSAQ was found to cover four of the six core intrinsic disorders, sleep insufficiency, and daytime sequela with 11 questions. Accordingly, the GSAQ is the most suitable for application as a general sleep disorders screener. Additional work is required to validate this instrument in the context of primary care. Finally, the future development of multiple sleep disorders screening questionnaires should not only cover all six intrinsic sleep disorders but also acquire some basic demographic information (age, sex, body mass index, presence/absence of bed partner, work status and shift) and some limited data regarding sleep sufficiency and the daytime consequences of sleep disturbance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Carbon nanotubes as vaccine scaffolds

PubMed Central

Scheinberg, David A.; McDevitt, Michael R.; Dao, Tao; Mulvey, Justin J.; Feinberg, Evan; Alidori, Simone

2013-01-01

Carbon nanotubes display characteristics that are potentially useful in their development as scaffolds for vaccine compositions. These features include stability in vivo, lack of intrinsic immunogenicity, low toxicity, and the ability to be appended with multiple copies of antigens. In addition, the particulate nature of carbon nanotubes and their unusual properties of rapid entry into antigen-presenting cells, such as dendritic cells, make them especially useful as carriers of antigens. Early attempts demonstrating carbon nanotube-based vaccines can be used in both infectious disease settings and cancer are promising. PMID:23899863

The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded

PubMed Central

Bourhis, Jean-Marie; Receveur-Bréchot, Véronique; Oglesbee, Michael; Zhang, Xinsheng; Buccellato, Matthew; Darbon, Hervé; Canard, Bruno; Finet, Stéphanie; Longhi, Sonia

2005-01-01

Measles virus is a negative-sense, single-stranded RNA virus within theMononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. Themeasles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, NTAIL (aa 401–525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459–507) of the viral phosphoprotein. With in NTAIL, an α-helical molecular recognition element (α-MoRE, aa 488–499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small-angle X-ray scattering, we have derived a low-resolution structural model of the complex between XD and NTAIL, which shows that most of NTAIL remains disordered in the complex despite P-induced folding within the α-MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N-terminal region of NTAIL, and of a bulky globular region, corresponding to XD and to the C terminus of NTAIL (aa 486–525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that NTAIL has an additional site (aa 517–525) involved in binding to XD but not in the unstructured-to-structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure. PMID:16046624

Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles.

PubMed

Liu, Yun; Wu, Jiahui; Sun, Nan; Tu, Chengjian; Shi, Xiaoying; Cheng, Hua; Liu, Simu; Li, Shuiming; Wang, Yong; Zheng, Yizhi; Uversky, Vladimir N

2017-07-07

Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R 0mm and R 15mm radicles (i.e., before radicle emergence and 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%). The heat-stable proteome of soybean radicles that contain many IDPs could protect lactate dehydrogenase (LDH) during freeze-thaw cycles. Comparison of the 795 heat-stable proteins in the R 0mm and R 15mm soybean radicles revealed that many of these proteins changed abundance during seedling growth with 170 and 89 proteins being more abundant in R 0mm and R 15mm , respectively. KEGG analysis identified 18 proteins from the cysteine and methionine metabolism pathways and nine proteins from the phenylpropanoid biosynthesis pathway. As an important type of IDP related to stress, 30 late embryogenesis abundant proteins were also found. Ten selected proteins with high levels of predicted intrinsic disorder were able to efficiently protect LDH from the freeze-thaw-induced inactivation, but the protective ability was not correlated with the disorder content of these proteins. These observations suggest that protection of the enzymes and other proteins in a stressed cell can be one of the biological functions of plant IDPs.

Protein conformational disorder and enzyme catalysis.

PubMed

Schulenburg, Cindy; Hilvert, Donald

2013-01-01

Though lacking a well-defined three-dimensional structure, intrinsically unstructured proteins are ubiquitous in nature. These molecules play crucial roles in many cellular processes, especially signaling and regulation. Surprisingly, even enzyme catalysis can tolerate substantial disorder. This observation contravenes conventional wisdom but is relevant to an understanding of how protein dynamics modulates enzyme function. This chapter reviews properties and characteristics of disordered proteins, emphasizing examples of enzymes that lack defined structures, and considers implications of structural disorder for catalytic efficiency and evolution.

MeV ion-induced movement of lattice disorder in single crystalline silicon

NASA Astrophysics Data System (ADS)

Sen, P.; Akhtar, J.; Russell, F. M.

2000-08-01

We provide experimental evidence for the transport of atomic disorder over large distances, in device grade single-crystalline silicon, following irradiation with 200 MeV silver ions. Pile-up of lattice defects or disorder is effected at predetermined locations, spatially separated from the irradiation site. These are revealed by STM scans with atomic resolution, of an intermediate region, spanning from irradiated to shadowed parts of the crystal surface. The experimental results are consistent with transport of disorder through breather-like intrinsic localised excitations.

Protecting clean critical points by local disorder correlations

NASA Astrophysics Data System (ADS)

Hoyos, J. A.; Laflorencie, Nicolas; Vieira, André.; Vojta, Thomas

2011-03-01

We show that a broad class of quantum critical points can be stable against locally correlated disorder even if they are unstable against uncorrelated disorder. Although this result seemingly contradicts the Harris criterion, it follows naturally from the absence of a random-mass term in the associated order-parameter field theory. We illustrate the general concept with explicit calculations for quantum spin-chain models. Instead of the infinite-randomness physics induced by uncorrelated disorder, we find that weak locally correlated disorder is irrelevant. For larger disorder, we find a line of critical points with unusual properties such as an increase of the entanglement entropy with the disorder strength. We also propose experimental realizations in the context of quantum magnetism and cold-atom physics. Financial support: Fapesp, CNPq, NSF, and Research Corporation.

Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif.

PubMed

Zeng, Danyun; Shen, Qingliang; Cho, Jae-Hyun

2017-02-26

Biological functions of intrinsically disordered proteins (IDPs), and proteins containing intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline-rich motifs (PRMs). Upon binding to their target proteins, IDPs undergo a disorder-to-order transition which is accompanied by a large conformational entropy penalty. Hence, the molecular mechanisms underlying control of conformational entropy are critical for understanding the binding affinity and selectivity of IDPs-mediated protein-protein interactions (PPIs). Here, we investigated the backbone conformational entropy change accompanied by binding of the N-terminal SH3 domain (nSH3) of CrkII and PRM derived from guanine nucleotide exchange factor 1 (C3G). In particular, we focused on the estimation of conformational entropy change of disordered PRM upon binding to the nSH3 domain. Quantitative characterization of conformational dynamics of disordered peptides like PRMs is limited. Hence, we combined various methods, including NMR model-free analysis, δ2D, DynaMine, and structure-based calculation of entropy loss. This study demonstrates that the contribution of backbone conformational entropy change is significant in the PPIs mediated by IDPs/IDRs. Copyright © 2017 Elsevier Inc. All rights reserved.

Weak Localization of Light in a Disordered Microcavity

NASA Astrophysics Data System (ADS)

Gurioli, M.; Bogani, F.; Cavigli, L.; Gibbs, H.; Khitrova, G.; Wiersma, D. S.

2005-05-01

We report the observation of weak localization of light in a semiconductor microcavity. The intrinsic disorder in a microcavity leads to multiple scattering and hence to static speckle. We show that averaging over realizations of the disorder reveals a coherent backscattering cone that has a coherent enhancement factor ≥2, as required by reciprocity. The coherent backscattering cone is observed along a ring-shaped pattern due to confinement by the microcavity.

Conformational Dissection of a Viral Intrinsically Disordered Domain Involved in Cellular Transformation

PubMed Central

Perrone, Sebastián; Salvay, Andres G.; Chemes, Lucía B.; de Prat-Gay, Gonzalo

2013-01-01

Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21–29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21–29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus. PMID:24086265

Plasticity of the Intrinsic Period of the Human Circadian Timing System

PubMed Central

Scheer, Frank A.J.L.; Wright, Kenneth P.; Kronauer, Richard E.; Czeisler, Charles A.

2007-01-01

Human expeditions to Mars will require adaptation to the 24.65-h Martian solar day-night cycle (sol), which is outside the range of entrainment of the human circadian pacemaker under lighting intensities to which astronauts are typically exposed. Failure to entrain the circadian time-keeping system to the desired rest-activity cycle disturbs sleep and impairs cognitive function. Furthermore, differences between the intrinsic circadian period and Earth's 24-h light-dark cycle underlie human circadian rhythm sleep disorders, such as advanced sleep phase disorder and non-24-hour sleep-wake disorders. Therefore, first, we tested whether exposure to a model-based lighting regimen would entrain the human circadian pacemaker at a normal phase angle to the 24.65-h Martian sol and to the 23.5-h day length often required of astronauts during short duration space exploration. Second, we tested here whether such prior entrainment to non-24-h light-dark cycles would lead to subsequent modification of the intrinsic period of the human circadian timing system. Here we show that exposure to moderately bright light (∼450 lux; ∼1.2 W/m2) for the second or first half of the scheduled wake episode is effective for entraining individuals to the 24.65-h Martian sol and a 23.5-h day length, respectively. Estimations of the circadian periods of plasma melatonin, plasma cortisol, and core body temperature rhythms collected under forced desynchrony protocols revealed that the intrinsic circadian period of the human circadian pacemaker was significantly longer following entrainment to the Martian sol as compared to following entrainment to the 23.5-h day. The latter finding of after-effects of entrainment reveals for the first time plasticity of the period of the human circadian timing system. Both findings have important implications for the treatment of circadian rhythm sleep disorders and human space exploration. PMID:17684566

Atrophia maculosa varioliformis cutis.

PubMed

Kuflik, Julianne H; Schwartz, Robert A; Becker, Kenneth A; Lambert, W Clark

2005-10-01

Atrophia maculosa varioliformis cutis is a rare disease characterized by spontaneously formed facial scars in young adults. Its etiology is unknown; there may be an underlying defect of dermal elastin. We discuss a patient with this unusual disorder and review its literature.

Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

PubMed

Prabhakaran, Panchami; Kale, Sangram S; Puranik, Vedavati G; Rajamohanan, P R; Chetina, Olga; Howard, Judith A K; Hofmann, Hans-Jörg; Sanjayan, Gangadhar J

2008-12-31

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.

Importance and challenges of measuring intrinsic foot muscle strength

PubMed Central

2012-01-01

Background Intrinsic foot muscle weakness has been implicated in a range of foot deformities and disorders. However, to establish a relationship between intrinsic muscle weakness and foot pathology, an objective measure of intrinsic muscle strength is needed. The aim of this review was to provide an overview of the anatomy and role of intrinsic foot muscles, implications of intrinsic weakness and evaluate the different methods used to measure intrinsic foot muscle strength. Method Literature was sourced from database searches of MEDLINE, PubMed, SCOPUS, Cochrane Library, PEDro and CINAHL up to June 2012. Results There is no widely accepted method of measuring intrinsic foot muscle strength. Methods to estimate toe flexor muscle strength include the paper grip test, plantar pressure, toe dynamometry, and the intrinsic positive test. Hand-held dynamometry has excellent interrater and intrarater reliability and limits toe curling, which is an action hypothesised to activate extrinsic toe flexor muscles. However, it is unclear whether any method can actually isolate intrinsic muscle strength. Also most methods measure only toe flexor strength and other actions such as toe extension and abduction have not been adequately assessed. Indirect methods to investigate intrinsic muscle structure and performance include CT, ultrasonography, MRI, EMG, and muscle biopsy. Indirect methods often discriminate between intrinsic and extrinsic muscles, but lack the ability to measure muscle force. Conclusions There are many challenges to accurately measure intrinsic muscle strength in isolation. Most studies have measured toe flexor strength as a surrogate measure of intrinsic muscle strength. Hand-held dynamometry appears to be a promising method of estimating intrinsic muscle strength. However, the contribution of extrinsic muscles cannot be excluded from toe flexor strength measurement. Future research should clarify the relative contribution of intrinsic and extrinsic muscles during intrinsic foot muscle strength testing. PMID:23181771

Protein domain definition should allow for conditional disorder

PubMed Central

Yegambaram, Kavestri; Bulloch, Esther MM; Kingston, Richard L

2013-01-01

Abstract: Proteins are often classified in a binary fashion as either structured or disordered. However this approach has several deficits. Firstly, protein folding is always conditional on the physiochemical environment. A protein which is structured in some circumstances will be disordered in others. Secondly, it hides a fundamental asymmetry in behavior. While all structured proteins can be unfolded through a change in environment, not all disordered proteins have the capacity for folding. Failure to accommodate these complexities confuses the definition of both protein structural domains and intrinsically disordered regions. We illustrate these points with an experimental study of a family of small binding domains, drawn from the RNA polymerase of mumps virus and its closest relatives. Assessed at face value the domains fall on a structural continuum, with folded, partially folded, and near unstructured members. Yet the disorder present in the family is conditional, and these closely related polypeptides can access the same folded state under appropriate conditions. Any heuristic definition of the protein domain emphasizing conformational stability divides this domain family in two, in a way that makes no biological sense. Structural domains would be better defined by their ability to adopt a specific tertiary structure: a structure that may or may not be realized, dependent on the circumstances. This explicitly allows for the conditional nature of protein folding, and more clearly demarcates structural domains from intrinsically disordered regions that may function without folding. PMID:23963781

Unusual developmental pattern of brain lateralization in young boys with autism spectrum disorder: Power analysis with child-sized magnetoencephalography.

PubMed

Hiraishi, Hirotoshi; Kikuchi, Mitsuru; Yoshimura, Yuko; Kitagawa, Sachiko; Hasegawa, Chiaki; Munesue, Toshio; Takesaki, Natsumi; Ono, Yasuki; Takahashi, Tsutomu; Suzuki, Michio; Higashida, Haruhiro; Asada, Minoru; Minabe, Yoshio

2015-03-01

Autism spectrum disorder (ASD) is often described as comprising an unusual brain growth pattern and aberrant brain lateralization. Although it is important to study the pathophysiology of the developing ASD cortex, examples of physiological brain lateralization in young children with ASD have yet to be well examined. Thirty-eight boys with ASD (aged 3-7 years) and 38 typically developing (TD) boys (aged 3-8 years) concentrated on video programs and their brain activities were measured non-invasively. We employed a customized child-sized magnetoencephalography system in which the sensors were located as close to the brain as possible for optimal recording in young children. To produce a credible laterality index of the brain oscillations, we defined two clusters of sensors corresponding to the right and left hemispheres. We focused on the laterality index ([left - right]/[left+right]) of the relative power band in seven frequency bands. The TD group displayed significantly rightward lateralized brain oscillations in the theta-1 frequency bands compared to the ASD group. This is the first study to demonstrate unusual brain lateralization of brain oscillations measured by magnetoencephalography in young children with ASD. © 2014 The Authors. Psychiatry and Clinical Neurosciences © 2014 Japanese Society of Psychiatry and Neurology.

Supporting Students with Emotional and Behavioral Disorders' Comprehension and Reading Fluency

ERIC Educational Resources Information Center

Garwood, Justin D.; Ciullo, Stephen; Brunsting, Nelson

2017-01-01

This article discusses two strategies to improve reading outcomes for middle and high school adolescents with emotional and behavioral disorders (EBD). The first is providing secondary students a choice of accessible, engaging activities to more actively engage them during reading instruction and foster intrinsic motivation to engage in literacy…

Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Callaway, David J. E.; Matsui, Tsutomu; Weiss, Thomas

The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The “tip of the whip” that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the bindingmore » of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. Furthermore NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.« less

Intrinsic disorder in the partitioning protein KorB persists after co-operative complex formation with operator DNA and KorA.

PubMed

Hyde, Eva I; Callow, Philip; Rajasekar, Karthik V; Timmins, Peter; Patel, Trushar R; Siligardi, Giuliano; Hussain, Rohanah; White, Scott A; Thomas, Christopher M; Scott, David J

2017-08-30

The ParB protein, KorB, from the RK2 plasmid is required for DNA partitioning and transcriptional repression. It acts co-operatively with other proteins, including the repressor KorA. Like many multifunctional proteins, KorB contains regions of intrinsically disordered structure, existing in a large ensemble of interconverting conformations. Using NMR spectroscopy, circular dichroism and small-angle neutron scattering, we studied KorB selectively within its binary complexes with KorA and DNA, and within the ternary KorA/KorB/DNA complex. The bound KorB protein remains disordered with a mobile C-terminal domain and no changes in the secondary structure, but increases in the radius of gyration on complex formation. Comparison of wild-type KorB with an N-terminal deletion mutant allows a model of the ensemble average distances between the domains when bound to DNA. We propose that the positive co-operativity between KorB, KorA and DNA results from conformational restriction of KorB on binding each partner, while maintaining disorder. © 2017 The Author(s).

Unique Challenges for Modeling Defect Dynamics in Concentrated Solid-Solution Alloys

NASA Astrophysics Data System (ADS)

Zhao, Shijun; Weber, William J.; Zhang, Yanwen

2017-11-01

Recently developed concentrated solid solution alloys (CSAs) are shown to have improved performance under irradiation that depends strongly on the number of alloying elements, alloying species, and their concentrations. In contrast to conventional dilute alloys, CSAs are composed of multiple principal elements situated randomly in a simple crystalline lattice. As a result, the intrinsic disorder has a profound influence on energy dissipation pathways and defect evolution when these CSAs are subjected to energetic particle irradiation. Extraordinary irradiation resistance, including suppression of void formation by two orders of magnitude at an elevated temperature, has been achieved with increasing compositional complexity in CSAs. Unfortunately, the loss of translational invariance associated with the intrinsic chemical disorder poses great challenges to theoretical modeling at the electronic and atomic levels. Based on recent computer simulation results for a set of novel Ni-containing, face-centered cubic CSAs, we review theoretical modeling progress in handling disorder in CSAs and underscore the impact of disorder on defect dynamics. We emphasize in particular the unique challenges associated with the description of defect dynamics in CSAs.

Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics

DOE PAGES

Callaway, David J. E.; Matsui, Tsutomu; Weiss, Thomas; ...

2017-03-08

The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The “tip of the whip” that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the bindingmore » of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. Furthermore NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.« less

Intrinsic disorder in spondins and some of their interacting partners

PubMed Central

Alowolodu, Oluwole; Johnson, Gbemisola; Addou, Iqbal; Zhdanova, Irina V.; Uversky, Vladimir N.

2016-01-01

ABSTRACT Spondins, which are proteins that inhibit and promote adherence of embryonic cells so as to aid axonal growth are part of the thrombospondin-1 family. Spondins function in several important biological processes, such as apoptosis, angiogenesis, etc. Spondins constitute a thrombospondin subfamily that includes F-spondin, a protein that interacts with Aβ precursor protein and inhibits its proteolytic processing; R-spondin, a 4-membered group of proteins that regulates Wnt pathway and have other functions, such as regulation of kidney proliferation, induction of epithelial proliferation, the tumor suppressant action; M-spondin that mediates mechanical linkage between the muscles and apodemes; and the SCO-spondin, a protein important for neuronal development. In this study, we investigated intrinsic disorder status of human spondins and their interacting partners, such as members of the LRP family, LGR family, Frizzled family, and several other binding partners in order to establish the existence and importance of disordered regions in spondins and their interacting partners by conducting a detailed analysis of their sequences, finding disordered regions, and establishing a correlation between their structure and biological functions. PMID:28232900

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

PubMed Central

Olson, Mark A.

2017-01-01

Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution. PMID:28197405

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome.

PubMed

Olson, Mark A

2017-01-01

Intrinsically disordered proteins that populate the so-called "Dark Proteome" offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution.

No Association between Cortical Gyrification or Intrinsic Curvature and Attention-deficit/Hyperactivity Disorder in Adolescents and Young Adults.

PubMed

Forde, Natalie J; Ronan, Lisa; Zwiers, Marcel P; Alexander-Bloch, Aaron F; Faraone, Stephen V; Oosterlaan, Jaap; Heslenfeld, Dirk J; Hartman, Catharina A; Buitelaar, Jan K; Hoekstra, Pieter J

2017-01-01

Magnetic resonance imaging (MRI) studies have highlighted subcortical, cortical, and structural connectivity abnormalities associated with attention-deficit/hyperactivity disorder (ADHD). Gyrification investigations of the cortex have been inconsistent and largely negative, potentially due to a lack of sensitivity of the previously used morphological parameters. The innovative approach of applying intrinsic curvature analysis, which is predictive of gyrification pattern, to the cortical surface applied herein allowed us greater sensitivity to determine whether the structural connectivity abnormalities thus far identified at a centimeter scale also occur at a millimeter scale within the cortical surface. This could help identify neurodevelopmental processes that contribute to ADHD. Structural MRI datasets from the NeuroIMAGE project were used [ n = 306 ADHD, n = 164 controls, and n = 148 healthy siblings of individuals with ADHD (age in years, mean(sd); 17.2 (3.4), 16.8 (3.2), and 17.7 (3.8), respectively)]. Reconstructions of the cortical surfaces were computed with FreeSurfer. Intrinsic curvature (taken as a marker of millimeter-scale surface connectivity) and local gyrification index were calculated for each point on the surface (vertex) with Caret and FreeSurfer, respectively. Intrinsic curvature skew and mean local gyrification index were extracted per region; frontal, parietal, temporal, occipital, cingulate, and insula. A generalized additive model was used to compare the trajectory of these measures between groups over age, with sex, scanner site, total surface area of hemisphere, and familiality accounted for. After correcting for sex, scanner site, and total surface area no group differences were found in the developmental trajectory of intrinsic curvature or local gyrification index. Despite the increased sensitivity of intrinsic curvature, compared to gyrification measures, to subtle morphological abnormalities of the cortical surface we found no milimeter-scale connectivity abnormalities associated with ADHD.

Intrinsic brain connectivity predicts impulse control disorders in patients with Parkinson's disease.

PubMed

Tessitore, Alessandro; De Micco, Rosa; Giordano, Alfonso; di Nardo, Federica; Caiazzo, Giuseppina; Siciliano, Mattia; De Stefano, Manuela; Russo, Antonio; Esposito, Fabrizio; Tedeschi, Gioacchino

2017-12-01

Impulse control disorders can be triggered by dopamine replacement therapies in patients with PD. Using resting-state functional MRI, we investigated the intrinsic brain network connectivity at baseline in a cohort of drug-naive PD patients who successively developed impulse control disorders over a 36-month follow-up period compared with patients who did not. Baseline 3-Tesla MRI images of 30 drug-naive PD patients and 20 matched healthy controls were analyzed. The impulse control disorders' presence and severity at follow-up were assessed by the Questionnaire for Impulsive-Compulsive Disorders in Parkinson's Disease Rating Scale. Single-subject and group-level independent component analysis was used to investigate functional connectivity differences within the major resting-state networks. We also compared internetwork connectivity between patients. Finally, a multivariate Cox regression model was used to investigate baseline predictors of impulse control disorder development. At baseline, decreased connectivity in the default-mode and right central executive networks and increased connectivity in the salience network were detected in PD patients with impulse control disorders at follow-up compared with those without. Increased default-mode/central executive internetwork connectivity was significantly associated with impulse control disorders development (P < 0.05). Our findings demonstrated that abnormal brain connectivity in the three large-scale networks characterizes drug-naive PD patients who will eventually develop impulse control disorders while on dopaminergic treatment. We hypothesize that these divergent cognitive and limbic network connectivity changes could represent a potential biomarker and an additional risk factor for the emergence of impulse control disorders. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

The clavicle: Normal and abnormal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, R.; Madewell, J.E.; Swischuk, L.E.

1989-07-01

The clavicle is an unusual long bone with many unique embryologic features. It is often involved in congenital and acquired disorders. Traumatic, inflammatory, neoplastic, metabolic and many other miscellaneous lesions may also affect the bone. Because of its ligamentous attachments and the presence of articulations at both ends, the clavicle can also be involved in arthritic diseases. This article illustrates the radiographic manifestations of many of the disorders of the clavicle that are commonly encountered in clinical practice.

Deciphering the mechanisms of binding induced folding at nearly atomic resolution: The Φ value analysis applied to IDPs.

PubMed

Gianni, Stefano; Dogan, Jakob; Jemth, Per

2014-01-01

The Φ value analysis is a method to analyze the structure of metastable states in reaction pathways. Such a methodology is based on the quantitative analysis of the effect of point mutations on the kinetics and thermodynamics of the probed reaction. The Φ value analysis is routinely used in protein folding studies and is potentially an extremely powerful tool to analyze the mechanism of binding induced folding of intrinsically disordered proteins. In this review we recapitulate the key equations and experimental advices to perform the Φ value analysis in the perspective of the possible caveats arising in intrinsically disordered systems. Finally, we briefly discuss some few examples already available in the literature.

In-cell NMR of intrinsically disordered proteins in prokaryotic cells.

PubMed

Ito, Yutaka; Mikawa, Tsutomu; Smith, Brian O

2012-01-01

In-cell NMR, i.e., the acquisition of heteronuclear multidimensional NMR of biomacromolecules inside living cells, is, to our knowledge, the only method for investigating the three-dimensional structure and dynamics of proteins at atomic detail in the intracellular environment. Since the inception of the method, intrinsically disordered proteins have been regarded as particular targets for in-cell NMR, due to their expected sensitivity to the molecular crowding in the intracellular environment. While both prokaryotic and eukaryotic cells can be used as host cells for in-cell NMR, prokaryotic in-cell NMR, particularly employing commonly used protein overexpression systems in Escherichia coli cells, is the most accessible approach. In this chapter we describe general procedures for obtaining in-cell NMR spectra in E. coli cells.

Mutations in actin used for structural studies partially disrupt β-thymosin/WH2 domains interaction.

PubMed

Deville, Célia; Girard-Blanc, Christine; Assrir, Nadine; Nhiri, Naïma; Jacquet, Eric; Bontems, François; Renault, Louis; Petres, Stéphane; van Heijenoort, Carine

2016-10-01

Understanding the structural basis of actin cytoskeleton remodeling requires stabilization of actin monomers, oligomers, and filaments in complex with partner proteins, using various biochemical strategies. Here, we report a dramatic destabilization of the dynamic interaction with a model β-thymosin/WH2 domain induced by mutations in actin. This result underlines that mutant actins should be used with prudence to characterize interactions with intrinsically disordered partners as destabilization of dynamic interactions, although identifiable by NMR, may be invisible to other structural techniques. It also highlights how both β-thymosin/WH2 domains and actin tune local structure and dynamics in regulatory processes involving intrinsically disordered domains. © 2016 Federation of European Biochemical Societies.

Anomalous uptake and circulatory characteristics of the plant-based small RNA MIR2911.

PubMed

Yang, Jian; Hotz, Tremearne; Broadnax, LaCassidy; Yarmarkovich, Mark; Elbaz-Younes, Ismail; Hirschi, Kendal D

2016-06-02

Inconsistent detection of plant-based dietary small RNAs in circulation has thwarted the use of dietary RNA therapeutics. Here we demonstrate mice consuming diets rich in vegetables displayed enhanced serum levels of the plant specific small RNA MIR2911. Differential centrifugation, size-exclusion chromatography, and proteinase K treatment of plant extracts suggest this RNA resides within a proteinase K-sensitive complex. Plant derived MIR2911 was more bioavailable than the synthetic RNA. Furthermore, MIR2911 exhibited unusual digestive stability compared with other synthetic plant microRNAs. The characteristics of circulating MIR2911 were also unusual as it was not associated with exosomes and fractionated as a soluble complex that was insensitive to proteinase K treatment, consistent with MIR2911 being stabilized by modifications conferred by the host. These results indicate that intrinsic stability and plant-based modifications orchestrate consumer uptake of this anomalous plant based small RNA and invite revisiting plant-based microRNA therapeutic approaches.

Anomalous uptake and circulatory characteristics of the plant-based small RNA MIR2911

PubMed Central

Yang, Jian; Hotz, Tremearne; Broadnax, LaCassidy; Yarmarkovich, Mark; Elbaz-Younes, Ismail; Hirschi, Kendal D.

2016-01-01

Inconsistent detection of plant-based dietary small RNAs in circulation has thwarted the use of dietary RNA therapeutics. Here we demonstrate mice consuming diets rich in vegetables displayed enhanced serum levels of the plant specific small RNA MIR2911. Differential centrifugation, size-exclusion chromatography, and proteinase K treatment of plant extracts suggest this RNA resides within a proteinase K-sensitive complex. Plant derived MIR2911 was more bioavailable than the synthetic RNA. Furthermore, MIR2911 exhibited unusual digestive stability compared with other synthetic plant microRNAs. The characteristics of circulating MIR2911 were also unusual as it was not associated with exosomes and fractionated as a soluble complex that was insensitive to proteinase K treatment, consistent with MIR2911 being stabilized by modifications conferred by the host. These results indicate that intrinsic stability and plant-based modifications orchestrate consumer uptake of this anomalous plant based small RNA and invite revisiting plant-based microRNA therapeutic approaches. PMID:27251858

Topological and behavioral disorder in collective motion

NASA Astrophysics Data System (ADS)

Quint, David

2014-03-01

A major underlying assumption in many studies on the collective motion of self-propelled agents has been that the environment is continuous, isotropic and ordered and agents are all identical. In the natural world there are many examples of disordered environments or heterogeneous swarms where collective motion can exist. Examples include bats that navigate natural caverns via echolocation, schools of fish that maneuver through dark and light areas, microbial colonies that move about in heterogeneous soil, quorum sensing bacteria, crowds of people that are evacuating a building and traffic flow in major cities. In general disorder can arise from two basic sources that inhibit/augment both movement and information flow, those that represent physical obstacles (i.e topological), (extrinsic), and those that arise from behavioral heterogeneties within the swarm itself (intrinsic). In either case, extrinsic or intrinsic, disorder can be quenched or dynamic in space or time or both. To understand the effect of the various forms of disorder that can be present in the environment of the agents, we study both discrete and continuous 2 d agent based models that utilize only local interactions and study the transition to the collectively moving state as a function of the amount of disorder or behavioral heterogeneities present in the environment. I will present our recent results and discuss the effect that disorder has on collective motion and the general physical mechanisms that swarms, either real or artificial, could utilize in order to overcome disorder in their environment.

The Young Offender.

ERIC Educational Resources Information Center

MacLeod, Hinson

1979-01-01

Looks at delinquency from the viewpoint of a training school chaplain and outlines factors believed to contribute to the development of delinquent behavior. Signs of maladjustment include overactivity, acute anxiety and fear, depression, psychosomatic disorders, unusual behavior, negative attitudes toward others and themselves, and resistance to…

Genetic and Diagnostic Biomarker Development in ASD Toddlers Using Resting State Functional MRI

DTIC Science & Technology

2016-09-01

networks during resting states. Autism spectrum disorder (ASD) begins prenatal, and early maldevelopment is present in many sites and systems that mediate...molecular and genomic evidence indicates autism spectrum disorder (ASD) begins prenatally, most likely by or before the late second trimester 10-15 as...ages 3 to 4 years. 2. KEYWORDS Autism spectrum disorder, ASD, early brain development, intrinsic functional brain networks, fMRI, infants, toddlers

Comprehensive dental management in a Hallermann-Streiff syndrome patient with unusual radiographic appearance of teeth.

PubMed

Gungor, O Erken; Nur, B Guzel; Yalcin, H; Karayilmaz, H; Mihci, E

2015-01-01

Hallermann-Streiff syndrome (HSS) is a genetic disorder characterized by proportionate dwarfism, birdlike facies, hypotrichosis, skin atrophy, dyscephaly, bilateral microphthalmia, congenital cataracts, a narrow, weak, beaked nose, a hypoplastic mandible, and orodental anomalies. Occurrence is sporadic and distinct patterns of inheritance have not been found. This case report describes the dental management of a 3-year-old girl patient with HSS, who had unusual radiographic appearance of teeth. Furthermore, dental treatments and a 30-month follow-up period of the patient with this rare tooth structure malformation have been presented.

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

PubMed Central

Wang, Yong; Chu, Xiakun; Longhi, Sonia; Roche, Philippe; Han, Wei; Wang, Erkang; Wang, Jin

2013-01-01

Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding–binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between “downhill folding,” “molten globule,” and “intrinsic disorder” in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a “kinetic divide-and-conquer” strategy that confers them high specificity without high affinity. PMID:24043820

Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions.

PubMed

Ganguly, Debabani; Chen, Jianhan

2011-04-01

Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. Copyright © 2011 Wiley-Liss, Inc.

The intrinsically disordered C-terminal region of Arabidopsis thaliana TCP8 transcription factor acts both as a transactivation and self-assembly domain.

PubMed

Valsecchi, Isabel; Guittard-Crilat, Emilie; Maldiney, Régis; Habricot, Yvette; Lignon, Sabrina; Lebrun, Régine; Miginiac, Emile; Ruelland, Eric; Jeannette, Emmanuelle; Lebreton, Sandrine

2013-09-01

TCPs are plant specific transcription factors with non-canonical basic helix-loop-helix domains. While Arabidopsis thaliana has 24 TCPs involved in cell proliferation and differentiation, their mode of action has not been fully elucidated. Using bioinformatic tools, we demonstrate that TCP transcription factors belong to the intrinsically disordered proteins (IDP) family and that disorder is higher in class I TCPs than in class II TCPs. In particular, using bioinformatic and biochemical approaches, we have characterized TCP8, a class I TCP. TCP8 exhibits three intrinsically disordered regions (IDR) made of more than 50 consecutive residues, in which phosphorylable Ser residues are mainly clustered. Phosphorylation of Ser-211 that belongs to the central IDR was confirmed by mass spectrometry. Yeast two-hybrid assays also showed that the C-terminal IDR corresponds to a transactivation domain. Moreover, biochemical experiments demonstrated that TCP8 tends to oligomerize in dimers, trimers and higher-order multimers. Bimolecular fluorescence complementation (BiFC) experiments carried out on a truncated form of TCP8 lacking the C-terminal IDR indicated that it is effectively required for the pronounced self-assembly of TCP8. These data were reinforced by the prediction of a coiled coil domain in this IDR. The C-terminal IDR acts thus as an oligomerization domain and also a transactivation domain. Moreover, many Molecular Recognition Features (MoRFs) were predicted, indicating that TCP8 could interact with several partners to fulfill a fine regulation of transcription in response to various stimuli.

Urea Dependent (15)N NMR-Relaxation Studies on PfP2 Multimers Reveal that the C-Terminal Behaves like an Independent Intrinsically Disordered Peptide.

PubMed

Mishra, Pushpa; Hosur, Ramakrishna V

2015-01-01

Intrinsically disordered proteins or such domains in globular proteins are believed to be playing important roles in protein functions by virtue of their ability to adapt themselves to requirements of different binding partners and thereby accord high specificity to the interaction. Eukaryotic ribosomal stalk is made up of a supramolecular assembly of P0, P1 and P2 proteins. In Plasmodium falciparum, homo-oligomers of P2 are also seen which seem to be involved in many non-ribosomal functions of the protein in the parasite, and in all of these the protein interacts with different interactors. Here we show by extensive (15)N NMR relaxation studies that the C-terminal stretch of about 45 residues of the protein always remains as a flexible disordered domain, regardless of the state of association of the protein. The relaxation behaviors and the derived rotational correlation times for this portion of the protein are essentially the same in the presence of different concentrations of urea which produce different mixtures of PfP2 oligomers in rapid exchange, whereas the rest of the protein shows substantial variations with urea concentration in the relaxation behaviors. In other words, the C-terminal domain behaves as if it were an independent intrinsically disordered peptide. This would augment the notion that the C-terminal domain of PfP2 would be acting as a scavenger for different interactors depending upon the different functions of the protein inside the parasite.

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins.

PubMed

Perez, Romel B; Tischer, Alexander; Auton, Matthew; Whitten, Steven T

2014-12-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs. © 2014 Wiley Periodicals, Inc.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape.

PubMed

Ferreon, Allan Chris M; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A

2012-10-30

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson's disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 21 [urea][TMAO] ratio has a net neutral effect on the protein's dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

PubMed Central

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson’s disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 2∶1 [urea]∶[TMAO] ratio has a net neutral effect on the protein’s dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments. PMID:22826265

Hair Breakage in Patients of African Descent: Role of Dermoscopy

PubMed Central

Quaresma, Maria Victória; Martinez Velasco, María Abril; Tosti, Antonella

2015-01-01

Dermoscopy represents a useful technique for the diagnosis and follow-up of hair and scalp disorders. To date, little has been published regarding dermoscopy findings of hair disorders in patients of African descent. This article illustrates how dermoscopy allows fast diagnosis of hair breakage due to intrinsic factors and chemical damage in African descent patients. PMID:27170942

Munchausen's Syndrome and Other Factitious Disorders in Children

PubMed Central

Jaghab, Kamil; Skodnek, Kenneth B.

2006-01-01

There has been increasing recognition in the pediatric literature for the past 20 years that illness falsification by caregivers must be included in the differential diagnosis of children presenting with persistent, unexplained symptoms or laboratory findings. However, there is considerably less awareness that pediatric symptoms can also be intentionally falsified by child and adolescent patients, and this unique group has remained virtually invisible. There have been reports that many children with factitious disorders also suffer from other mental disorders, particularly personality disorders. We report an unusual case of Munchausen's syndrome in a 15-year-old patient with sickle cell disease. We also review other reported pediatric factitious disorders in literature. Our purpose is to make clinicians aware of this less known disorder in children and to discuss the similarities and differences these disorders have in children compared to adults with the same disorders. PMID:21103164

Two interesting cases highlighting an oblivious specialty of psychoneuroendocrinology.

PubMed

Hari Kumar, K V S; Dhull, Pawan; Somasekharan, Manoj; Seshadri, K

2012-01-01

Psychoneuroendocrinology deals with the overlap disorders pertaining to three different specialties. Awareness about the somatic manifestations of psychiatric diseases and vice versa is a must for all the clinicians. The knowledge of this interlinked specialty is essential because of the obscure presentation of certain disorders. Our first case was treated as depressive disorder, whereas the diagnosis was hypogonadism with empty sella. Our second patient was managed as schizophrenia and the evaluation revealed bilateral basal ganglia calcification and a diagnosis of Fahr's disease. We report these cases for their unusual presentation and to highlight the importance of this emerging specialty.

Translational animal models of autism and neurodevelopmental disorders.

PubMed

Crawley, Jacqueline N

2012-09-01

Autism is a neurodevelopmental disorder whose diagnosis is based on three behavioral criteria: unusual reciprocal social interactions, deficits in communication, and stereotyped repetitive behaviors with restricted interests. A large number of de novo single gene mutations and chromosomal deletions are associated with autism spectrum disorders. Based on the strong genetic evidence, mice with targeted mutations in homologous genes have been generated as translational research tools. Mouse models of autism have revealed behavioral and biological outcomes of mutations in risk genes. The field is now poised to employ the most robust phenotypes in the most replicable mouse models for preclinical screening of novel therapeutics.

Paroxysmal myoclonic dystonia with vocalisations: new entity or variant of preexisting syndromes?

PubMed Central

Feinberg, T E; Shapiro, A K; Shapiro, E

1986-01-01

From among 1377 patients with movement disorders, four patients had an unusual movement disorder characterised by paroxysmal bursts of involuntary, regular, repetitive, rhythmic, bilateral, coordinated, simultaneous, stereotypic myoclonus and vocalisations, often associated with tonic symptoms, interference with voluntary functioning, presence of hyperactivity, attention and learning disabilities, and resistance to treatment with haloperidol and other drugs. This symptom complex may represent a new disease entity, referred to here as paroxysmal myoclonic dystonia with vocalisations or a variant or combination of other movement disorders such as Gilles de la Tourette, myoclonic, or dystonic syndromes. PMID:3457101

Unusual Enhancement in Intrinsic Thermal Conductivity of Multilayer Graphene by Tensile Strains

DOE PAGES

Kuang, Youdi; Lindsay, Lucas R.; Huang, Baoling

2015-01-01

High basal plane thermal conductivity k of multi-layer graphene makes it promising for thermal management applications. Here we examine the effects of tensile strain on thermal transport in this system. Using a first principles Boltzmann-Peierls equation for phonon transport approach, we calculate the room-temperature in-plane lattice k of multi-layer graphene (up to four layers) and graphite under different isotropic tensile strains. The calculated in-plane k of graphite, finite mono-layer graphene and 3-layer graphene agree well with previous experiments. The dimensional transitions of the intrinsic k and the extent of the diffusive transport regime from mono-layer graphene to graphite are presented.more » We find a peak enhancement of intrinsic k for multi-layer graphene and graphite with increasing strain and the largest enhancement amplitude is about 40%. In contrast the calculated intrinsic k with tensile strain decreases for diamond and diverges for graphene, we show that the competition between the decreased mode heat capacities and the increased lifetimes of flexural phonons with increasing strain contribute to this k behavior. Similar k behavior is observed for 2-layer hexagonal boron nitride systems, suggesting that it is an inherent thermal transport property in multi-layer systems assembled of purely two dimensional atomic layers. This study provides insights into engineering k of multi-layer graphene and boron nitride by strain and into the nature of thermal transport in quasi-two-dimensional and highly anisotropic systems.« less

When Disorder Looks Like Order: A New Model to Explain Radial Magnetic Fields in Young Supernova Remnants

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, J. L.; Gaensler, B. M.; Jaffe, T.

Radial magnetic fields are observed in all known young, shell-type supernova remnants in our Galaxy, including Cas A, Tycho, Kepler, and SN1006, and yet the nature of these radial fields has not been thoroughly explored. Using a 3D model, we consider the existence and observational implications of an intrinsically radial field. We also present a new explanation of the origin of the radial pattern observed from polarization data as resulting from a selection effect due to the distribution of cosmic-ray electrons (CREs). We show that quasi-parallel acceleration can concentrate CREs at regions where the magnetic field is radial, making amore » completely turbulent field appear ordered, when it is in fact disordered. We discuss observational properties that may help distinguish between an intrinsically radial magnetic field and the case where it only appears radial due to the CRE distribution. We also show that the case of an intrinsically radial field with a quasi-perpendicular CRE acceleration mechanism has intriguing similarities to the observed polarization properties of SN1006.« less

Thermal conductivity of graphene and graphite: collective excitations and mean free paths.

PubMed

Fugallo, Giorgia; Cepellotti, Andrea; Paulatto, Lorenzo; Lazzeri, Michele; Marzari, Nicola; Mauri, Francesco

2014-11-12

We characterize the thermal conductivity of graphite, monolayer graphene, graphane, fluorographane, and bilayer graphene, solving exactly the Boltzmann transport equation for phonons, with phonon-phonon collision rates obtained from density functional perturbation theory. For graphite, the results are found to be in excellent agreement with experiments; notably, the thermal conductivity is 1 order of magnitude larger than what found by solving the Boltzmann equation in the single mode approximation, commonly used to describe heat transport. For graphene, we point out that a meaningful value of intrinsic thermal conductivity at room temperature can be obtained only for sample sizes of the order of 1 mm, something not considered previously. This unusual requirement is because collective phonon excitations, and not single phonons, are the main heat carriers in these materials; these excitations are characterized by mean free paths of the order of hundreds of micrometers. As a result, even Fourier's law becomes questionable in typical sample sizes, because its statistical nature makes it applicable only in the thermodynamic limit to systems larger than a few mean free paths. Finally, we discuss the effects of isotopic disorder, strain, and chemical functionalization on thermal performance. Only chemical functionalization is found to play an important role, decreasing the conductivity by a factor of 2 in hydrogenated graphene, and by 1 order of magnitude in fluorogenated graphene.

Intrinsically disordered and pliable Starmaker-like protein from medaka (Oryzias latipes) controls the formation of calcium carbonate crystals.

PubMed

Różycka, Mirosława; Wojtas, Magdalena; Jakób, Michał; Stigloher, Christian; Grzeszkowiak, Mikołaj; Mazur, Maciej; Ożyhar, Andrzej

2014-01-01

Fish otoliths, biominerals composed of calcium carbonate with a small amount of organic matrix, are involved in the functioning of the inner ear. Starmaker (Stm) from zebrafish (Danio rerio) was the first protein found to be capable of controlling the formation of otoliths. Recently, a gene was identified encoding the Starmaker-like (Stm-l) protein from medaka (Oryzias latipes), a putative homologue of Stm and human dentine sialophosphoprotein. Although there is no sequence similarity between Stm-l and Stm, Stm-l was suggested to be involved in the biomineralization of otoliths, as had been observed for Stm even before. The molecular properties and functioning of Stm-l as a putative regulatory protein in otolith formation have not been characterized yet. A comprehensive biochemical and biophysical analysis of recombinant Stm-l, along with in silico examinations, indicated that Stm-l exhibits properties of a coil-like intrinsically disordered protein. Stm-l possesses an elongated and pliable structure that is able to adopt a more ordered and rigid conformation under the influence of different factors. An in vitro assay of the biomineralization activity of Stm-l indicated that Stm-l affected the size, shape and number of calcium carbonate crystals. The functional significance of intrinsically disordered properties of Stm-l and the possible role of this protein in controlling the formation of calcium carbonate crystals is discussed.

Intrinsically Disordered and Pliable Starmaker-Like Protein from Medaka (Oryzias latipes) Controls the Formation of Calcium Carbonate Crystals

PubMed Central

Różycka, Mirosława; Wojtas, Magdalena; Jakób, Michał; Stigloher, Christian; Grzeszkowiak, Mikołaj; Mazur, Maciej; Ożyhar, Andrzej

2014-01-01

Fish otoliths, biominerals composed of calcium carbonate with a small amount of organic matrix, are involved in the functioning of the inner ear. Starmaker (Stm) from zebrafish (Danio rerio) was the first protein found to be capable of controlling the formation of otoliths. Recently, a gene was identified encoding the Starmaker-like (Stm-l) protein from medaka (Oryzias latipes), a putative homologue of Stm and human dentine sialophosphoprotein. Although there is no sequence similarity between Stm-l and Stm, Stm-l was suggested to be involved in the biomineralization of otoliths, as had been observed for Stm even before. The molecular properties and functioning of Stm-l as a putative regulatory protein in otolith formation have not been characterized yet. A comprehensive biochemical and biophysical analysis of recombinant Stm-l, along with in silico examinations, indicated that Stm-l exhibits properties of a coil-like intrinsically disordered protein. Stm-l possesses an elongated and pliable structure that is able to adopt a more ordered and rigid conformation under the influence of different factors. An in vitro assay of the biomineralization activity of Stm-l indicated that Stm-l affected the size, shape and number of calcium carbonate crystals. The functional significance of intrinsically disordered properties of Stm-l and the possible role of this protein in controlling the formation of calcium carbonate crystals is discussed. PMID:25490041

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

NASA Astrophysics Data System (ADS)

Knott, Michael; Best, Robert B.

2014-05-01

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

Site-Specific Modulation of Charge Controls the Structure and Stimulus Responsiveness of Intrinsically Disordered Peptide Brushes.

PubMed

Bhagawati, Maniraj; Rubashkin, Matt G; Lee, Jessica P; Ananthanarayanan, Badriprasad; Weaver, Valerie M; Kumar, Sanjay

2016-06-14

Intrinsically disordered proteins (IDPs) are an important and emerging class of materials for tailoring biointerfaces. While the importance of chain charge and resultant electrostatic interactions in controlling conformational properties of IDPs is beginning to be explored through in silico approaches, there is a dearth of experimental studies motivated toward a systematic study of these effects. In an effort to explore this relationship, we measured the conformations of two peptides derived from the intrinsically disordered neurofilament (NF) side arm domain: one depicting the wild-type sequence with four lysine-serine-proline repeats (KSP peptide) and another in which the serine residues were replaced with aspartates (KDP peptide), a strategy sometimes used to mimic phosphorylation. Using a variety of biophysical measurements including a novel application of scanning angle interference microscopy, we demonstrate that the KDP peptide assumes comparatively more expanded conformations in solution and forms significantly thicker brushes when immobilized on planar surfaces at high densities. In both settings, the peptides respond to changes in ambient ionic strength, with each peptide showing distinct stimulus-responsive characteristics. While the KDP peptide undergoes compaction with increasing ionic strength as would be expected for a polyampholyte, the KSP peptide shows biphasic behavior, with an initial compaction followed by an expanded state at a higher ionic strength. Together these results support the notion that modulation of charge on IDPs can regulate conformational and interfacial properties.

Hydrophobicity diversity in globular and nonglobular proteins measured with the Gini index.

PubMed

Carugo, Oliviero

2017-12-01

Amino acids and their properties are variably distributed in proteins and different compositions determine all protein features, ranging from solubility to stability and functionality. Gini index, a tool to estimate distribution uniformity, is widely used in macroeconomics and has numerous statistical applications. Here, Gini index is used to analyze the distribution of hydrophobicity in proteins and to compare hydrophobicity distribution in globular and intrinsically disordered proteins. Based on the analysis of carefully selected high-quality data sets of proteins extracted from the Protein Data Bank (http://www.rcsb.org) and from the DisProt database (http://www.disprot.org/), it is observed that hydrophobicity is distributed in a more diverse way in intrinsically disordered proteins than in folded and soluble globular proteins. This correlates with the observation that the amino acid composition deviates from the uniformity (estimate with the Shannon and the Gini-Simpson indices) more in intrinsically disordered proteins than in globular and soluble proteins. Although statistical tools tike the Gini index have received little attention in molecular biology, these results show that they allow one to estimate sequence diversity and that they are useful to delineate trends that can hardly be described, otherwise, in simple and concise ways. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy

PubMed Central

Soranno, Andrea; Buchli, Brigitte; Nettels, Daniel; Cheng, Ryan R.; Müller-Späth, Sonja; Pfeil, Shawn H.; Hoffmann, Armin; Lipman, Everett A.; Makarov, Dmitrii E.; Schuler, Benjamin

2012-01-01

Internal friction, which reflects the “roughness” of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners. PMID:22492978

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.

PubMed

Soranno, Andrea; Buchli, Brigitte; Nettels, Daniel; Cheng, Ryan R; Müller-Späth, Sonja; Pfeil, Shawn H; Hoffmann, Armin; Lipman, Everett A; Makarov, Dmitrii E; Schuler, Benjamin

2012-10-30

Internal friction, which reflects the "roughness" of the energy landscape, plays an important role for proteins by modulating the dynamics of their folding and other conformational changes. However, the experimental quantification of internal friction and its contribution to folding dynamics has remained challenging. Here we use the combination of single-molecule Förster resonance energy transfer, nanosecond fluorescence correlation spectroscopy, and microfluidic mixing to determine the reconfiguration times of unfolded proteins and investigate the mechanisms of internal friction contributing to their dynamics. Using concepts from polymer dynamics, we determine internal friction with three complementary, largely independent, and consistent approaches as an additive contribution to the reconfiguration time of the unfolded state. We find that the magnitude of internal friction correlates with the compactness of the unfolded protein: its contribution dominates the reconfiguration time of approximately 100 ns of the compact unfolded state of a small cold shock protein under native conditions, but decreases for more expanded chains, and approaches zero both at high denaturant concentrations and in intrinsically disordered proteins that are expanded due to intramolecular charge repulsion. Our results suggest that internal friction in the unfolded state will be particularly relevant for the kinetics of proteins that fold in the microsecond range or faster. The low internal friction in expanded intrinsically disordered proteins may have implications for the dynamics of their interactions with cellular binding partners.

Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity

PubMed Central

Lai, Julian; Koh, Chuan Hock; Tjota, Monika; Pieuchot, Laurent; Raman, Vignesh; Chandrababu, Karthik Balakrishna; Yang, Daiwen; Wong, Limsoon; Jedd, Gregory

2012-01-01

Like animals and plants, multicellular fungi possess cell-to-cell channels (septal pores) that allow intercellular communication and transport. Here, using a combination of MS of Woronin body-associated proteins and a bioinformatics approach that identifies related proteins based on composition and character, we identify 17 septal pore-associated (SPA) proteins that localize to the septal pore in rings and pore-centered foci. SPA proteins are not homologous at the primary sequence level but share overall physical properties with intrinsically disordered proteins. Some SPA proteins form aggregates at the septal pore, and in vitro assembly assays suggest aggregation through a nonamyloidal mechanism involving mainly α-helical and disordered structures. SPA loss-of-function phenotypes include excessive septation, septal pore degeneration, and uncontrolled Woronin body activation. Together, our data identify the septal pore as a complex subcellular compartment and focal point for the assembly of unstructured proteins controlling diverse aspects of intercellular connectivity. PMID:22955885

Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation.

PubMed

Boothby, Thomas C; Tapia, Hugo; Brozena, Alexandra H; Piszkiewicz, Samantha; Smith, Austin E; Giovannini, Ilaria; Rebecchi, Lorena; Pielak, Gary J; Koshland, Doug; Goldstein, Bob

2017-03-16

Tardigrades are microscopic animals that survive a remarkable array of stresses, including desiccation. How tardigrades survive desiccation has remained a mystery for more than 250 years. Trehalose, a disaccharide essential for several organisms to survive drying, is detected at low levels or not at all in some tardigrade species, indicating that tardigrades possess potentially novel mechanisms for surviving desiccation. Here we show that tardigrade-specific intrinsically disordered proteins (TDPs) are essential for desiccation tolerance. TDP genes are constitutively expressed at high levels or induced during desiccation in multiple tardigrade species. TDPs are required for tardigrade desiccation tolerance, and these genes are sufficient to increase desiccation tolerance when expressed in heterologous systems. TDPs form non-crystalline amorphous solids (vitrify) upon desiccation, and this vitrified state mirrors their protective capabilities. Our study identifies TDPs as functional mediators of tardigrade desiccation tolerance, expanding our knowledge of the roles and diversity of disordered proteins involved in stress tolerance. Copyright © 2017 Elsevier Inc. All rights reserved.

An intrinsic vasopressin system in the olfactory bulb is involved in social recognition

PubMed Central

Tobin, Vicky A.; Hashimoto, Hirofumi; Wacker, Douglas W.; Takayanagi, Yuki; Langnaese, Kristina; Caquineau, Celine; Noack, Julia; Landgraf, Rainer; Onaka, Tatsushi; Leng, Gareth; Meddle, Simone L.; Engelmann, Mario; Ludwig, Mike

2010-01-01

Many peptides, when released as chemical messengers within the brain, have powerful influences on complex behaviours. Most strikingly, vasopressin and oxytocin, once thought of as circulating hormones whose actions were confined to peripheral organs, are now known to be released in the brain where they play fundamentally important roles in social behaviours1. In humans, disruptions of these peptide systems have been linked to several neurobehavioural disorders, including Prader-Willi syndrome, affective disorders, and obsessive-compulsive disorder, and polymorphisms of the vasopressin V1a receptor have been linked to autism2,3. Here we report that the rat olfactory bulb contains a large population of interneurones which express vasopressin, that blocking the actions of vasopressin in the olfactory bulb impairs the social recognition abilities of rats, and that vasopressin agonists and antagonists can modulate the processing of information by olfactory bulb neurones. The findings indicate that social information is processed in part by a vasopressin system intrinsic to the olfactory system. PMID:20182426

Wrecked regulation of intrinsically disordered proteins in diseases: pathogenicity of deregulated regulators

PubMed Central

Uversky, Vladimir N.

2014-01-01

Biologically active proteins without stable tertiary structure are common in all known proteomes. Functions of these intrinsically disordered proteins (IDPs) are typically related to regulation, signaling, and control. Cellular levels of these important regulators are tightly regulated by a variety mechanisms ranging from firmly controlled expression to precisely targeted degradation. Functions of IDPs are controlled by binding to specific partners, alternative splicing, and posttranslational modifications among other means. In the norm, right amounts of precisely activated IDPs have to be present in right time at right places. Wrecked regulation brings havoc to the ordered world of disordered proteins, leading to protein misfolding, misidentification, and missignaling that give rise to numerous human diseases, such as cancer, cardiovascular disease, neurodegenerative diseases, and diabetes. Among factors inducing pathogenic transformations of IDPs are various cellular mechanisms, such as chromosomal translocations, damaged splicing, altered expression, frustrated posttranslational modifications, aberrant proteolytic degradation, and defective trafficking. This review presents some of the aspects of deregulated regulation of IDPs leading to human diseases. PMID:25988147

Fibrillation mechanism of a model intrinsically disordered protein revealed by 2D correlation deep UV resonance Raman spectroscopy.

PubMed

Sikirzhytski, Vitali; Topilina, Natalya I; Takor, Gaius A; Higashiya, Seiichiro; Welch, John T; Uversky, Vladimir N; Lednev, Igor K

2012-05-14

Understanding of numerous biological functions of intrinsically disordered proteins (IDPs) is of significant interest to modern life science research. A large variety of serious debilitating diseases are associated with the malfunction of IDPs including neurodegenerative disorders and systemic amyloidosis. Here we report on the molecular mechanism of amyloid fibrillation of a model IDP (YE8) using 2D correlation deep UV resonance Raman spectroscopy. YE8 is a genetically engineered polypeptide, which is completely unordered at neutral pH yet exhibits all properties of a fibrillogenic protein at low pH. The very first step of the fibrillation process involves structural rearrangements of YE8 at the global structure level without the detectable appearance of secondary structural elements. The formation of β-sheet species follows the global structural changes and proceeds via the simultaneous formation of turns and β-strands. The kinetic mechanism revealed is an important new contribution to understanding of the general fibrillation mechanism proposed for IDP.

Pseudologia Fantastica in the Emergency Department: A Case Report and Review of the Literature

PubMed Central

Teslyar, Polina; Friedman, Rohn

2017-01-01

Psychiatrists commonly encounter deception in the emergency department. This article presents the case of a patient who presents to the emergency department with an unusual and elaborate web of deceptions along multiple themes including feigning medical illness, multiple losses, and grandiose academic and athletic achievements. We review the clinical characteristics of pseudologia fantastica and discuss how this patient's constellation of malingering, factitious disorder, and personality disorder suggests this diagnosis. PMID:28573061

The intrinsic disorder related alloy scattering in ZrNiSn half-Heusler thermoelectric materials

PubMed Central

Xie, Hanhui; Wang, Heng; Fu, Chenguang; Liu, Yintu; Snyder, G. Jeffrey; Zhao, Xinbing; Zhu, Tiejun

2014-01-01

The intrinsic structural disorder dramatically affects the thermal and electronic transport in semiconductors. Although normally considered an ordered compound, the half-Heusler ZrNiSn displays many transport characteristics of a disordered alloy. Similar to the (Zr,Hf)NiSn based solid solutions, the unsubstituted ZrNiSn compound also exhibits charge transport dominated by alloy scattering, as demonstrated in this work. The unexpected charge transport, even in ZrNiSn which is normally considered fully ordered, can be explained by the Ni partially filling interstitial sites in this half-Heusler system. The influence of the disordering and defects in crystal structure on the electron transport process has also been quantitatively analyzed in ZrNiSn1-xSbx with carrier concentration nH ranging from 5.0×1019 to 2.3×1021 cm−3 by changing Sb dopant content. The optimized carrier concentration nH ≈ 3–4×1020 cm−2 results in ZT ≈ 0.8 at 875K. This work suggests that MNiSn (M = Hf, Zr, Ti) and perhaps most other half-Heusler thermoelectric materials should be considered highly disordered especially when trying to understand the electronic and phonon structure and transport features. PMID:25363573

Structural Disorder within Henipavirus Nucleoprotein and Phosphoprotein: From Predictions to Experimental Assessment

PubMed Central

Darbon, Hervé; Longhi, Sonia

2010-01-01

Henipaviruses are newly emerged viruses within the Paramyxoviridae family. Their negative-strand RNA genome is packaged by the nucleoprotein (N) within α-helical nucleocapsid that recruits the polymerase complex made of the L protein and the phosphoprotein (P). To date structural data on Henipaviruses are scarce, and their N and P proteins have never been characterized so far. Using both computational and experimental approaches we herein show that Henipaviruses N and P proteins possess large intrinsically disordered regions. By combining several disorder prediction methods, we show that the N-terminal domain of P (PNT) and the C-terminal domain of N (NTAIL) are both mostly disordered, although they contain short order-prone segments. We then report the cloning, the bacterial expression, purification and characterization of Henipavirus PNT and NTAIL domains. By combining gel filtration, dynamic light scattering, circular dichroism and nuclear magnetic resonance, we show that both NTAIL and PNT belong to the premolten globule sub-family within the class of intrinsically disordered proteins. This study is the first reported experimental characterization of Henipavirus P and N proteins. The evidence that their respective N-terminal and C-terminal domains are highly disordered under native conditions is expected to be invaluable for future structural studies by helping to delineate N and P protein domains amenable to crystallization. In addition, following previous hints establishing a relationship between structural disorder and protein interactivity, the present results suggest that Henipavirus PNT and NTAIL domains could be involved in manifold protein-protein interactions. PMID:20657787

Field induced spontaneous quasiparticle decay and renormalization of quasiparticle dispersion in a quantum antiferromagnet

DOE PAGES

Hong, Tao; Qiu, Y.; Matsumoto, M.; ...

2017-05-05

The notion of a quasiparticle, such as a phonon, a roton or a magnon, is used in modern condensed matter physics to describe an elementary collective excitation. The intrinsic zero-temperature magnon damping in quantum spin systems can be driven by the interaction of the one-magnon states and multi-magnon continuum. However, detailed experimental studies on this quantum many-body effect induced by an applied magnetic field are rare. Here we present a high-resolution neutron scattering study in high fields on an S=1/2 antiferromagnet C 9H 18N 2CuBr 4. Finally, compared with the non-interacting linear spin–wave theory, our results demonstrate a variety ofmore » phenomena including field-induced renormalization of one-magnon dispersion, spontaneous magnon decay observed via intrinsic linewidth broadening, unusual non-Lorentzian two-peak structure in the excitation spectra and a dramatic shift of spectral weight from one-magnon state to the two-magnon continuum.« less

Field induced spontaneous quasiparticle decay and renormalization of quasiparticle dispersion in a quantum antiferromagnet

NASA Astrophysics Data System (ADS)

Hong, Tao; Qiu, Y.; Matsumoto, M.; Tennant, D. A.; Coester, K.; Schmidt, K. P.; Awwadi, F. F.; Turnbull, M. M.; Agrawal, H.; Chernyshev, A. L.

2017-05-01

The notion of a quasiparticle, such as a phonon, a roton or a magnon, is used in modern condensed matter physics to describe an elementary collective excitation. The intrinsic zero-temperature magnon damping in quantum spin systems can be driven by the interaction of the one-magnon states and multi-magnon continuum. However, detailed experimental studies on this quantum many-body effect induced by an applied magnetic field are rare. Here we present a high-resolution neutron scattering study in high fields on an S=1/2 antiferromagnet C9H18N2CuBr4. Compared with the non-interacting linear spin-wave theory, our results demonstrate a variety of phenomena including field-induced renormalization of one-magnon dispersion, spontaneous magnon decay observed via intrinsic linewidth broadening, unusual non-Lorentzian two-peak structure in the excitation spectra and a dramatic shift of spectral weight from one-magnon state to the two-magnon continuum.

Intrinsic ferromagnetism in hexagonal boron nitride nanosheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Si, M. S.; Gao, Daqiang, E-mail: gaodq@lzu.edu.cn, E-mail: xueds@lzu.edu.cn; Yang, Dezheng

2014-05-28

Understanding the mechanism of ferromagnetism in hexagonal boron nitride nanosheets, which possess only s and p electrons in comparison with normal ferromagnets based on localized d or f electrons, is a current challenge. In this work, we report an experimental finding that the ferromagnetic coupling is an intrinsic property of hexagonal boron nitride nanosheets, which has never been reported before. Moreover, we further confirm it from ab initio calculations. We show that the measured ferromagnetism should be attributed to the localized π states at edges, where the electron-electron interaction plays the role in this ferromagnetic ordering. More importantly, we demonstratemore » such edge-induced ferromagnetism causes a high Curie temperature well above room temperature. Our systematical work, including experimental measurements and theoretical confirmation, proves that such unusual room temperature ferromagnetism in hexagonal boron nitride nanosheets is edge-dependent, similar to widely reported graphene-based materials. It is believed that this work will open new perspectives for hexagonal boron nitride spintronic devices.« less

Field induced spontaneous quasiparticle decay and renormalization of quasiparticle dispersion in a quantum antiferromagnet

PubMed Central

Hong, Tao; Qiu, Y.; Matsumoto, M.; Tennant, D. A.; Coester, K.; Schmidt, K. P.; Awwadi, F. F.; Turnbull, M. M.; Agrawal, H.; Chernyshev, A. L.

2017-01-01

The notion of a quasiparticle, such as a phonon, a roton or a magnon, is used in modern condensed matter physics to describe an elementary collective excitation. The intrinsic zero-temperature magnon damping in quantum spin systems can be driven by the interaction of the one-magnon states and multi-magnon continuum. However, detailed experimental studies on this quantum many-body effect induced by an applied magnetic field are rare. Here we present a high-resolution neutron scattering study in high fields on an S=1/2 antiferromagnet C9H18N2CuBr4. Compared with the non-interacting linear spin–wave theory, our results demonstrate a variety of phenomena including field-induced renormalization of one-magnon dispersion, spontaneous magnon decay observed via intrinsic linewidth broadening, unusual non-Lorentzian two-peak structure in the excitation spectra and a dramatic shift of spectral weight from one-magnon state to the two-magnon continuum. PMID:28474679

Field induced spontaneous quasiparticle decay and renormalization of quasiparticle dispersion in a quantum antiferromagnet.

PubMed

Hong, Tao; Qiu, Y; Matsumoto, M; Tennant, D A; Coester, K; Schmidt, K P; Awwadi, F F; Turnbull, M M; Agrawal, H; Chernyshev, A L

2017-05-05

The notion of a quasiparticle, such as a phonon, a roton or a magnon, is used in modern condensed matter physics to describe an elementary collective excitation. The intrinsic zero-temperature magnon damping in quantum spin systems can be driven by the interaction of the one-magnon states and multi-magnon continuum. However, detailed experimental studies on this quantum many-body effect induced by an applied magnetic field are rare. Here we present a high-resolution neutron scattering study in high fields on an S=1/2 antiferromagnet C 9 H 18 N 2 CuBr 4 . Compared with the non-interacting linear spin-wave theory, our results demonstrate a variety of phenomena including field-induced renormalization of one-magnon dispersion, spontaneous magnon decay observed via intrinsic linewidth broadening, unusual non-Lorentzian two-peak structure in the excitation spectra and a dramatic shift of spectral weight from one-magnon state to the two-magnon continuum.

A fabrication guide for planar silicon quantum dot heterostructures

NASA Astrophysics Data System (ADS)

Spruijtenburg, Paul C.; Amitonov, Sergey V.; van der Wiel, Wilfred G.; Zwanenburg, Floris A.

2018-04-01

We describe important considerations to create top-down fabricated planar quantum dots in silicon, often not discussed in detail in literature. The subtle interplay between intrinsic material properties, interfaces and fabrication processes plays a crucial role in the formation of electrostatically defined quantum dots. Processes such as oxidation, physical vapor deposition and atomic-layer deposition must be tailored in order to prevent unwanted side effects such as defects, disorder and dewetting. In two directly related manuscripts written in parallel we use techniques described in this work to create depletion-mode quantum dots in intrinsic silicon, and low-disorder silicon quantum dots defined with palladium gates. While we discuss three different planar gate structures, the general principles also apply to 0D and 1D systems, such as self-assembled islands and nanowires.

Variable steroid receptor responses: Intrinsically disordered AF1 is the key

PubMed Central

Simons, S. Stoney; Kumar, Raj

2013-01-01

Steroid hormones, acting through their cognate receptor proteins, see widespread clinical applications due to their ability to alter the induction or repression of numerous genes. However, steroid usage is limited by the current inability to control off-target, or non-specific, side-effects. Recent results from three separate areas of research with glucocorticoid and other steroid receptors (cofactor-induced changes in receptor structure, the ability of ligands to alter remote regions of receptor structure, and how cofactor concentration affects both ligand potency and efficacy) indicate that a key element of receptor activity is the intrinsically disordered amino-terminal domain. These results are combined to construct a novel framework within which to logically pursue various approaches that could afford increased selectivity in steroid-based therapies. PMID:23792173

Intrinsically disordered RGG/RG domains mediate degenerate specificity in RNA binding

PubMed Central

Ozdilek, Bagdeser A.; Thompson, Valery F.; Ahmed, Nasiha S.; White, Connor I.

2017-01-01

Abstract RGG/RG domains are the second most common RNA binding domain in the human genome, yet their RNA-binding properties remain poorly understood. Here, we report a detailed analysis of the RNA binding characteristics of intrinsically disordered RGG/RG domains from Fused in Sarcoma (FUS), FMRP and hnRNPU. For FUS, previous studies defined RNA binding as mediated by its well-folded domains; however, we show that RGG/RG domains are the primary mediators of binding. RGG/RG domains coupled to adjacent folded domains can achieve affinities approaching that of full-length FUS. Analysis of RGG/RG domains from FUS, FMRP and hnRNPU against a spectrum of contrasting RNAs reveals that each display degenerate binding specificity, while still displaying different degrees of preference for RNA. PMID:28575444

Extrinsic mechanism obstructing the opening of a prosthetic mitral valve: an unusual case of suture entrapment.

PubMed

Ozkan, Mehmet; Astarcioglu, Mehmet Ali; Karakoyun, Suleyman; Balkanay, Mehmet

2012-02-01

Obstruction to a prosthetic cardiac valve is a well-recognized complication of cardiac valve replacement. Malfunction of the mobile component of a prosthetic valve to open or close correctly may occur in consequence of intrinsic or extrinsic causes (thrombus, vegetation, entrapment of left ventricular myocardium, suture entanglement, and pannus formation) that may result prosthetic valve stenosis and/or insufficiency. In the case we report a 48-year-old female with valve dysfunction occurred early after surgery, as one valve leaflet was only able to partially open due to suture entrapment. © 2011, Wiley Periodicals, Inc.

An unusual cause of gynaecomastia.

PubMed

Subbiah, Sridhar; Walia, Rama; Kumar, Santhosh; Nahar, Uma; Bhansali, Anil

2011-07-20

Gynaecomastia in adolescents and young adults is a common endocrine disorder with usually benign aetiology. However, gynaecomastia in middle-aged men is uncommon and warrants intensive search to unravel its aetiology. The authors report a 42-year-old male who presented with gynaecomastia due to feminising adrenocortical carcinoma.

Extreme metabolic alkalosis with fludrocortisone therapy.

PubMed Central

Burns, A.; Brown, T. M.; Semple, P.

1983-01-01

We present an unusual case of extreme metabolic alkalosis resulting from severe hypokalaemia caused by unmonitored fludrocortisone therapy. Biochemical aspects of the disorder are discussed, as is the successful treatment with diuretics and potassium replacement. Some dangers of this therapy and necessary precautions are emphasized. PMID:6622340

An unusual autopsy case of lethal hypothermia exacerbated by body lice-induced severe anemia.

PubMed

Nara, Akina; Nagai, Hisashi; Yamaguchi, Rutsuko; Makino, Yohsuke; Chiba, Fumiko; Yoshida, Ken-ichi; Yajima, Daisuke; Iwase, Hirotaro

2016-05-01

Pediculus humanus humanus (known as body lice) are commonly found in the folds of clothes, and can cause skin disorders when they feed on human blood, resulting in an itching sensation. Body lice are known as vectors of infectious diseases, including typhus, recurrent fever, and trench fever. An infestation with blood-sucking body lice induces severe cutaneous pruritus, and this skin disorder is known as "vagabond's disease." A body lice infestation is sometimes complicated with iron deficiency anemia. In the present case, a man in his late 70s died of lethal hypothermia in the outdoors during the winter season. The case history and autopsy findings revealed that the cause of the lethal hypothermia was iron deficiency anemia, which was associated with a prolonged infestation of blood-sucking body lice. Also, he had vagabond's disease because the skin on his body was abnormal and highly pigmented. This is an unusual autopsy case since the body lice contributed to the cause of the death.

A Candidate for an Intrinsic Dusty Absorber with a Metal-rich Damped Lyα Absorption Line System in the Quasar J170542.91+354340.2

NASA Astrophysics Data System (ADS)

Pan, Xiang; Zhou, Hongyan; Ge, Jian; Jiang, Peng; Yang, Bin; Lu, Honglin; Ji, Tuo; Zhang, Shaohua; Shi, Xiheng

2017-02-01

We present a detailed analysis of the unusual damped Lyα absorption line system (DLA) toward the quasar SDSS J170542.91+354340.2 at a redshift of 2, previously reported by Noterdaeme et al. as one of the very few CO absorbers known to date at high z. This DLA is exceptional in that: (1) its extinction curve is similar to peculiar Milky Way sightlines penetrating star formation regions; (2) its absorption components are redshifted at a speed of several hundred km s-1 compared to broad Balmer emission lines; (3) its gas-phase metallicity is super-solar as evaluated from more than 30 absorption lines; (4) detection of residual flux in the DLA trough and variability of {{C}} {{IV}} absorption is possible. Based on these facts, we argue that this dusty DLA is a good candidate for an intrinsic quasar 2175 Å absorber, and can originate from star formation regions of the quasar’s host galaxy. We discuss in detail the gas and dust properties, and the dust depletion. Follow-up observations, such as spectropolarimetry and optical/infrared spectroscopy, will help to confirm the system’s intrinsic nature and to explore how dust grains behave in the extreme environments proximate to quasars.

Strain-Induced Extrinsic High-Temperature Ferromagnetism in the Fe-Doped Hexagonal Barium Titanate

PubMed Central

Zorko, A.; Pregelj, M.; Gomilšek, M.; Jagličić, Z.; Pajić, D.; Telling, M.; Arčon, I.; Mikulska, I.; Valant, M.

2015-01-01

Diluted magnetic semiconductors possessing intrinsic static magnetism at high temperatures represent a promising class of multifunctional materials with high application potential in spintronics and magneto-optics. In the hexagonal Fe-doped diluted magnetic oxide, 6H-BaTiO3-δ, room-temperature ferromagnetism has been previously reported. Ferromagnetism is broadly accepted as an intrinsic property of this material, despite its unusual dependence on doping concentration and processing conditions. However, the here reported combination of bulk magnetization and complementary in-depth local-probe electron spin resonance and muon spin relaxation measurements, challenges this conjecture. While a ferromagnetic transition occurs around 700 K, it does so only in additionally annealed samples and is accompanied by an extremely small average value of the ordered magnetic moment. Furthermore, several additional magnetic instabilities are detected at lower temperatures. These coincide with electronic instabilities of the Fe-doped 3C-BaTiO3-δ pseudocubic polymorph. Moreover, the distribution of iron dopants with frozen magnetic moments is found to be non-uniform. Our results demonstrate that the intricate static magnetism of the hexagonal phase is not intrinsic, but rather stems from sparse strain-induced pseudocubic regions. We point out the vital role of internal strain in establishing defect ferromagnetism in systems with competing structural phases. PMID:25572803

Photoconductivity of Activated Carbon Fibers

DOE R&D Accomplishments Database

Kuriyama, K.; Dresselhaus, M. S.

1990-08-01

The photoconductivity is measured on a high-surface-area disordered carbon material, namely activated carbon fibers, to investigate their electronic properties. Measurements of decay time, recombination kinetics and temperature dependence of the photoconductivity generally reflect the electronic properties of a material. The material studied in this paper is a highly disordered carbon derived from a phenolic precursor, having a huge specific surface area of 1000--2000m{sup 2}/g. Our preliminary thermopower measurements suggest that this carbon material is a p-type semiconductor with an amorphous-like microstructure. The intrinsic electrical conductivity, on the order of 20S/cm at room temperature, increases with increasing temperature in the range 30--290K. In contrast with the intrinsic conductivity, the photoconductivity in vacuum decreases with increasing temperature. The recombination kinetics changes from a monomolecular process at room temperature to a biomolecular process at low temperatures. The observed decay time of the photoconductivity is {approx equal}0.3sec. The magnitude of the photoconductive signal was reduced by a factor of ten when the sample was exposed to air. The intrinsic carrier density and the activation energy for conduction are estimated to be {approx equal}10{sup 21}/cm{sup 3} and {approx equal}20meV, respectively. The majority of the induced photocarriers and of the intrinsic carriers are trapped, resulting in the long decay time of the photoconductivity and the positive temperature dependence of the conductivity.

Structural disorder in plant proteins: where plasticity meets sessility.

PubMed

Covarrubias, Alejandra A; Cuevas-Velazquez, Cesar L; Romero-Pérez, Paulette S; Rendón-Luna, David F; Chater, Caspar C C

2017-09-01

Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks. Given the versatility of intrinsic structural disorder within proteins, this feature appears as one of the leading characters of such complex functional circuits, critical for plant adaptation and survival in their wild habitats. In this review, we present information of those intrinsically disordered proteins (IDPs) from plants for which their high level of predicted structural disorder has been correlated with a particular function, or where there is experimental evidence linking this structural feature with its protein function. Using examples of plant IDPs involved in the control of cell cycle, metabolism, hormonal signaling and regulation of gene expression, development and responses to stress, we demonstrate the critical importance of IDPs throughout the life of the plant.

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions.

PubMed

Saravanan, Konda Mani; Dunker, A Keith; Krishnaswamy, Sankaran

2017-12-27

More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.

Understanding the autistic dental patient.

PubMed

Green, Danielle; Flanagan, Dennis

2008-01-01

Autism spectrum disorder (ASD) is one of many pervasive developmental disorders (PDD); others include Rett syndrome, childhood disintegrative disorder (also known as Heller's syndrome), pervasive developmental disorder not otherwise specified (PDD-NOS), and the higher functioning Asperger's syndrome. Because ASD is the most common of the developmental disabilities, it is not unusual for dentists to have ASD patients among their patient population. As the name indicates, ASD varies widely in its clinical manifestations; however, dentists are likely to encounter difficulties with communication and socialization. Although communication may be difficult, it is not impossible. A thorough understanding of this complex neurological disorder and displaying patience are vital for the dentist. This article seeks to familiarize readers with ASD characteristics and co-morbid conditions that may affect dental treatment and provide some management strategies for this unique population.

Part-crystalline part-liquid state and electrical/thermal transport in materials with chemical-bond hierarchy

NASA Astrophysics Data System (ADS)

Zhang, Wenqng

2015-03-01

A concept of part-crystalline part-liquid state (or liquid-like), and even part-crystalline part-glass state (or glass-like), was demonstrated in some materials such as Cu3SbSe3 with chemical-bond-hierarchy, in which certain constituent species weakly bond to other part of the crystal. Such a material could intrinsically manifest the coexistence of rigid crystalline sublattices and other fluctuating noncrystalline sublattices with thermally induced large amplitude vibrations and even flow of the group of species atoms. The large-amplitude vibrations and movement of atoms can generate unusual severe phonon scattering and thermal damping due to the collective low-frequency vibrations similar to the Boson peak in amorphous or liquid materials. While different phase or state may have large energetic discrepancy, whether the thermally-induced part-crystalline state is undergoing phase transition becomes an interesting issue. In addition, our earlier work reported that second-order phase transition could induce extreme electron and phonon scattering in thermoelectrics. The above work clearly demonstrated that the unusual effect from structural fluctuations on thermal and electrical transport in thermoelectrics should be paid attention to. While materials with these structural changes can retain extremely low lattice thermal conductivity and unusual electron transport and become promising candidates for high-performance thermoelectrics, underlying mechanism is yet to be explored.

Platysmal myoclonus in subclinical hyperthyroidism.

PubMed

Teoh, Hock-Luen; Lim, Erle Chuen-Hian

2005-08-01

Hyperthyroidism is associated with various movement disorders, such as chorea and tremors. We report on a young Chinese woman with an unusual presentation of myoclonus, involving both platysmal muscles, in association with subclinical hyperthyroidism. The myoclonus was preceded by symptoms of hyperthyroidism, namely weight loss, menstrual disturbances, and heat intolerance. The movements abated with clonazepam and hyperthyroidism was treated with carbimazole. The myoclonus recurred briefly when she stopped taking clonazepam, but she has since remained well and euthyroid. Copyright 2005 Movement Disorder Society

Classical and unusual imaging appearances of melorheostosis.

PubMed

Suresh, S; Muthukumar, T; Saifuddin, A

2010-08-01

This comprehensive review will discuss the classical and unusual radiological features of melorheostosis, which is an uncommon, non-hereditary, benign, sclerosing mesodermal disease with an incidence of 0.9 cases per million. The presentation of melorheostosis in the appendicular skeleton (more commonly involved) and in the axial skeleton (very few documented case reports) will be discussed. The aim of the review is to illustrate the associations and rare, but recognized, complications of the disorder. The role of cross-sectional imaging in the form of magnetic resonance imaging (MRI) and computed tomography (CT) in revealing the spectrum of disease manifestation and differentiation from other disease entities and malignancy will be explored.

The trigeminal trophic syndrome: an unusual cause of nasal ulceration.

PubMed

Monrad, Seetha U; Terrell, Jeffrey E; Aronoff, David M

2004-06-01

Trigeminal trophic syndrome (TTS) is an unusual complication after peripheral or central damage to the trigeminal nerve, characterized by anesthesia, paresthesias, and ala nasi ulceration. We describe a patient with classic TTS after trigeminal rhizotomy who underwent several extensive evaluations for nasal ulceration and received prolonged immunosuppressive therapy for a presumed autoimmune disorder before the correct diagnosis was made. An understanding of the predisposing factors and clinical presentation of TTS is important to ensure a timely diagnosis of this difficult-to-treat illness. Differentiation of TTS from malignancy, infection, or vasculitis is possible on the basis of clinical history, tissue biopsy, and serologic evaluation.

Oral Rehabilitation for Amniotic Band Syndrome: An Unusual Presentation

PubMed Central

Sharma, Krishna

2015-01-01

ABSTRACT Amniotic band syndrome (ABS) is a congenital disorder caused by entrapment of fetal parts in fibrous amniotic bands while in utero. The syndrome is underdiagnosed and its presentation is variable. The syndrome has been well described in the pediatric, orthopedic and obstetric literature; however, despite the discernable craniomaxillofacial involvement, ABS has not been reported in the dental literature very often. The present report describes a case of a patient with ABS and concomitant dental findings. How to cite this article: Hotwani K, Sharma K. Oral Rehabilitation for Amniotic Band Syndrome: An Unusual Presentation. Int J Clin Pediatr Dent 2015;8(1):55-57. PMID:26124582

Oral Rehabilitation for Amniotic Band Syndrome: An Unusual Presentation.

PubMed

Hotwani, Kavita; Sharma, Krishna

2015-01-01

Amniotic band syndrome (ABS) is a congenital disorder caused by entrapment of fetal parts in fibrous amniotic bands while in utero. The syndrome is underdiagnosed and its presentation is variable. The syndrome has been well described in the pediatric, orthopedic and obstetric literature; however, despite the discernable craniomaxillofacial involvement, ABS has not been reported in the dental literature very often. The present report describes a case of a patient with ABS and concomitant dental findings. How to cite this article: Hotwani K, Sharma K. Oral Rehabilitation for Amniotic Band Syndrome: An Unusual Presentation. Int J Clin Pediatr Dent 2015;8(1):55-57.

Intrinsically disordered proteins as molecular shields†

PubMed Central

Chakrabortee, Sohini; Tripathi, Rashmi; Watson, Matthew; Kaminski Schierle, Gabriele S.; Kurniawan, Davy P.; Kaminski, Clemens F.; Wise, Michael J.; Tunnacliffe, Alan

2017-01-01

The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 – while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins – HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Förster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability, but a bioinformatics survey does not support this, since there are no significant differences in the degree of disorder between desiccation tolerant and intolerant species. It seems clear therefore that molecular shield function is largely an intermolecular activity implemented by specialist IDPs, distinct from molecular chaperones, but with a role in proteostasis. PMID:21909508

Intrinsically disordered proteins as molecular shields.

PubMed

Chakrabortee, Sohini; Tripathi, Rashmi; Watson, Matthew; Schierle, Gabriele S Kaminski; Kurniawan, Davy P; Kaminski, Clemens F; Wise, Michael J; Tunnacliffe, Alan

2012-01-01

The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 - while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins - HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Förster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability, but a bioinformatics survey does not support this, since there are no significant differences in the degree of disorder between desiccation tolerant and intolerant species. It seems clear therefore that molecular shield function is largely an intermolecular activity implemented by specialist IDPs, distinct from molecular chaperones, but with a role in proteostasis.

Thermodynamic analysis of the disorder-to-α-helical transition of 18.5-kDa myelin basic protein reveals an equilibrium intermediate representing the most compact conformation.

PubMed

Vassall, Kenrick A; Jenkins, Andrew D; Bamm, Vladimir V; Harauz, George

2015-05-22

The intrinsically disordered, 18.5-kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that is essential to proper myelin formation in the central nervous system. MBP acts in oligodendrocytes both to adjoin membrane leaflets to each other in forming myelin and as a hub in numerous protein-protein and protein-membrane interaction networks. Like many intrinsically disordered proteins (IDPs), MBP multifunctionality arises from its high conformational plasticity and its ability to undergo reversible disorder-to-order transitions. One such transition is the disorder-to-α-helical conformational change that is induced upon MBP-membrane binding. Here, we have investigated the disorder-to-α-helical transition of MBP-derived α-peptides and the full-length 18.5-kDa protein. This transition was induced through titration of the membrane-mimetic solvent trifluoroethanol into both protein and peptide solutions, and conformational change was monitored using circular dichroism spectroscopy, 1-anilinonaphthalene-8-sulfonic acid binding, tryptophan fluorescence quenching, and Förster (fluorescence) resonance energy transfer measurements. The data suggest that the disorder-to-α-helical transition of MBP follows a 3-state model: disordered↔intermediate↔α-helical, with each of the identified equilibrium states likely representing a conformational ensemble. The disordered state is characterized by slight compaction with little regular secondary structure, whereas the intermediate is also disordered but globally more compact. Surprisingly, the α-helical conformation is less compact than the intermediate. This study suggests that multifunctionality in MBP could arise from differences in the population of energetically distinct ensembles under different conditions and also provides an example of an IDP that undergoes cooperative global conformation change. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments.

PubMed

Moukhtar, Julien; Faivre-Moskalenko, Cendrine; Milani, Pascale; Audit, Benjamin; Vaillant, Cedric; Fontaine, Emeline; Mongelard, Fabien; Lavorel, Guillaume; St-Jean, Philippe; Bouvet, Philippe; Argoul, Françoise; Arneodo, Alain

2010-04-22

Sequence dependency of DNA intrinsic bending properties has been emphasized as a possible key ingredient to in vivo chromatin organization. We use atomic force microscopy (AFM) in air and liquid to image intrinsically straight (synthetic), uncorrelated (hepatitis C RNA virus) and persistent long-range correlated (human) DNA fragments in various ionic conditions such that the molecules freely equilibrate on the mica surface before being captured in a particular conformation. 2D thermodynamic equilibrium is experimentally verified by a detailed statistical analysis of the Gaussian nature of the DNA bend angle fluctuations. We show that the worm-like chain (WLC) model, commonly used to describe the average conformation of long semiflexible polymers, reproduces remarkably well the persistence length estimates for the first two molecules as consistently obtained from (i) mean square end-to-end distance measurement and (ii) mean projection of the end-to-end vector on the initial orientation. Whatever the operating conditions (air or liquid, concentration of metal cations Mg(2+) and/or Ni(2+)), the persistence length found for the uncorrelated viral DNA underestimates the value obtained for the straight DNA. We show that this systematic difference is the signature of the presence of an uncorrelated structural intrinsic disorder in the hepatitis C virus (HCV) DNA fragment that superimposes on local curvatures induced by thermal fluctuations and that only the entropic disorder depends upon experimental conditions. In contrast, the WLC model fails to describe the human DNA conformations. We use a mean-field extension of the WLC model to account for the presence of long-range correlations (LRC) in the intrinsic curvature disorder of human genomic DNA: the stronger the LRC, the smaller the persistence length. The comparison of AFM imaging of human DNA with LRC DNA simulations confirms that the rather small mean square end-to-end distance observed, particularly for G+C-rich human DNA molecules, more likely results from a large-scale intrinsic curvature due to a persistent distribution of DNA curvature sites than from some increased flexibility.

Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation

PubMed Central

Brady, Jacob P.; Farber, Patrick J.; Sekhar, Ashok; Lin, Yi-Hsuan; Huang, Rui; Bah, Alaji; Chan, Hue Sun; Forman-Kay, Julie D.; Kay, Lewis E.

2017-01-01

Membrane encapsulation is frequently used by the cell to sequester biomolecules and compartmentalize their function. Cells also concentrate molecules into phase-separated protein or protein/nucleic acid “membraneless organelles” that regulate a host of biochemical processes. Here, we use solution NMR spectroscopy to study phase-separated droplets formed from the intrinsically disordered N-terminal 236 residues of the germ-granule protein Ddx4. We show that the protein within the concentrated phase of phase-separated Ddx4, Ddx4cond, diffuses as a particle of 600-nm hydrodynamic radius dissolved in water. However, NMR spectra reveal sharp resonances with chemical shifts showing Ddx4cond to be intrinsically disordered. Spin relaxation measurements indicate that the backbone amides of Ddx4cond have significant mobility, explaining why high-resolution spectra are observed, but motion is reduced compared with an equivalently concentrated nonphase-separating control. Observation of a network of interchain interactions, as established by NOE spectroscopy, shows the importance of Phe and Arg interactions in driving the phase separation of Ddx4, while the salt dependence of both low- and high-concentration regions of phase diagrams establishes an important role for electrostatic interactions. The diffusion of a series of small probes and the compact but disordered 4E binding protein 2 (4E-BP2) protein in Ddx4cond are explained by an excluded volume effect, similar to that found for globular protein solvents. No changes in structural propensities of 4E-BP2 dissolved in Ddx4cond are observed, while changes to DNA and RNA molecules have been reported, highlighting the diverse roles that proteinaceous solvents play in dictating the properties of dissolved solutes. PMID:28894006

Interfacial Properties of NTAIL, an Intrinsically Disordered Protein.

PubMed

Bénarouche, Anaïs; Habchi, Johnny; Cagna, Alain; Maniti, Ofelia; Girard-Egrot, Agnès; Cavalier, Jean-François; Longhi, Sonia; Carrière, Frédéric

2017-12-19

Intrinsically disordered proteins (IDPs) lack stable secondary and tertiary structure under physiological conditions in the absence of their biological partners and thus exist as dynamic ensembles of interconverting conformers, often highly soluble in water. However, in some cases, IDPs such as the ones involved in neurodegenerative diseases can form protein aggregates and their aggregation process may be triggered by the interaction with membranes. Although the interfacial behavior of globular proteins has been extensively studied, experimental data on IDPs at the air/water (A/W) and water/lipid interfaces are scarce. We studied here the intrinsically disordered C-terminal domain of the Hendra virus nucleoprotein (N TAIL ) and compared its interfacial properties to those of lysozyme that is taken as a model globular protein of similar molecular mass. Adsorption of N TAIL at the A/W interface was studied in the absence and presence of phospholipids using Langmuir films, polarization modulated-infrared reflection-absorption spectroscopy, and an automated drop tensiometer for interfacial tension and elastic modulus determination with oscillating bubbles. N TAIL showed a significant surface activity, with a higher adsorption capacity at the A/W interface and penetration into egg phosphatidylcholine monolayer compared to lysozyme. Whereas lysozyme remains folded upon compression of the protein layer at the A/W interface and shows a quasi-pure elastic behavior, N TAIL shows a much higher molecular area and forms a highly viscoelastic film with a high dilational modulus. To our knowledge, a new disorder-to-order transition is thus observed for the N TAIL protein that folds into an antiparallel β-sheet at the A/W interface and presents strong intermolecular interactions. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

An unusual cause of gynaecomastia

PubMed Central

Subbiah, Sridhar; Walia, Rama; Kumar, Santhosh; Nahar, Uma; Bhansali, Anil

2011-01-01

Gynaecomastia in adolescents and young adults is a common endocrine disorder with usually benign aetiology. However, gynaecomastia in middle-aged men is uncommon and warrants intensive search to unravel its aetiology. The authors report a 42-year-old male who presented with gynaecomastia due to feminising adrenocortical carcinoma. PMID:22689603

Understanding Williams Syndrome: Behavioral Patterns and Interventions.

ERIC Educational Resources Information Center

Semel, Eleanor; Rosner, Sue R.

This guide to Williams syndrome (WS), a congenital disorder characterized by developmental/cognitive limitations but relatively high verbal and social skills, explains the strengths, difficulties and variations found among individuals with the condition and offers guidelines for intervention in the unusual properties of the WS behavioral profile.…

Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks

PubMed Central

Pechmann, Sebastian; Frydman, Judith

2014-01-01

Evolution is driven by mutations, which lead to new protein functions but come at a cost to protein stability. Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability. Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability. We here examine factors that systematically promote non-conservative mutations at the proteome level. Intrinsically disordered regions in proteins play pivotal roles in protein interactions, but many questions regarding their evolution remain unanswered. Similarly, whether and how molecular chaperones, which have been shown to buffer destabilizing mutations in individual proteins, generally provide robustness during proteome evolution remains unclear. To this end, we introduce an evolutionary parameter λ that directly estimates the rate of non-conservative substitutions. Our analysis of λ in Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens sequences reveals how co- and post-translationally acting chaperones differentially promote non-conservative substitutions in their substrates, likely through buffering of their destabilizing effects. We further find that λ serves well to quantify the evolution of intrinsically disordered proteins even though the unstructured, thus generally variable regions in proteins are often flanked by very conserved sequences. Crucially, we show that both intrinsically disordered proteins and highly re-wired proteins in protein interaction networks, which have evolved new interactions and functions, exhibit a higher λ at the expense of enhanced chaperone assistance. Our findings thus highlight an intricate interplay of molecular chaperones and protein disorder in the evolvability of protein networks. Our results illuminate the role of chaperones in enabling protein evolution, and underline the importance of the cellular context and integrated approaches for understanding proteome evolution. We feel that the development of λ may be a valuable addition to the toolbox applied to understand the molecular basis of evolution. PMID:24968255

Translational animal models of autism and neurodevelopmental disorders

PubMed Central

Crawley, Jacqueline N.

2012-01-01

Autism is a neurodevelopmental disorder whose diagnosis is based on three behavioral criteria: unusual reciprocal social interactions, deficits in communication, and stereotyped repetitive behaviors with restricted interests. A large number of de novo single gene mutations and chromosomal deletions are associated with autism spectrum disorders. Based on the strong genetic evidence, mice with targeted mutations in homologous genes have been generated as translational research tools. Mouse models of autism have revealed behavioral and biological outcomes of mutations in risk genes. The field is now poised to employ the most robust phenotypes in the most replicable mouse models for preclinical screening of novel therapeutics. PMID:23226954

The Use of T-tube Cholangiocatheter Stents in the Treatment of Pediatric Tracheomalacia

PubMed Central

Mohammad Vahid Hosseini, Seyed; Zarenezhad, Mohammad; Sabet, Babak; Shoar, Mehrdad Malek; Kangari, Gholamreza

2013-01-01

Tracheomalacia is a common disorder in neonate and infants, which can lead to life-threatening airway occlusion, because of external pressure or intrinsic defect of tracheobroncial cartilage. Aortopexy and Stents are effective in relieving tracheomalacia in the latter patients. In this case we are to show how t-tube cholangiocatheter is effective and easy available in sever tracheomalacia neonates with intrinsic defect. It can be easily replaced and causes no infection, erosion, or sever complication in 9 months period. PMID:24470855

The Use of T-tube Cholangiocatheter Stents in the Treatment of Pediatric Tracheomalacia.

PubMed

Mohammad Vahid Hosseini, Seyed; Zarenezhad, Mohammad; Sabet, Babak; Shoar, Mehrdad Malek; Kangari, Gholamreza

2013-01-01

Tracheomalacia is a common disorder in neonate and infants, which can lead to life-threatening airway occlusion, because of external pressure or intrinsic defect of tracheobroncial cartilage. Aortopexy and Stents are effective in relieving tracheomalacia in the latter patients. In this case we are to show how t-tube cholangiocatheter is effective and easy available in sever tracheomalacia neonates with intrinsic defect. It can be easily replaced and causes no infection, erosion, or sever complication in 9 months period.

Spin-orbit driven magnetic insulating state with J eff=1/2 character in a 4d oxide

DOE PAGES

Calder, S.; Li, Ling; Okamoto, Satoshi; ...

2015-11-30

The unusual magnetic and electronic ground states of 5d iridates has been shown to be driven by intrinsically enhanced spin-orbit coupling (SOC). The influence of appreciable but reduced SOC in creating the manifested magnetic insulating states in 4d oxides is less clear, with one hurdle being the existence of such compounds. Here we present experimental and theoretical results on Sr 4RhO 6 that reveal SOC dominated behavior. Neutron measurements show the octahedra are both spatially separated and locally ideal, making the electronic ground state susceptible to alterations by SOC. Magnetic ordering is observed with a similar structure to an analogousmore » J eff=1/2 Mott iridate. We consider the underlying role of SOC in this rhodate with density functional theory and x-ray absorption spectroscopy and find a magnetic insulating ground state with J eff =1/2 character.The unusual magnetic and electronic ground states of 5d iridates have been shown to be driven by intrinsically enhanced spin-orbit coupling (SOC). The influence of appreciable but reduced SOC in creating the manifested magnetic insulating states in 4d oxides is less clear, with one hurdle being the existence of such compounds. Here, we present experimental and theoretical results on Sr 4RhO 6 that reveal SOC dominated behavior. Neutron measurements show the octahedra are both spatially separated and locally ideal, making the electronic ground state susceptible to alterations by SOC. Magnetic ordering is observed with a similar structure to an analogous J eff=1/2 Mott iridate. We consider the underlying role of SOC in this rhodate with density functional theory and x-ray absorption spectroscopy, and find a magnetic insulating ground state with J eff=12 character.« less

Topologically Diverse Human Membrane Proteins Partition to Liquid-Disordered Domains in Phase-Separated Lipid Vesicles.

PubMed

Schlebach, Jonathan P; Barrett, Paul J; Day, Charles A; Kim, Ji Hun; Kenworthy, Anne K; Sanders, Charles R

2016-02-23

The integration of membrane proteins into "lipid raft" membrane domains influences many biochemical processes. The intrinsic structural properties of membrane proteins are thought to mediate their partitioning between membrane domains. However, whether membrane topology influences the targeting of proteins to rafts remains unclear. To address this question, we examined the domain preference of three putative raft-associated membrane proteins with widely different topologies: human caveolin-3, C99 (the 99 residue C-terminal domain of the amyloid precursor protein), and peripheral myelin protein 22. We find that each of these proteins are excluded from the ordered domains of giant unilamellar vesicles containing coexisting liquid-ordered and liquid-disordered phases. Thus, the intrinsic structural properties of these three topologically distinct disease-linked proteins are insufficient to confer affinity for synthetic raft-like domains.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riback, Joshua A.; Bowman, Micayla A.; Zmyslowski, Adam M.

A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the generalmore » expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.« less

Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing.

PubMed

Hotta, Kinya; Ranganathan, Soumya; Liu, Ruchuan; Wu, Fei; Machiyama, Hiroaki; Gao, Rong; Hirata, Hiroaki; Soni, Neelesh; Ohe, Takashi; Hogue, Christopher W V; Madhusudhan, M S; Sawada, Yasuhiro

2014-04-01

Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD) of p130Cas (or BCAR1) has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2-9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing β-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing.

Elephantine but not elephantiasis: Subcutaneous zygomycosis.

PubMed

Girish, Meenakshi; Arora, Amit; Bhalla, Lucky; Salodkar, Atul

2011-09-01

Subcutaneous zygomycosis is an unusual disorder caused by a rare fungus, Basidiobolus ranarum. We report this entity in a 4- yr- old boy. Biopsy showed the Splendore Hoeppli phenomenon and the culture yielded Basidiobolus ranarum. The child responded to saturated solution of potassium iodide within 1 month of starting treatment.

44 CFR 15.7 - Disturbances.

Code of Federal Regulations, 2012 CFR

2012-10-01

... SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.7 Disturbances. At both Mt. Weather and NETC we prohibit any unwarranted loitering, disorderly conduct, or other conduct at Mt. Weather and NETC that: (a) Creates loud or unusual noise or a...

44 CFR 15.7 - Disturbances.

Code of Federal Regulations, 2011 CFR

2011-10-01

... SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.7 Disturbances. At both Mt. Weather and NETC we prohibit any unwarranted loitering, disorderly conduct, or other conduct at Mt. Weather and NETC that: (a) Creates loud or unusual noise or a...

44 CFR 15.7 - Disturbances.

Code of Federal Regulations, 2013 CFR

2013-10-01

... SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.7 Disturbances. At both Mt. Weather and NETC we prohibit any unwarranted loitering, disorderly conduct, or other conduct at Mt. Weather and NETC that: (a) Creates loud or unusual noise or a...

44 CFR 15.7 - Disturbances.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.7 Disturbances. At both Mt. Weather and NETC we prohibit any unwarranted loitering, disorderly conduct, or other conduct at Mt. Weather and NETC that: (a) Creates loud or unusual noise or a...

44 CFR 15.7 - Disturbances.

Code of Federal Regulations, 2014 CFR

2014-10-01

... SECURITY GENERAL CONDUCT AT THE MT. WEATHER EMERGENCY ASSISTANCE CENTER AND AT THE NATIONAL EMERGENCY TRAINING CENTER § 15.7 Disturbances. At both Mt. Weather and NETC we prohibit any unwarranted loitering, disorderly conduct, or other conduct at Mt. Weather and NETC that: (a) Creates loud or unusual noise or a...

OPAL: prediction of MoRF regions in intrinsically disordered protein sequences.

PubMed

Sharma, Ronesh; Raicar, Gaurav; Tsunoda, Tatsuhiko; Patil, Ashwini; Sharma, Alok

2018-06-01

Intrinsically disordered proteins lack stable 3-dimensional structure and play a crucial role in performing various biological functions. Key to their biological function are the molecular recognition features (MoRFs) located within long disordered regions. Computationally identifying these MoRFs from disordered protein sequences is a challenging task. In this study, we present a new MoRF predictor, OPAL, to identify MoRFs in disordered protein sequences. OPAL utilizes two independent sources of information computed using different component predictors. The scores are processed and combined using common averaging method. The first score is computed using a component MoRF predictor which utilizes composition and sequence similarity of MoRF and non-MoRF regions to detect MoRFs. The second score is calculated using half-sphere exposure (HSE), solvent accessible surface area (ASA) and backbone angle information of the disordered protein sequence, using information from the amino acid properties of flanks surrounding the MoRFs to distinguish MoRF and non-MoRF residues. OPAL is evaluated using test sets that were previously used to evaluate MoRF predictors, MoRFpred, MoRFchibi and MoRFchibi-web. The results demonstrate that OPAL outperforms all the available MoRF predictors and is the most accurate predictor available for MoRF prediction. It is available at http://www.alok-ai-lab.com/tools/opal/. ashwini@hgc.jp or alok.sharma@griffith.edu.au. Supplementary data are available at Bioinformatics online.

Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment

PubMed Central

Mollica, Luca; Bessa, Luiza M.; Hanoulle, Xavier; Jensen, Malene Ringkjøbing; Blackledge, Martin; Schneider, Robert

2016-01-01

In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context. PMID:27668217

Genome-scale prediction of proteins with long intrinsically disordered regions.

PubMed

Peng, Zhenling; Mizianty, Marcin J; Kurgan, Lukasz

2014-01-01

Proteins with long disordered regions (LDRs), defined as having 30 or more consecutive disordered residues, are abundant in eukaryotes, and these regions are recognized as a distinct class of biologically functional domains. LDRs facilitate various cellular functions and are important for target selection in structural genomics. Motivated by the lack of methods that directly predict proteins with LDRs, we designed Super-fast predictor of proteins with Long Intrinsically DisordERed regions (SLIDER). SLIDER utilizes logistic regression that takes an empirically chosen set of numerical features, which consider selected physicochemical properties of amino acids, sequence complexity, and amino acid composition, as its inputs. Empirical tests show that SLIDER offers competitive predictive performance combined with low computational cost. It outperforms, by at least a modest margin, a comprehensive set of modern disorder predictors (that can indirectly predict LDRs) and is 16 times faster compared to the best currently available disorder predictor. Utilizing our time-efficient predictor, we characterized abundance and functional roles of proteins with LDRs over 110 eukaryotic proteomes. Similar to related studies, we found that eukaryotes have many (on average 30.3%) proteins with LDRs with majority of proteomes having between 25 and 40%, where higher abundance is characteristic to proteomes that have larger proteins. Our first-of-its-kind large-scale functional analysis shows that these proteins are enriched in a number of cellular functions and processes including certain binding events, regulation of catalytic activities, cellular component organization, biogenesis, biological regulation, and some metabolic and developmental processes. A webserver that implements SLIDER is available at http://biomine.ece.ualberta.ca/SLIDER/. Copyright © 2013 Wiley Periodicals, Inc.

Intrinsic point defects in off-stoichiometric Cu2ZnSnSe4: A neutron diffraction study

NASA Astrophysics Data System (ADS)

Gurieva, Galina; Valle Rios, Laura Elisa; Franz, Alexandra; Whitfield, Pamela; Schorr, Susan

2018-04-01

This work is an experimental study of intrinsic point defects in off-stoichiometric kesterite type CZTSe by means of neutron powder diffraction. We revealed the existence of copper vacancies (VCu), various cation anti site defects (CuZn, ZnCu, ZnSn, SnZn, and CuZn), as well as interstitials (Cui, Zni) in a wide range of off-stoichiometric polycrystalline powder samples synthesized by the solid state reaction. The results show that the point defects present in off-stoichiometric CZTSe agree with the off-stoichiometry type model, assuming certain cation substitutions accounting for charge balance. In addition to the known off-stoichiometry types A-H, new types (I-L) have been introduced. For the very first time, a correlation between the chemical composition of the CZTSe kesterite type phase and the occurring intrinsic point defects is presented. In addition to the off-stoichiometry type specific defects, the Cu/Zn disorder is always present in the CZTSe phase. In Cu-poor/Zn-rich CZTSe, a composition considered as the one that delivers the best photovoltaic performance, mainly copper vacancies, ZnCu and ZnSn anti sites are present. Also, this compositional region shows the lowest degree of Cu/Zn disorder.

The impairment of HCCS leads to MLS syndrome by activating a non-canonical cell death pathway in the brain and eyes

PubMed Central

Indrieri, Alessia; Conte, Ivan; Chesi, Giancarlo; Romano, Alessia; Quartararo, Jade; Tatè, Rosarita; Ghezzi, Daniele; Zeviani, Massimo; Goffrini, Paola; Ferrero, Ileana; Bovolenta, Paola; Franco, Brunella

2013-01-01

Mitochondrial-dependent (intrinsic) programmed cell death (PCD) is an essential homoeostatic mechanism that selects bioenergetically proficient cells suitable for tissue/organ development. However, the link between mitochondrial dysfunction, intrinsic apoptosis and developmental anomalies has not been demonstrated to date. Now we provide the evidence that non-canonical mitochondrial-dependent apoptosis explains the phenotype of microphthalmia with linear skin lesions (MLS), an X-linked developmental disorder caused by mutations in the holo-cytochrome c-type synthase (HCCS) gene. By taking advantage of a medaka model that recapitulates the MLS phenotype we demonstrate that downregulation of hccs, an essential player of the mitochondrial respiratory chain (MRC), causes increased cell death via an apoptosome-independent caspase-9 activation in brain and eyes. We also show that the unconventional activation of caspase-9 occurs in the mitochondria and is triggered by MRC impairment and overproduction of reactive oxygen species (ROS). We thus propose that HCCS plays a key role in central nervous system (CNS) development by modulating a novel non-canonical start-up of cell death and provide the first experimental evidence for a mechanistic link between mitochondrial dysfunction, intrinsic apoptosis and developmental disorders. PMID:23239471

Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations.

PubMed

Ilie, Ioana M; Nayar, Divya; den Otter, Wouter K; van der Vegt, Nico F A; Briels, Wim J

2018-06-12

Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Molecular Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theoretical framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril. Our study shows that individual fragments in solution have a propensity toward attaining non-β conformations, indicating that in a fibril β-strands are stabilized by interactions with other strands. We show that most dimers of hydrogen-bonded fragments are unstable in solution, while hydrogen bonding stabilizes the collective binding of five fragments to the end of a fibril. Hydrophobic effects make further contributions to the stability of fibrils. This study is the first of its kind where structural and binding preferences of the five major fragments of the hydrophobic core of α-synuclein have been investigated. This approach improves sampling of intrinsically disordered proteins, provides information on the binding mechanism between the core sequences of α-synuclein, and enables the parametrization of coarse grained models.

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations.

PubMed

Bernetti, Mattia; Masetti, Matteo; Pietrucci, Fabio; Blackledge, Martin; Jensen, Malene Ringkjobing; Recanatini, Maurizio; Mollica, Luca; Cavalli, Andrea

2017-10-19

Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev N TAIL , a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics. To validate our simulation strategy, we compared the predicted NMR properties against available experimental data. Our simulations reveal a rough free-energy surface comprising multiple local minima, which are separated by low energy barriers. Moreover, we identified interconversion rates between the main kinetic states, which lie in the sub-μs time scales, as suggested in previous works for Sev N TAIL . Therefore, the emerging picture is in agreement with the atomic-level properties possessed by the free IDP in solution. By providing both a thermodynamic and kinetic characterization of this IDP test case, our study demonstrates how computational methods can be effective tools for studying this challenging class of proteins.

Intrinsically Disordered Energy Landscapes

PubMed Central

Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

2015-01-01

Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium. PMID:25999294

Rapid Proteasomal Degradation of Posttranscriptional Regulators of the TIS11/Tristetraprolin Family Is Induced by an Intrinsically Unstructured Region Independently of Ubiquitination

PubMed Central

Ngoc, Long Vo; Wauquier, Corinne; Soin, Romuald; Bousbata, Sabrina; Twyffels, Laure; Kruys, Véronique

2014-01-01

The TIS11/tristetraprolin (TTP) CCCH tandem zinc finger proteins are major effectors in the destabilization of mRNAs bearing AU-rich elements (ARE) in their 3′ untranslated regions. In this report, we demonstrate that the Drosophila melanogaster dTIS11 protein is short-lived due to its rapid ubiquitin-independent degradation by the proteasome. Our data indicate that this mechanism is tightly associated with the intrinsically unstructured, disordered N- and C-terminal domains of the protein. Furthermore, we show that TTP, the mammalian TIS11/TTP protein prototype, shares the same three-dimensional characteristics and is degraded by the same proteolytic pathway as dTIS11, thereby indicating that this mechanism has been conserved across evolution. Finally, we observed a phosphorylation-dependent inhibition of dTIS11 and TTP degradation by the proteasome in vitro, raising the possibility that such modifications directly affect proteasomal recognition for these proteins. As a group, RNA-binding proteins (RNA-BPs) have been described as enriched in intrinsically disordered regions, thus raising the possibility that the mechanism that we uncovered for TIS11/TTP turnover is widespread among other RNA-BPs. PMID:25246635

Anomalously Soft Non-Euclidean Springs

NASA Astrophysics Data System (ADS)

Levin, Ido; Sharon, Eran

2016-01-01

In this work we study the mechanical properties of a frustrated elastic ribbon spring—the non-Euclidean minimal spring. This spring belongs to the family of non-Euclidean plates: it has no spontaneous curvature, but its lateral intrinsic geometry is described by a non-Euclidean reference metric. The reference metric of the minimal spring is hyperbolic, and can be embedded as a minimal surface. We argue that the existence of a continuous set of such isometric minimal surfaces with different extensions leads to a complete degeneracy of the bulk elastic energy of the minimal spring under elongation. This degeneracy is removed only by boundary layer effects. As a result, the mechanical properties of the minimal spring are unusual: the spring is ultrasoft with a rigidity that depends on the thickness t as t7 /2 and does not explicitly depend on the ribbon's width. Moreover, we show that as the ribbon is widened, the rigidity may even decrease. These predictions are confirmed by a numerical study of a constrained spring. This work is the first to address the unusual mechanical properties of constrained non-Euclidean elastic objects.

Intrinsic to extrinsic phonon lifetime transition in a GaAs-AlAs superlattice.

PubMed

Hofmann, F; Garg, J; Maznev, A A; Jandl, A; Bulsara, M; Fitzgerald, E A; Chen, G; Nelson, K A

2013-07-24

We have measured the lifetimes of two zone-center longitudinal acoustic phonon modes, at 320 and 640 GHz, in a 14 nm GaAs/2 nm AlAs superlattice structure. By comparing measurements at 296 and 79 K we separate the intrinsic contribution to phonon lifetime determined by phonon-phonon scattering from the extrinsic contribution due to defects and interface roughness. At 296 K, the 320 GHz phonon lifetime has approximately equal contributions from intrinsic and extrinsic scattering, whilst at 640 GHz it is dominated by extrinsic effects. These measurements are compared with intrinsic and extrinsic scattering rates in the superlattice obtained from first-principles lattice dynamics calculations. The calculated room-temperature intrinsic lifetime of longitudinal phonons at 320 GHz is in agreement with the experimentally measured value of 0.9 ns. The model correctly predicts the transition from predominantly intrinsic to predominantly extrinsic scattering; however the predicted transition occurs at higher frequencies. Our analysis indicates that the 'interfacial atomic disorder' model is not entirely adequate and that the observed frequency dependence of the extrinsic scattering rate is likely to be determined by a finite correlation length of interface roughness.

Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex

PubMed Central

Hayama, Ryo; Sparks, Samuel; Hecht, Lee M.; Dutta, Kaushik; Karp, Jerome M.; Cabana, Christina M.; Rout, Michael P.; Cowburn, David

2018-01-01

Intrinsically disordered proteins (IDPs) play important roles in many biological systems. Given the vast conformational space that IDPs can explore, the thermodynamics of the interactions with their partners is closely linked to their biological functions. Intrinsically disordered regions of Phe–Gly nucleoporins (FG Nups) that contain multiple phenylalanine–glycine repeats are of particular interest, as their interactions with transport factors (TFs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex. Here, we used NMR and isothermal titration calorimetry to thermodynamically characterize these multivalent interactions. These analyses revealed that a combination of low per-FG motif affinity and the enthalpy–entropy balance prevents high-avidity interaction between FG Nups and TFs, whereas the large number of FG motifs promotes frequent FG–TF contacts, resulting in enhanced selectivity. Our thermodynamic model underlines the importance of functional disorder of FG Nups. It helps explain the rapid and selective translocation of TFs through the nuclear pore complex and further expands our understanding of the mechanisms of “fuzzy” interactions involving IDPs. PMID:29374059

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emin, David, E-mail: emin@unm.edu

Charge carriers that execute multi-phonon hopping generally interact strongly enough with phonons to form polarons. A polaron's sluggish motion is linked to slowly shifting atomic displacements that severely reduce the intrinsic width of its transport band. Here a means to estimate hopping polarons' bandwidths from Seebeck-coefficient measurements is described. The magnitudes of semiconductors' Seebeck coefficients are usually quite large (>k/|q| = 86 μV/K) near room temperature. However, in accord with the third law of thermodynamics, Seebeck coefficients must vanish at absolute zero. Here, the transition of the Seebeck coefficient of hopping polarons to its low-temperature regime is investigated. The temperature and sharpness ofmore » this transition depend on the concentration of carriers and on the width of their transport band. This feature provides a means of estimating the width of a polaron's transport band. Since the intrinsic broadening of polaron bands is very small, less than the characteristic phonon energy, the net widths of polaron transport bands in disordered semiconductors approach the energetic disorder experienced by their hopping carriers, their disorder energy.« less

Intrinsically disordered proteins drive enamel formation via an evolutionarily conserved self-assembly motif.

PubMed

Wald, Tomas; Spoutil, Frantisek; Osickova, Adriana; Prochazkova, Michaela; Benada, Oldrich; Kasparek, Petr; Bumba, Ladislav; Klein, Ophir D; Sedlacek, Radislav; Sebo, Peter; Prochazka, Jan; Osicka, Radim

2017-02-28

The formation of mineralized tissues is governed by extracellular matrix proteins that assemble into a 3D organic matrix directing the deposition of hydroxyapatite. Although the formation of bones and dentin depends on the self-assembly of type I collagen via the Gly-X-Y motif, the molecular mechanism by which enamel matrix proteins (EMPs) assemble into the organic matrix remains poorly understood. Here we identified a Y/F-x-x-Y/L/F-x-Y/F motif, evolutionarily conserved from the first tetrapods to man, that is crucial for higher order structure self-assembly of the key intrinsically disordered EMPs, ameloblastin and amelogenin. Using targeted mutations in mice and high-resolution imaging, we show that impairment of ameloblastin self-assembly causes disorganization of the enamel organic matrix and yields enamel with disordered hydroxyapatite crystallites. These findings define a paradigm for the molecular mechanism by which the EMPs self-assemble into supramolecular structures and demonstrate that this process is crucial for organization of the organic matrix and formation of properly structured enamel.

Soft Phonon Modes Leading to Ultralow Thermal Conductivity and High Thermoelectric Performance in AgCuTe.

PubMed

Roychowdhury, Subhajit; Jana, Manoj K; Pan, Jaysree; Guin, Satya N; Sanyal, Dirtha; Waghmare, Umesh V; Biswas, Kanishka

2018-04-03

Crystalline solids with intrinsically low lattice thermal conductivity (κ L ) are crucial to realizing high-performance thermoelectric (TE) materials. Herein, we show an ultralow κ L of 0.35 Wm -1  K -1 in AgCuTe, which has a remarkable TE figure-of-merit, zT of 1.6 at 670 K when alloyed with 10 mol % Se. First-principles DFT calculation reveals several soft phonon modes in its room-temperature hexagonal phase, which are also evident from low-temperature heat-capacity measurement. These phonon modes, dominated by Ag vibrations, soften further with temperature giving a dynamic cation disorder and driving the superionic transition. Intrinsic factors cause an ultralow κ L in the room-temperature hexagonal phase, while the dynamic disorder of Ag/Cu cations leads to reduced phonon frequencies and mean free paths in the high-temperature rocksalt phase. Despite the cation disorder at elevated temperatures, the crystalline conduits of the rigid anion sublattice give a high power factor. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Support for chemistry symposia at the 2011 American Association for the Advancement of Science meeting, February 17-21 2011

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charles Casey

2011-08-20

This proposal supported Chemistry Symposia at the 2011 American Association for the Advancement of Science (AAAS) Meeting in Washington, DC February 17-21, 2011. The Chemistry Section of AAAS presented an unusually strong set of symposia for the 2011 AAAS meeting to help celebrate the 2011 International Year of Chemistry. The AAAS meeting provided an unusual opportunity to convey the excitement and importance of chemistry to a very broad audience and allowed access to a large contingent of the scientific press. Excellent suggestions for symposia were received from AAAS Chemistry Fellows and from the chairs of the American Chemical Society Technicalmore » Divisions. The AAAS Chemistry executive committee selected topics that would have wide appeal to scientists, the public, and the press for formal proposals of symposia. The symposia proposals were peer reviewed by AAAS. The Chemistry Section made a strong case to the program selection committee for approval of the chemistry symposia and 6 were approved for the 2011 annual meeting. The titles of the approved symposia were: (1) Powering the Planet: Generation of Clean Fuels from Sunlight and Water, (2) Biological Role and Consequences of Intrinsic Protein Disorder, (3) Chemically Speaking: How Organisms Talk to Each Other, (4) Molecular Self-Assembly and Artificial Molecular Machines, (5) Frontiers in Organic Materials for Information Processing, Energy and Sensors, and (6) Celebrating Marie Curie's 100th Anniversary of Her Nobel Prize in Chemistry. The Chemistry Section of AAAS is provided with funds to support only 1-2 symposia a year. Because of the much greater number of symposia approved in conjunction with observance of the 2011 International Year of Chemistry, additional support was sought from DOE to help support the 30 invited speakers and 8 symposia moderators/organizers. Support for the symposia provided the opportunity to highlight the excitement of current chemical research, to educate the public about the achievements of chemistry and its contributions to the well-being of humankind. The 2011 AAAS Annual Meeting provided an important opportunity to play a prominent role in the global celebration of the 2011 International Year of Chemistry.« less

MODELING THE HARD TeV SPECTRA OF BLAZARS 1ES 0229+200 AND 3C 66A WITH AN INTERNAL ABSORPTION SCENARIO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zacharopoulou, O.; Aharonian, F. A.; Khangulyan, D.

2011-09-10

We study the applicability of the idea of internal absorption of {gamma}-rays produced through synchrotron radiation of ultrarelativistic protons in highly magnetized blobs to 1ES 0229+200 and 3C 66A, the two TeV blazars which show unusually hard intrinsic {gamma}-ray spectra after being corrected for the intergalactic absorption. We show that for certain combinations of reasonable model parameters, even with quite modest energy requirements, the scenario allows a self-consistent explanation of the non-thermal emission of these objects in the keV, GeV, and TeV energy bands.

Monitoring solar-type stars for luminosity variations

NASA Technical Reports Server (NTRS)

Lockwood, G. W.; Skiff, B. A.

1988-01-01

Since 1984, researchers have made more than 1500 differential photometric b (471 nm) and y (551 nm) measurements of three dozen solar-like lower main sequence stars whose chromospheric activity was previosly studied by O. C. Wilson. Here, researchers describe their methodology and the statistical tests used to distinguish intrinsic stellar variability from observational and instrument errors. The incidence of detected variability among the program and comparison stars is summarized. Among the 100 plus pairs of stars measured differentially, only a dozen were found that were unusually constant, with peak-to-peak amplitudes of seasonal mean brightness smaller than 0.3 percent (0.003 mag) over a two-to-three-year interval.

A family with unusual Waardenburg syndrome type I (WSI), cleft lip (palate), and Hirschsprung disease is not linked to PAX 3.

PubMed

Pierpont, J W; St Jacques, D; Seaver, L H; Erickson, R P

1995-03-01

An unusual family with Waardenburg syndrome type 1 (WSI), cleft lip (palate), and Hirschsprung disease is not linked to the PAX 3 gene since there is an obligate crossover which has occurred between PAX 3 DNA markers and the disorder in this family. This family may also have anticipation of the WSI traits as the proband's grandmother is nonpenetrant, his mother has dystopia canthorum, and severe cleft lip (palate), while the proband has dystopia canthorum, severe cleft lip (palate), and Hirschsprung disease. Thus, a locus other than PAX 3 is implicated in this Waardenburg-like syndrome with Hirschsprung disease and cleft lip (palate).

Hashimoto thyroiditis with an unusual presentation of cardiac tamponade in Noonan syndrome.

PubMed

Lee, Mi Ji; Kim, Byung Young; Ma, Jae Sook; Choi, Young Earl; Kim, Young Ok; Cho, Hwa Jin; Kim, Chan Jong

2016-11-01

Noonan syndrome is an autosomal dominant, multisystem disorder. Autoimmune thyroiditis with hypothyroidism is an infrequent feature in patients with Noonan syndrome. A 16-year-old boy was admitted because of chest discomfort and dyspnea; an echocardiogram revealed pericardial effusion. Additional investigations led to a diagnosis of severe hypothyroidism due to Hashimoto thyroiditis. The patient was treated with L-thyroxine at 0.15 mg daily. However, during admission, he developed symptoms of cardiac tamponade. Closed pericardiostomy was performed, after which the patient's chest discomfort improved, and his vital signs stabilized. Herein, we report a case of an adolescent with Noonan syndrome, who was diagnosed with Hashimoto thyroiditis with an unusual presentation of cardiac tamponade.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

PubMed

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-10-26

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1α CAD.

PubMed

Lindström, Ida; Andersson, Eva; Dogan, Jakob

2018-05-18

Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1α (Hif-1α CAD). A total of 17 Hif-1α CAD point-mutations were generated and a Φ-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1α CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is "disordered-like", with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.

ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins

PubMed Central

Song, Dong; Wang, Wei; Ye, Wei; Ji, Dingjue; Luo, Ray; Chen, Hai-Feng

2017-01-01

Intrinsically disordered proteins (IDPs) are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These IDPs are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27 are insufficient in sampling the conformational characters of IDPs. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of IDPs. Further test suggests that the calculated secondary chemical shifts under ff14IDPs force field are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs force field is a robust model for improving the conformation sampling of IDPs. PMID:27484738

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

PubMed Central

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-01-01

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. PMID:26498066

A multiprotein binding interface in an intrinsically disordered region of the tumor suppressor protein interferon regulatory factor-1.

PubMed

Narayan, Vikram; Halada, Petr; Hernychová, Lenka; Chong, Yuh Ping; Žáková, Jitka; Hupp, Ted R; Vojtesek, Borivoj; Ball, Kathryn L

2011-04-22

The interferon-regulated transcription factor and tumor suppressor protein IRF-1 is predicted to be largely disordered outside of the DNA-binding domain. One of the advantages of intrinsically disordered protein domains is thought to be their ability to take part in multiple, specific but low affinity protein interactions; however, relatively few IRF-1-interacting proteins have been described. The recent identification of a functional binding interface for the E3-ubiquitin ligase CHIP within the major disordered domain of IRF-1 led us to ask whether this region might be employed more widely by regulators of IRF-1 function. Here we describe the use of peptide aptamer-based affinity chromatography coupled with mass spectrometry to define a multiprotein binding interface on IRF-1 (Mf2 domain; amino acids 106-140) and to identify Mf2-binding proteins from A375 cells. Based on their function as known transcriptional regulators, a selection of the Mf2 domain-binding proteins (NPM1, TRIM28, and YB-1) have been validated using in vitro and cell-based assays. Interestingly, although NPM1, TRIM28, and YB-1 all bind to the Mf2 domain, they have differing amino acid specificities, demonstrating the degree of combinatorial diversity and specificity available through linear interaction motifs.

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.

PubMed

Zerze, Gül H; Best, Robert B; Mittal, Jeetain

2015-11-19

We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions.

Dual cases of type 1 narcolepsy with schizophrenia and other psychotic disorders.

PubMed

Canellas, Francesca; Lin, Ling; Julià, Maria Rosa; Clemente, Antonio; Vives-Bauza, Cristofol; Ollila, Hanna M; Hong, Seung Chul; Arboleya, Susana M; Einen, Mali A; Faraco, Juliette; Fernandez-Vina, Marcelo; Mignot, Emmanuel

2014-09-15

Cases of narcolepsy in association with psychotic features have been reported but never fully characterized. These patients present diagnostic and treatment challenges and may shed new light on immune associations in schizophrenia. Our case series was gathered at two narcolepsy specialty centers over a 9-year period. A questionnaire was created to improve diagnosis of schizophrenia or another psychotic disorder in patients with narcolepsy. Pathophysiological investigations included full HLA Class I and II typing, testing for known systemic and intracellular/synaptic neuronal antibodies, recently described neuronal surface antibodies, and immunocytochemistry on brain sections to detect new antigens. Ten cases were identified, one with schizoaffective disorder, one with delusional disorder, two with schizophreniform disorder, and 6 with schizophrenia. In all cases, narcolepsy manifested first in childhood or adolescence, followed by psychotic symptoms after a variable interval. These patients had auditory hallucinations, which was the most differentiating clinical feature in comparison to narcolepsy patients without psychosis. Narcolepsy therapy may have played a role in triggering psychotic symptoms but these did not reverse with changes in narcolepsy medications. Response to antipsychotic treatment was variable. Pathophysiological studies did not reveal any known autoantibodies or unusual brain immunostaining pattern. No strong HLA association outside of HLA DQB1*06:02 was found, although increased DRB3*03 and DPA1*02:01 was notable. Narcolepsy can occur in association with schizophrenia, with significant diagnostic and therapeutic challenges. Dual cases maybe under diagnosed, as onset is unusually early, often in childhood. Narcolepsy and psychosis may share an autoimmune pathology; thus, further investigations in larger samples are warranted. © 2014 American Academy of Sleep Medicine.

Pulmonary Vasculitis and a Horseshoe Kidney in Noonan Syndrome.

PubMed

Puvabanditsin, Surasak; Abellar, Rosanna; Madubuko, Adaora; Mehta, Rajeev; Walzer, Lauren

2018-01-01

We report a term male neonate with congenital myeloproliferative disorder, thrombocytopenia, a horseshoe kidney, feeding difficulty secondary to dysphagia/foregut dysmotility, and respiratory failure. Prenatal molecular genetic analysis revealed a fetus carrying c.184T>G (p.Tyr62Asp) pathogenic variant in PTPN11 . The infant eventually succumbed to respiratory failure. Bacterial and viral cultures/studies were all no growth/negative. Pulmonary capillaritis and vasculitis were noted at autopsy. This report presents a new case of Noonan syndrome with unusual associated disorders and a review of the literature.

Pulmonary Vasculitis and a Horseshoe Kidney in Noonan Syndrome

PubMed Central

Abellar, Rosanna; Madubuko, Adaora; Mehta, Rajeev

2018-01-01

We report a term male neonate with congenital myeloproliferative disorder, thrombocytopenia, a horseshoe kidney, feeding difficulty secondary to dysphagia/foregut dysmotility, and respiratory failure. Prenatal molecular genetic analysis revealed a fetus carrying c.184T>G (p.Tyr62Asp) pathogenic variant in PTPN11. The infant eventually succumbed to respiratory failure. Bacterial and viral cultures/studies were all no growth/negative. Pulmonary capillaritis and vasculitis were noted at autopsy. This report presents a new case of Noonan syndrome with unusual associated disorders and a review of the literature. PMID:29670795

Inherited disorders in the Afrikaner population of southern Africa. Part I. Historical and demographic background, cardiovascular, neurological, metabolic and intestinal conditions.

PubMed

Botha, M C; Beighton, P

1983-10-08

Certain genetic disorders occur with unusually high frequency in the Afrikaner population of southern Africa. Conditions of this type (reviewed in Part I of this article) include familial hypercholesterolaemia, progressive familial heart block, Huntington's chorea, porphyria variegata, Gaucher's disease, cystic fibrosis and familial colonic polyposis. This genetic situation is explicable to some extent on the basis of the demographic development of the Afrikaner population during the 14 generations since the arrival of the first immigrants from Holland more than 330 years ago.

Brief Report: Autism-Like Traits Are Associated with Enhanced Ability to Disembed Visual Forms

ERIC Educational Resources Information Center

Sabatino DiCriscio, Antoinette; Troiani, Vanessa

2017-01-01

Atypical visual perceptual skills are thought to underlie unusual visual attention in autism spectrum disorders. We assessed whether individual differences in visual processing skills scaled with quantitative traits associated with the broader autism phenotype (BAP). Visual perception was assessed using the Figure-ground subtest of the Test of…

Severity of Hyperacusis Predicts Individual Differences in Speech Perception in Williams Syndrome

ERIC Educational Resources Information Center

Elsabbagh, M.; Cohen, H.; Cohen, M.; Rosen, S.; Karmiloff-Smith, A.

2011-01-01

Background: Williams Syndrome (WS) is a neurodevelopmental disorder of genetic origin, characterised by relative proficiency in language in the face of serious impairment in several other domains. Individuals with WS display an unusual sensitivity to noise, known as hyperacusis. Methods: In this study, we examined the extent to which hyperacusis…

"Helicobacter Pylori" Infection in Five Inpatient Units for People with Intellectual Disability and Psychiatric Disorder

ERIC Educational Resources Information Center

Clarke, David; Vemuri, Murali; Gunatilake, Deepthi; Tewari, Sidhartha

2008-01-01

Background: A high prevalence of "Helicobacter pylori" infection has been reported among people with intellectual disability, especially those residing in hospital and similar settings. Surveys of inpatients have found unusually high rates of gastrointestinal malignancy, to which "H. pylori" infection predisposes. Methods: "Helicobacter pylori"…

Bringing Back the Body: A Retrospective on the Development of Objectification Theory

ERIC Educational Resources Information Center

Fredrickson, Barbara L.; Hendler, Lee Meyerhoff; Nilsen, Stephanie; O'Barr, Jean Fox; Roberts, Tomi-Ann

2011-01-01

In this article, Barbara L. Fredrickson reflects back on two early papers--"Objectification Theory: Toward Understanding Women's Lived Experiences and Mental Health Risks" and "A Mediational Model Linking Self-Objectification, Body Shame, and Disordered Eating"--and puts them into larger context. Both papers share an unusual origin story. To tell…

Expanded Access Protocol (EAP) Using the CliniMACS® Device for Pediatric Haplocompatible Donor Stem Cell Transplant

ClinicalTrials.gov

2017-11-22

Acute Lymphoblastic Leukemia; Acute Myeloid Leukemia; Chronic Myeloid Leukemia; Myelodysplastic Syndrome; Lymphomas; Bone Marrow Failure; Hemoglobinopathy; Immune Deficiency; Osteopetrosis; Cytopenias; Leukocyte Disorders; Anemia Due to Intrinsic Red Cell Abnormality

Schizophrenia and the structure of language: the linguist's view.

PubMed

Covington, Michael A; He, Congzhou; Brown, Cati; Naçi, Lorina; McClain, Jonathan T; Fjordbak, Bess Sirmon; Semple, James; Brown, John

2005-09-01

Patients with schizophrenia often display unusual language impairments. This is a wide ranging critical review of the literature on language in schizophrenia since the 19th century. We survey schizophrenic language level by level, from phonetics through phonology, morphology, syntax, semantics, and pragmatics. There are at least two kinds of impairment (perhaps not fully distinct): thought disorder, or failure to maintain a discourse plan, and schizophasia, comprising various dysphasia-like impairments such as clanging, neologism, and unintelligible utterances. Thought disorder appears to be primarily a disruption of executive function and pragmatics, perhaps with impairment of the syntax-semantics interface; schizophasia involves disruption at other levels. Phonetics is also often abnormal (manifesting as flat intonation or unusual voice quality), but phonological structure, morphology, and syntax are normal or nearly so (some syntactic impairments have been demonstrated). Access to the lexicon is clearly impaired, manifesting as stilted speech, word approximation, and neologism. Clanging (glossomania) is straightforwardly explainable as distraction by self-monitoring. Recent research has begun to relate schizophrenia, which is partly genetic, to the genetic endowment that makes human language possible.

Impact of environment on dynamics of exciton complexes in a WS2 monolayer

NASA Astrophysics Data System (ADS)

Jakubczyk, Tomasz; Nogajewski, Karol; Molas, Maciej R.; Bartos, Miroslav; Langbein, Wolfgang; Potemski, Marek; Kasprzak, Jacek

2018-07-01

Scientific curiosity to uncover original optical properties and functionalities of atomically thin semiconductors, stemming from unusual Coulomb interactions in the two-dimensional geometry and multi-valley band structure, drives the research on monolayers of transition metal dichalcogenides (TMDs). While recent works ascertained the exotic energetic schemes of exciton complexes in TMDs, we here infer their unusual coherent dynamics occurring on subpicosecond time scale. The dynamics is largely affected by the disorder landscape on the submicron scale, thus can be uncovered using four-wave mixing in the frequency domain, which enables microscopic investigations and imaging. Focusing on a WS2 monolayer, we observe that exciton coherence is lost primarily due to interaction with phonons and relaxation processes towards optically dark excitonic states. Notably, when temperature is low and disorder weak, excitons large coherence volume results in enhanced oscillator strength, allowing to reach the regime of radiatively limited dephasing. Additionally, we observe long valley coherence for the negatively charged exciton complex. We therefore elucidate the crucial role of exciton environment in the TMDs on its dynamics and show that revealed mechanisms are ubiquitous within this family.

Infectious complications of the primary immunodeficiencies.

PubMed

Stiehm, E R; Chin, T W; Haas, A; Peerless, A G

1986-07-01

The primary manifestation of the immunodeficiencies is undue susceptibility to infection. This means too many, too severe, too prolonged, too complicated and too unusual infections. Infections in immunodeficiency have a characteristic cause depending on the nature of the immune deficiency. Antibody deficiencies are associated with infections with gram-positive infections. Cellular immune deficiencies are associated with mycobacterial, protozoan, fungus, virus, and opportunistic bacterial infection. Phagocytic disorders are associated with staphylococcal, fungal, and gram-negative organisms. Complement disorders are associated by neisserial infections. Infections have also been implicated in the pathogenesis of some immunodeficiencies in some circumstances. These include human T lymphotropic virus type III (HTLV-III), rubella virus, cytomegalovirus, and Epstein-Barr virus. Several infectious syndromes in specific immunodeficiencies have been identified. Examples include enteric cytopathic human orphan (ECHO) virus encephalitis in agammaglobulinemia, and meningococcal meningitis in C6 deficiency. Infections can also be induced by live vaccines given in immunodeficiency (e.g., paralytic polio in agammaglobulinemia.) Unusual infectious syndromes will be illustrated including parainfluenza infection in severe combined and immunodeficiency, Legionella pneumonia in chronic granulomatous disease, and Cryptosporidium infection in hyper-IgM immunodeficiency.

Cytophagic and S-100 protein immunoreactive myeloid leukemia cutis.

PubMed

Thomas, Crystal G; Patel, Rajiv M; Bergfeld, Wilma F

2010-03-01

Myeloid leukemia cutis (LC) is the cutaneous involvement by neoplastic leukocytes of the myeloid series. Myeloid LC may occur de novo or concurrently with acute myeloid leukemias, chronic myeloid leukemias, other myeloproliferative disorders or myelodysplastic syndromes. We describe an unusual case of cytophagic S-100 protein immunoreactive leukemia cutis presenting in an 87-year-old woman without prior history of myeloid leukemia or other hematologic disorders. We outline key histologic and immunohistochemical features that aide in the diagnosis of LC. The presence of cytophagocytosis on histologic examination, a phenomenon more commonly associated with lymphoid rather than myeloid malignancies, provided a clue to the possibility of a malignant process. The atypical myeloid infiltrate showed S-100 protein positivity, an unusual finding that may be seen in LC. Although not commonly reported in LC, the presence of S-100 protein positivity and cytophagocytosis should not lead to the premature exclusion of LC as a possible diagnosis until a thorough clinical, histologic and immunohistochemical evaluation is performed. In addition, the presence of cytophagocytosis has been shown to have prognostic significance for patients with myeloid leukemia.

Mapping multivalency and differential affinities within large intrinsically disordered protein complexes with segmental motion analysis.

PubMed

Milles, Sigrid; Lemke, Edward A

2014-07-07

Intrinsically disordered proteins (IDPs) can bind to multiple interaction partners. Numerous binding regions in the IDP that act in concert through complex cooperative effects facilitate such interactions, but complicate studying IDP complexes. To address this challenge we developed a combined fluorescence correlation and time-resolved polarization spectroscopy approach to study the binding properties of the IDP nucleoporin153 (Nup153) to nuclear transport receptors (NTRs). The detection of segmental backbone mobility of Nup153 within the unperturbed complex provided a readout of local, region-specific binding properties that are usually masked in measurements of the whole IDP. The binding affinities of functionally and structurally diverse NTRs to distinct regions of Nup153 can differ by orders of magnitudes-a result with implications for the diversity of transport routes in nucleocytoplasmic transport. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings.

PubMed

Sanchez-Martinez, M; Crehuet, R

2014-12-21

We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.

Stochastic transport in the presence of spatial disorder: Fluctuation-induced corrections to homogenization

NASA Astrophysics Data System (ADS)

Russell, Matthew J.; Jensen, Oliver E.; Galla, Tobias

2016-10-01

Motivated by uncertainty quantification in natural transport systems, we investigate an individual-based transport process involving particles undergoing a random walk along a line of point sinks whose strengths are themselves independent random variables. We assume particles are removed from the system via first-order kinetics. We analyze the system using a hierarchy of approaches when the sinks are sparsely distributed, including a stochastic homogenization approximation that yields explicit predictions for the extrinsic disorder in the stationary state due to sink strength fluctuations. The extrinsic noise induces long-range spatial correlations in the particle concentration, unlike fluctuations due to the intrinsic noise alone. Additionally, the mean concentration profile, averaged over both intrinsic and extrinsic noise, is elevated compared with the corresponding profile from a uniform sink distribution, showing that the classical homogenization approximation can be a biased estimator of the true mean.

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

PubMed Central

Quiroz, Felipe García; Chilkoti, Ashutosh

2015-01-01

Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level. PMID:26390327

Meta-structure correlation in protein space unveils different selection rules for folded and intrinsically disordered proteins.

PubMed

Naranjo, Yandi; Pons, Miquel; Konrat, Robert

2012-01-01

The number of existing protein sequences spans a very small fraction of sequence space. Natural proteins have overcome a strong negative selective pressure to avoid the formation of insoluble aggregates. Stably folded globular proteins and intrinsically disordered proteins (IDPs) use alternative solutions to the aggregation problem. While in globular proteins folding minimizes the access to aggregation prone regions, IDPs on average display large exposed contact areas. Here, we introduce the concept of average meta-structure correlation maps to analyze sequence space. Using this novel conceptual view we show that representative ensembles of folded and ID proteins show distinct characteristics and respond differently to sequence randomization. By studying the way evolutionary constraints act on IDPs to disable a negative function (aggregation) we might gain insight into the mechanisms by which function-enabling information is encoded in IDPs.

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective

PubMed Central

Maxwell, Peter I.

2017-01-01

Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high‐energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra‐atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (Oi –1, Ci, Ni, Ni +1) and some sidechain hydrogen atoms (Hγ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the Oi –1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:28841241

Anticoagulant and antithrombotic evaluation of native fucosylated chondroitin sulfates and their derivatives as selective inhibitors of intrinsic factor Xase.

PubMed

Wu, Mingyi; Wen, Dandan; Gao, Na; Xiao, Chuang; Yang, Lian; Xu, Li; Lian, Wu; Peng, Wenlie; Jiang, Jianmin; Zhao, Jinhua

2015-03-06

Fucosylated chondroitin sulfate (FCS), a structurally unusual glycosaminoglycan, has distinct anticoagulant properties, and is an especially strong inhibitor of the intrinsic factor Xase (anti-Xase). To obtain a highly selective inhibitor of human Xase, we purified six native FCSs with various sulfation patterns, prepared a series of FCS derivatives, and then elucidated the relationship between the structures and the anticoagulant activities of FCSs. FCSs 1-3 containing higher Fuc2S4S exhibit stronger AT-dependent anti-IIa activities, whereas 4-6 containing more Fuc3S4S produce potent HCII-dependent anti-IIa activities. Saccharides containing a minimum of 6-8 trisaccharide units, free carboxyl groups, and full fucosylation of GlcA may be required for potent anti-Xase activity, and approximately six trisaccharide units and partial fucosylation of GlcA may contribute to potent HCII-dependent activity. Decreasing of the molecular weights markedly reduces their AT-dependent anti-IIa activities, and even eliminates human platelet and factor XII activation. Furthermore, in vitro and in vivo studies suggested that fractions of 6-12 kDa may be very promising compounds as putative selective intrinsic Xase inhibitors with antithrombotic action, but without the consequences of major bleeding and factor XII activation. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Metadisorder for designer light in random systems

PubMed Central

Yu, Sunkyu; Piao, Xianji; Hong, Jiho; Park, Namkyoo

2016-01-01

Disorder plays a critical role in signal transport by controlling the correlation of a system, as demonstrated in various complex networks. In wave physics, disordered potentials suppress wave transport, because of their localized eigenstates, from the interference between multiple scattering paths. Although the variation of localization with tunable disorder has been intensively studied as a bridge between ordered and disordered media, the general trend of disorder-enhanced localization has remained unchanged, and the existence of complete delocalization in highly disordered potentials has not been explored. We propose the concept of “metadisorder”: randomly coupled optical systems in which eigenstates can be engineered to achieve unusual localization. We demonstrate that one of the eigenstates in a randomly coupled system can always be arbitrarily molded, regardless of the degree of disorder, by adjusting the self-energy of each element. Ordered waves with the desired form are then achieved in randomly coupled systems, including plane waves and globally collective resonances. We also devise counterintuitive functionalities in disordered systems, such as “small-world–like” transport from non–Anderson-type localization, phase-conserving disorder, and phase-controlled beam steering. PMID:27757414

Energetics of intrinsic defects in NiO and the consequences for its resistive random access memory performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawson, J. A., E-mail: jad95@cam.ac.uk; Guo, Y.; Robertson, J.

2015-09-21

Energetics for a variety of intrinsic defects in NiO are calculated using state-of-the-art ab initio hybrid density functional theory calculations. At the O-rich limit, Ni vacancies are the lowest cost defect for all Fermi energies within the gap, in agreement with the well-known p-type behaviour of NiO. However, the ability of the metal electrode in a resistive random access memory metal-oxide-metal setup to shift the oxygen chemical potential towards the O-poor limit results in unusual NiO behaviour and O vacancies dominating at lower Fermi energy levels. Calculated band diagrams show that O vacancies in NiO are positively charged at themore » operating Fermi energy giving it the advantage of not requiring a scavenger metal layer to maximise drift. Ni and O interstitials are generally found to be higher in energy than the respective vacancies suggesting that significant recombination of O vacancies and interstitials does not take place as proposed in some models of switching behaviour.« less

SIL1-related Marinesco-Sjoegren syndrome (MSS) with associated motor neuronopathy and bradykinetic movement disorder.

PubMed

Byrne, Susan; Dlamini, Nomazulu; Lumsden, Daniel; Pitt, Matthew; Zaharieva, Irina; Muntoni, Francesco; King, Andrew; Robert, Leema; Jungbluth, Heinz

2015-07-01

Marinesco-Sjoegren syndrome (MSS) is a recessively inherited multisystem disorder caused by mutations in SIL1 and characterized by cerebellar atrophy with ataxia, cataracts, a skeletal muscle myopathy, and variable degrees of developmental delay. Pathogenic mechanisms implicated to date include mitochondrial, nuclear envelope and lysosomal-autophagic pathway abnormalities. Here we present a 5-year-old girl with SIL1-related MSS and additional unusual features of an associated motor neuronopathy and a bradykinetic movement disorder preceding the onset of ataxia. These findings suggest that an associated motor neuronopathy may be part of the phenotypical spectrum of SIL1-related MSS and should be actively investigated in genetically confirmed cases. The additional observation of a bradykinetic movement disorder suggests an intriguing continuum between neurodevelopmental and neurodegenerative multisystem disorders intricately linked in the same cellular pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

The BG21 isoform of Golli myelin basic protein is intrinsically disordered with a highly flexible amino-terminal domain.

PubMed

Ahmed, Mumdooh A M; Bamm, Vladimir V; Harauz, George; Ladizhansky, Vladimir

2007-08-28

The genes of the oligodendrocyte lineage (Golli) encode a family of developmentally regulated isoforms of myelin basic protein. The "classic" MBP isoforms arise from transcription start site 3, whereas Golli-specific isoforms arise from transcription start site 1, and comprise both Golli-specific and classic MBP sequences. The Golli isoform BG21 has been suggested to play roles in myelination and T cell activation pathways. It is an intrinsically disordered protein, thereby presenting a large effective surface area for interaction with other proteins such as Golli-interacting protein. We have used multidimensional heteronuclear NMR spectroscopy to achieve sequence-specific resonance assignments of the recombinant murine BG21 in physiologically relevant buffer, to analyze its secondary structure using chemical shift indexing (CSI), and to investigate its backbone dynamics using 15N spin relaxation measurements. We have assigned 184 out of 199 residues unambiguously. The CSI analysis revealed little ordered secondary structure under these conditions, with only some small fragments having a slight tendency toward alpha-helicity, which may represent putative recognition motifs. The 15N relaxation and NOE measurements confirmed the general behavior of the protein as an extended polypeptide chain, with the N-terminal Golli-specific portion (residues S5-T69) being exceptionally flexible, even in comparison to other intrinsically disordered proteins that have been studied this way. The high degree of flexibility of this N-terminal region may be to provide additional plasticity, or conformational adaptability, in protein-protein interactions. Another highly mobile segment, A126-S127-G128-G129, may function as a hinge.

Dissecting partner recognition by an intrinsically disordered protein using descriptive random mutagenesis.

PubMed

Gruet, Antoine; Dosnon, Marion; Vassena, Andrea; Lombard, Vincent; Gerlier, Denis; Bignon, Christophe; Longhi, Sonia

2013-09-23

In view of getting insights into the molecular determinants of the binding efficiency of intrinsically disordered proteins (IDPs), we used random mutagenesis. As a proof of concept, we chose the interaction between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein and assessed how amino acid substitutions introduced at random within NTAIL affect partner recognition. In contrast with directed evolution approaches, we did not apply any selection and used the gene library approach not for production purposes but for achieving a better understanding of the NTAIL/XD interaction. For that reason, and to differentiate our approach from similar approaches that make use of systematic (i.e., targeted) mutagenesis, we propose to call it "descriptive random mutagenesis" (DRM). NTAIL variants generated by error-prone PCR were picked at random in the absence of selection pressure and were characterized in terms of sequence and binding abilities toward XD. DRM not only identified determinants of NTAIL/XD interaction that were in good agreement with previous work but also provided new insights. In particular, we discovered that the primary interaction site is poorly evolvable in terms of binding abilities toward XD. We also identified a critical NTAIL residue whose role in stabilizing the NTAIL/XD complex had previously escaped detection, and we identified NTAIL regulatory sites that dampen the interaction while being located outside the primary interaction site. Results show that DRM is a valuable approach to study binding abilities of IDPs. © 2013 Elsevier Ltd. All rights reserved.

Composition-related structural transition of random peptides: insight into the boundary between intrinsically disordered proteins and folded proteins.

PubMed

Kang, Wen-Bin; He, Chuan; Liu, Zhen-Xing; Wang, Jun; Wang, Wei

2018-05-16

Previous studies based on bioinformatics showed that there is a sharp distinction of structural features and residue composition between the intrinsically disordered proteins and the folded proteins. What induces such a composition-related structural transition? How do various kinds of interactions work in such processes? In this work, we investigate these problems based on a survey on peptides randomly composed of charged residues (including glutamic acids and lysines) and the residues with different hydrophobicity, such as alanines, glycines, or phenylalanines. Based on simulations using all-atom model and replica-exchange Monte Carlo method, a coil-globule transition is observed for each peptide. The corresponding transition temperature is found to be dependent on the contents of the hydrophobic and charged residues. For several cases, when the mean hydrophobicity is larger than a certain threshold, the transition temperature is higher than the room temperature, and vise versa. These thresholds of hydrophobicity and net charge are quantitatively consistent with the border line observed from the study of bioinformatics. These results outline the basic physical reasons for the compositional distinction between the intrinsically disordered proteins and the folded proteins. Furthermore, the contributions of various interactions to the structural variation of peptides are analyzed based on the contact statistics and the charge-pattern dependence of the gyration radii of the peptides. Our observations imply that the hydrophobicity contributes essentially to such composition-related transitions. Thus, we achieve a better understanding on composition-structure relation of the natural proteins and the underlying physics.

Protein intrinsic disorder in plants.

PubMed

Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

2013-09-12

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

Protein intrinsic disorder in plants

PubMed Central

Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A.; Solano, Roberto

2013-01-01

To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks. PMID:24062761

How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?

PubMed

Bonetti, Daniela; Troilo, Francesca; Brunori, Maurizio; Longhi, Sonia; Gianni, Stefano

2018-04-24

The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N TAIL ) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of N TAIL upon binding to XD by measuring the effect on both the folding and binding steps of N TAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of N TAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Hierarchy of Information Processing in the Brain: A Novel 'Intrinsic Ignition' Framework.

PubMed

Deco, Gustavo; Kringelbach, Morten L

2017-06-07

A general theory of brain function has to be able to explain local and non-local network computations over space and time. We propose a new framework to capture the key principles of how local activity influences global computation, i.e., describing the propagation of information and thus the broadness of communication driven by local activity. More specifically, we consider the diversity in space (nodes or brain regions) over time using the concept of intrinsic ignition, which are naturally occurring intrinsic perturbations reflecting the capability of a given brain area to propagate neuronal activity to other regions in a given brain state. Characterizing the profile of intrinsic ignition for a given brain state provides insight into the precise nature of hierarchical information processing. Combining this data-driven method with a causal whole-brain computational model can provide novel insights into the imbalance of brain states found in neuropsychiatric disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases.

PubMed

Boomsma, Wouter; Nielsen, Sofie V; Lindorff-Larsen, Kresten; Hartmann-Petersen, Rasmus; Ellgaard, Lars

2016-01-01

The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work indicates that San1 is not a unique case, and that several other yeast and human E3 ligases have sequence properties that may allow them to recognize substrates by a similar mechanism as San1.

Life Goals Increase Self-regulation Among Male Patients with Alcohol Use Disorder.

PubMed

Won, Sung-Doo; Kim, Im-Yel

2018-01-24

Alcohol use disorder (AUD) has been conceptualized as a chronic self-regulation failure. The aim of this study was to examine the most probable pathways related to self-regulation among patients with AUD. In this study, a hypothetical model was proposed that focused on the relationship between risk factors (extrinsic life goals, emotion dysregulation) and protective factors (intrinsic life goals, self-control, and abstinence self-efficacy). Male patients with AUD (N = 188) were recruited from alcohol centers of four psychiatric hospitals between March 2015 and September 2015. All participants completed psychological assessments, including the Future Oriented Goals Scale (FOGS), the Alcohol Abstinence Self-Efficacy Scale (AASE), the Brief Self-Control Scale (BSCS), and the Difficulties in Emotion Regulation Scale (DERS) as well as sociodemographic characteristics. The final model was found to be a good fit to data. In testing indirect effects, it was shown that intrinsic life goals via emotion dysregulation, self-control, and alcohol abstinence self-efficacy decreased alcohol self-regulation failure. On the other hand, extrinsic life goals via these factors increased alcohol self-regulation failure. Conclusions/Importance: These results suggest that intrinsic goals might indirectly be the important and protective factors for AUD. Moreover, the findings implicate that self-regulation through goal setting may be necessary to alleviate symptoms and improve function among patients with AUD.

Intrinsic, Functional, and Structural Properties of β-Thymosins and β-Thymosin/WH2 Domains in the Regulation and Coordination of Actin Self-Assembly Dynamics and Cytoskeleton Remodeling.

PubMed

Renault, L

2016-01-01

β-Thymosins are a family of heat-stable multifunctional polypeptides that are expressed as small proteins of about 5kDa (~45 amino acids) almost exclusively in multicellular animals. They were first isolated from the thymus. As full-length or truncated polypeptides, they appear to stimulate a broad range of extracellular activities in various signaling pathways, including tissue repair and regeneration, inflammation, cell migration, and immune defense. However, their cell surface receptors and structural mechanisms of regulations in these multiple pathways remain still poorly understood. Besides their extracellular activities, they belong to a larger family of small, intrinsically disordered actin-binding domains called WH2/β-thymosin domains that have been identified in more than 1800 multidomain proteins found in different taxonomic domains of life and involved in various actin-based motile processes including cell morphogenesis, motility, adhesions, tissue development, intracellular trafficking, or pathogen infections. This review briefly surveys the main recent findings to understand how these small, intrinsically disordered but functional domains can interact with many unrelated partners and can thus integrate and coordinate various intracellular activities in actin self-assembly dynamics and cell signaling pathways linked to their cytoskeleton remodeling. © 2016 Elsevier Inc. All rights reserved.

Religiosity, mood symptoms, and quality of life in bipolar disorder.

PubMed

Stroppa, André; Moreira-Almeida, Alexander

2013-06-01

The aim of the present study was to investigate the relationship between religiosity and mood, quality of life, number of hospitalizations, and number of severe suicide attempts among bipolar disorder patients. In a cross-sectional study of bipolar disorder outpatients (N = 168), we assessed symptoms of mania [Young Mania Rating Scale (YMRS)], depression [Montgomery-Åsberg Depression Rating Scale (MADRS)], religiosity (Duke Religious Index), religious coping (Brief RCOPE), and quality of life [World Health Organization Quality of Life-Brief Version (WHOQOL-BREF)]. Sociodemographic data, number of suicide attempts, and number of hospitalizations were obtained through an interview with the individual and analysis of the patient's medical records. Logistical and linear regressions of the association between the religious indicators and clinical variables were conducted, controlling for sociodemographic variables. A total of 148 (88.1%) individuals reported some type of religious affiliation. Intrinsic religiosity [odds ratio (OR) = 0.19, 95% confidence interval (CI): 0.06-0.57, p = 0.003] and positive religious coping strategies (OR = 0.25, CI: 0.09-0.71, p = 0.01) were associated with fewer depressive symptoms. All four domains of quality of life were directly and significantly correlated with intrinsic religiosity. Positive religious coping was correlated with higher levels of the psychological (β = 0.216, p = 0.002) and environmental (β = 0.178, p = 0.028) quality-of-life domains. Negative religious coping was associated with lower scores on the psychological domain of quality of life (β = -0.182, p = 0.025). Intrinsic religiosity and positive religious coping are strongly associated with fewer depressive symptoms and improved quality of life. Negative religious coping is associated with worse quality of life. Religiosity is a relevant aspect of patients' lives and should be taken into consideration by physicians when assessing and managing bipolar disorder patients. Further longitudinal studies are needed to determine the causality and therapeutic implications of our findings. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Probed Serial Recall in Williams Syndrome: Lexical Influences on Phonological Short-Term Memory

ERIC Educational Resources Information Center

Brock, Jan; McCormack, Teresa; Boucher, Jill

2005-01-01

Williams syndrome is a genetic disorder that, it has been claimed, results in an unusual pattern of linguistic strengths and weaknesses. The current study investigated the hypothesis that there is a reduced influence of lexical knowledge on phonological short-term memory in Williams syndrome. Fourteen children with Williams syndrome and 2…

Superimposed Segmental Manifestation of Juvenile Amyopathic Dermatomyositis in a 9-year-old Boy

PubMed Central

Bulur, Isil; Erdogan, Hilal Kaya; Saracoglu, Zeynep Nurhan; Happle, Rudolf; Canaz, Funda

2017-01-01

Dermatomyositis is a well-known autoimmune disorder. On the other hand, juvenile amyopathic dermatomyositis (JADM) occurs rather rarely. Here, we report an unusual case in a 9-year-old Turkish boy showing a unilateral linear inflammatory skin lesion that was followed, after 16 months, by the appearance of bilateral disseminated features JADM. PMID:28794565

Ingressive Speech Errors: A Service Evaluation of Speech-Sound Therapy in a Child Aged 4;6

ERIC Educational Resources Information Center

Hrastelj, Laura; Knight, Rachael-Anne

2017-01-01

Background: A pattern of ingressive substitutions for word-final sibilants can be identified in a small number of cases in child speech disorder, with growing evidence suggesting it is a phonological difficulty, despite the unusual surface form. Phonological difficulty implies a problem with the cognitive process of organizing speech into sound…

Neurophysiological Indices of Atypical Auditory Processing and Multisensory Integration Are Associated with Symptom Severity in Autism

ERIC Educational Resources Information Center

Brandwein, Alice B.; Foxe, John J.; Butler, John S.; Frey, Hans-Peter; Bates, Juliana C.; Shulman, Lisa H.; Molholm, Sophie

2015-01-01

Atypical processing and integration of sensory inputs are hypothesized to play a role in unusual sensory reactions and social-cognitive deficits in autism spectrum disorder (ASD). Reports on the relationship between objective metrics of sensory processing and clinical symptoms, however, are surprisingly sparse. Here we examined the relationship…

Brief Report: Non-Random X Chromosome Inactivation in Females with Autism

ERIC Educational Resources Information Center

Talebizadeh, Z.; Bittel, D. C.; Veatch, O. J.; Kibiryeva, N.; Butler, M. G.

2005-01-01

Autism is a heterogeneous neurodevelopmental disorder with a 3-4 times higher sex ratio in males than females. X chromosome genes may contribute to this higher sex ratio through unusual skewing of X chromosome inactivation. We studied X chromosome skewness in 30 females with classical autism and 35 similarly aged unaffected female siblings as…

Association between Psychopathic Disorder and Serum Antibody to Herpes Simplex Virus (Type 1)

PubMed Central

Cleobury, J. F.; Skinner, G. R. B.; Thouless, M. E.; Wildy, P.

1971-01-01

The sera of a small of patients has been examined for herpes simplex virus antibody. Three clinically-defined groups of patients were compared: (a) aggressive psychopaths, (b) psychiatric controls, and (c) general hospital patients. The first group had an unusually high average kinetic neutralization constant against type 1 herpes simplex virus. PMID:5543996

Association between psychopathic disorder and serum antibody to herpes simplex virus (type 1).

PubMed

Cleobury, J F; Skinner, G R; Thouless, M E; Wildy, P

1971-02-20

The sera of a small of patients has been examined for herpes simplex virus antibody. Three clinically-defined groups of patients were compared: (a) aggressive psychopaths, (b) psychiatric controls, and (c) general hospital patients. The first group had an unusually high average kinetic neutralization constant against type 1 herpes simplex virus.

The Psychometric Properties of a New Measure of Sensory Behaviors in Autistic Children

ERIC Educational Resources Information Center

Neil, Louise; Green, Dido; Pellicano, Elizabeth

2017-01-01

Unusual reactions to sensory input became part of the diagnostic criteria for autism spectrum disorder in the DSM-5. Measures accurately assessing these symptoms are important for clinical decisions. This study examined the reliability and validity of the Sensory Behavior Questionnaire, a parent-report scale designed to assess frequency and impact…

Entomophagy and Coprophagy in Undifferentiated Schizophrenia

PubMed Central

Lingeswaran, Anand; Vijayakumar, Vinayak; Dinesh, John

2009-01-01

Coprophagia or the ingestion of feces, considered to be a variant of pica, has been associated with medical disorders like seizure disorders, cerebral atrophy, and tumors and with psychiatric disorders like mental retardation, alcoholism, depression, obsessive compulsive disorder, schizophrenia, schizoaffective disorder, fetishes, delirium, and dementia. But entomophagy or the practice of eating live or dead insects as food by humans has only been reported as part of eating habits by some cultures in the world and not in association with any medical or neuropsychiatric disorders. Till date, there is no report in medical literature of entomophagy as an association with any neuropsychiatric or medical illnesses. Coprophagy and entomophagy has not been together reported as well. We describe the first ever case report of a 19-year- old male patient diagnosed with undifferentiated schizophrenia and associated with both entomophagy and coprophagy. His schizophrenic symptoms, the entomophagic, coprophagic behaviors improved with olanzapine therapy. Entomophagy and coprophagy, two very unusual human behaviors, can be seen in association with schizophrenia. PMID:21938094

Entomophagy and coprophagy in undifferentiated schizophrenia.

PubMed

Lingeswaran, Anand; Vijayakumar, Vinayak; Dinesh, John

2009-01-01

Coprophagia or the ingestion of feces, considered to be a variant of pica, has been associated with medical disorders like seizure disorders, cerebral atrophy, and tumors and with psychiatric disorders like mental retardation, alcoholism, depression, obsessive compulsive disorder, schizophrenia, schizoaffective disorder, fetishes, delirium, and dementia. But entomophagy or the practice of eating live or dead insects as food by humans has only been reported as part of eating habits by some cultures in the world and not in association with any medical or neuropsychiatric disorders. Till date, there is no report in medical literature of entomophagy as an association with any neuropsychiatric or medical illnesses. Coprophagy and entomophagy has not been together reported as well. We describe the first ever case report of a 19-year- old male patient diagnosed with undifferentiated schizophrenia and associated with both entomophagy and coprophagy. His schizophrenic symptoms, the entomophagic, coprophagic behaviors improved with olanzapine therapy. Entomophagy and coprophagy, two very unusual human behaviors, can be seen in association with schizophrenia.

Etiology and pathogenesis of anxiety disorders.

PubMed

Sher, L

2001-07-01

The author suggests that biological abnormalities related to the development of anxiety disorders can be classified as real or relative. Individuals with 'real abnormalities' are not able to function under any circumstances, including the circumstances that are natural for humans. Persons with 'relative abnormalities' can function under the natural circumstances, but are not able to function in situations that are unnatural for humans. Unnatural situations include being in elevators, flying airplanes, driving cars, etc. The author suggests that all humans can be classified into four groups: 1. Individuals with excellent 'adaptational reserve' never develop anxiety disorders; 2. Individuals with good adaptational reserve develop anxiety disorders only if they are subjected to extremely stressful, unusual situations (e.g. being a hostage); 3. Individuals with moderate adaptational reserve develop anxiety disorders if they are exposed to unnatural situations. They have 'relative abnormalities'; 4. Individuals with poor adaptational reserve develop anxiety disorders in situations that are natural for humans. They have 'real abnormalities'. Copyright 2001 Harcourt Publishers Ltd.

Guanidinoacetate methyltransferase (GAMT) deficiency: late onset of movement disorder and preserved expressive language.

PubMed

O'Rourke, Declan J; Ryan, Stephanie; Salomons, Gajja; Jakobs, Cornelis; Monavari, Ahmad; King, Mary D

2009-05-01

Guanidinoacetate methyltransferase (GAMT) deficiency is a disorder of creatine biosynthesis, characterized by early-onset learning disability and epilepsy in most affected children. Severe expressive language delay is a constant feature even in the mildest clinical phenotypes.We report the clinical, biochemical, imaging, and treatment data of two female siblings (18y and 13y) with an unusual phenotype of GAMT deficiency. The oldest sibling had subacute onset of a movement disorder at age 17 years, later than has been previously reported. The younger sibling had better language skills than previously described in this disorder. After treatment with creatine, arginine restriction and ornithine-supplemented diet, seizure severity and movement disorder were reduced but cognition did not improve. This report confirms that GAMT deficiency, a heterogeneous, potentially treatable disorder, detected by increased levels of guanidinoacetate in body fluids (e.g. plasma or urine) or by an abnormal creatine peak on magnetic resonance spectroscopy, should be considered in patients of any age with unexplained, apparently static learning disability and epilepsy.

Anomalous glassy dynamics in simple models of dense biological tissue

NASA Astrophysics Data System (ADS)

Sussman, Daniel M.; Paoluzzi, M.; Marchetti, M. Cristina; Manning, M. Lisa

2018-02-01

In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that vertex models have quite unusual behavior in the zero-temperature limit, with rigidity transitions that are controlled by residual stresses and therefore exhibit very different scaling and phenomenology compared to particulate systems. Here we investigate the finite-temperature phase of two-dimensional Voronoi and Vertex models, and show that they have highly unusual, sub-Arrhenius scaling of dynamics with temperature. We connect the anomalous glassy dynamics to features of the potential energy landscape associated with zero-temperature inherent states.

NMOSD triggered by yellow fever vaccination - An unusual clinical presentation with segmental painful erythema.

PubMed

Schöberl, F; Csanadi, E; Eren, O; Dieterich, M; Kümpfel, T

2017-01-01

Neuromyelitis Optica Spectrum Disorder (NMOSD) is an immune-mediated disease of the central nervous system with the presence of aquaporin 4-antibodies (AQP4-abs) in most cases. We describe a patient who developed NMOSD after a yellow fever vaccination. He presented to us with an unusual painful erythema Th7-9 triggered by touch in the respective skin area due to a cervical spinal cord lesion affecting the dorsolateral parts of C6/7. To our knowledge, this is the first case of NMOSD with such a clinical presentation expanding the clinical spectrum of NMOSD. It is important to be aware of that a yellow fever vaccination can trigger NMOSD. Copyright © 2016 Elsevier B.V. All rights reserved.

Self-Reported Sleep Disturbances in Patients with Dissociative Identity Disorder and Post-Traumatic Stress Disorder and How They Relate to Cognitive Failures and Fantasy Proneness

PubMed Central

van Heugten – van der Kloet, Dalena; Huntjens, Rafaele; Giesbrecht, Timo; Merckelbach, Harald

2014-01-01

Sleep disturbances, fantasy proneness, cognitive failures, and dissociative symptoms are related to each other. However, the co-occurrence of these phenomena has been primarily studied in non-clinical samples. We investigated the correlations between these phenomena in dissociative identity disorder (DID) patients, post-traumatic stress disorder (PTSD) patients, and healthy controls. Both patient groups reported more sleep problems and lower sleep quality and displayed higher levels of fantasy proneness and cognitive failures than controls. However, the two patient groups did not differ with regard to these variables. Moreover, a higher level of unusual sleep experiences tended to predict participants belonging to the DID group, while specifically a lower sleep quality and more cognitive failures tended to predict participants belonging to the PTSD group. PMID:24600412

Self-reported sleep disturbances in patients with dissociative identity disorder and post-traumatic stress disorder and how they relate to cognitive failures and fantasy proneness.

PubMed

van Heugten-van der Kloet, Dalena; Huntjens, Rafaele; Giesbrecht, Timo; Merckelbach, Harald

2014-01-01

Sleep disturbances, fantasy proneness, cognitive failures, and dissociative symptoms are related to each other. However, the co-occurrence of these phenomena has been primarily studied in non-clinical samples. We investigated the correlations between these phenomena in dissociative identity disorder (DID) patients, post-traumatic stress disorder (PTSD) patients, and healthy controls. Both patient groups reported more sleep problems and lower sleep quality and displayed higher levels of fantasy proneness and cognitive failures than controls. However, the two patient groups did not differ with regard to these variables. Moreover, a higher level of unusual sleep experiences tended to predict participants belonging to the DID group, while specifically a lower sleep quality and more cognitive failures tended to predict participants belonging to the PTSD group.

Effect of disorder on the pressure-induced superconducting state of CeAu 2Si 2

NASA Astrophysics Data System (ADS)

Ren, Z.; Giriat, G.; Scheerer, G. W.; Lapertot, G.; Jaccard, D.

2015-03-01

CeAu2Si2 is a newly discovered pressure-induced heavy fermion superconductor, which shows very unusual interplay between superconductivity and magnetism under pressure. Here we compare the results of high-pressure measurements on single-crystalline CeAu2Si2 samples with different levels of disorder. It is found that while the magnetic properties are essentially sample independent, superconductivity is rapidly suppressed when the residual resistivity of the sample increases. We show that the depression of bulk Tc can be well understood in terms of pair breaking by nonmagnetic disorder, which strongly suggests an unconventional pairing state in pressurized CeAu2Si2 . Furthermore, increasing the level of disorder leads to the emergence of another phase transition at T* within the magnetic phase, which might be in competition with superconductivity.

MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.

PubMed

Necci, Marco; Piovesan, Damiano; Dosztányi, Zsuzsanna; Tosatto, Silvio C E

2017-05-01

Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases. MobiDB-lite is available as part of the MobiDB database from URL: http://mobidb.bio.unipd.it/. An executable can be downloaded from URL: http://protein.bio.unipd.it/mobidblite/. silvio.tosatto@unipd.it. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64).

PubMed

Poznar, Monika; Hołubowicz, Rafał; Wojtas, Magdalena; Gapiński, Jacek; Banachowicz, Ewa; Patkowski, Adam; Ożyhar, Andrzej; Dobryszycki, Piotr

2017-11-01

Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Tick receptor for outer surface protein A from Ixodes ricinus — the first intrinsically disordered protein involved in vector-microbe recognition

NASA Astrophysics Data System (ADS)

Urbanowicz, Anna; Lewandowski, Dominik; Szpotkowski, Kamil; Figlerowicz, Marek

2016-04-01

The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.

Amyloid-like fibrils formed from intrinsically disordered caseins: physicochemical and nanomechanical properties.

PubMed

Pan, Kang; Zhong, Qixin

2015-08-07

Amyloid-like fibrils are studied because of their significance in understanding pathogenesis and creating functional materials. Amyloid-like fibrils have been studied by heating globular proteins at acidic conditions. In the present study, intrinsically disordered α-, β-, and κ-caseins were studied to form amyloid-like fibrils at pH 2.0 and 90 °C. No fibrils were observed for α-caseins, and acid hydrolysis was found to be the rate-limiting step of fibrillation of β- and κ-caseins. An increase of β-sheet structure was observed after fibrillation. Nanomechanic analysis of long amyloid-like fibrils using peak-force quantitative nanomechanical atomic force microscopy showed the lowest and highest Young's modulus for β-casein (2.35 ± 0.29 GPa) and κ-casein (4.14 ± 0.66 GPa), respectively. The dispersion with β-casein fibrils had a viscosity more than 10 and 5 times higher than those of κ-casein and β-lactoglobulin, respectively, at 0.1 s(-1) at comparable concentrations. The current findings may assist not only the understanding of amyloid fibril formation but also the development of novel functional materials from disordered proteins.

IDPT: Insights into potential intrinsically disordered proteins through transcriptomic analysis of genes for prostate carcinoma epigenetic data.

PubMed

Mallik, Saurav; Sen, Sagnik; Maulik, Ujjwal

2016-07-15

Involvement of intrinsically disordered proteins (IDPs) with various dreadful diseases like cancer is an interesting research topic. In order to gain novel insights into the regulation of IDPs, in this article, we perform a transcriptomic analysis of mRNAs (genes) for transcripts encoding IDPs on a human multi-omics prostate carcinoma dataset having both gene expression and methylation data. In this regard, firstly the genes that consist of both the expression and methylation data, and that are corresponding to the cancer-related prostate-tissue-specific disordered proteins of MobiDb database, are selected. We apply standard t-test for determining differentially expressed genes as well as differentially methylated genes. A network having these genes and their targeter miRNAs from Diana Tarbase v7.0 database and corresponding Transcription Factors from TRANSFAC and ITFP databases, is then built. Thereafter, we perform literature search, and KEGG pathway and Gene Ontology analyses using DAVID database. Finally, we report several significant potential gene-markers (with the corresponding IDPs) that have inverse relationship between differential expression and methylation patterns, and that are hub genes of the TF-miRNA-gene network. Copyright © 2016 Elsevier B.V. All rights reserved.

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

Comparison of skin barrier function and sensory nerve electric current perception threshold between IgE-high extrinsic and IgE-normal intrinsic types of atopic dermatitis.

PubMed

Mori, T; Ishida, K; Mukumoto, S; Yamada, Y; Imokawa, G; Kabashima, K; Kobayashi, M; Bito, T; Nakamura, M; Ogasawara, K; Tokura, Y

2010-01-01

Background Two types of atopic dermatitis (AD) have been proposed, with different pathophysiological mechanisms underlying this seemingly heterogeneous disorder. The extrinsic type shows high IgE levels presumably as a consequence of skin barrier damage and feasible allergen permeation, whereas the intrinsic type exhibits normal IgE levels and is not mediated by allergen-specific IgE. Objectives To investigate the relationship between pruritus perception threshold and skin barrier function of patients with AD in a comparison between the extrinsic and intrinsic types. Methods Enrolled in this study were 32 patients with extrinsic AD, 17 with intrinsic AD and 24 healthy individuals. The barrier function of the stratum corneum was assessed by skin surface hydration and transepidermal water loss (TEWL), and pruritus perception was evaluated by the electric current perception threshold (CPT) of sensory nerves upon neuroselective transcutaneous electric stimulation. Results Skin surface hydration was significantly lower and TEWL was significantly higher in extrinsic AD than intrinsic AD or normal controls. Although there was no statistically significant difference in CPT among extrinsic AD, intrinsic AD and normal controls, CPT was significantly correlated with skin surface hydration and inversely with TEWL in intrinsic AD and normal controls, but not extrinsic AD. Finally, CPT was correlated with the visual analogue scale of itch in the nonlesional skin of patients with extrinsic but not intrinsic AD. Conclusions Patients with extrinsic AD have an impaired barrier, which increases the pre-existing pruritus but rather decreases sensitivity to external stimuli. In contrast, patients with intrinsic AD retain a normal barrier function and sensory reactivity to external pruritic stimuli.

Dyssomnias, parasomnias, and sleep disorders associated with medical and psychiatric diseases.

PubMed

Barthlen, G M; Stacy, C

1994-03-01

Sleep disorders can be intrinsic, as are insomnia or narcolepsy, or can be accounted for by external factors, such as noise, altitude, drug or alcohol abuse, or shift work. The arousal disorders, common in children, are usually benign and disappear by puberty. Sleep-wake transition disorders such as sleep starts are benign as well, and may occur at any age. The parasomnias comprise different entities such as nightmares, REM-sleep behavior disorder, sleep enuresis, and bruxism. Diagnosis and treatment often require a multidisciplinary approach. Virtually every psychiatric, neurologic, or medical disease, when of sufficient severity, leaves its specific fingerprint on sleep; some disorders, such as peptic ulcer disease, gastroesophageal reflux, or epilepsy, tend to be exacerbated during sleep. Fortunately, most sleep disorders are amenable to therapy, which can include counseling, sleep hygiene, withholding of an offending agent, behavioral therapy, light therapy, or cautious drug therapy.

[Metabolic alkalosis despite hyperlactatemia and hypercapnia. Interpretation and therapy with help of the Stewart concept].

PubMed

Chappell, D; Hofmann-Kiefer, K; Jacob, M; Conzen, P; Rehm, M

2008-02-01

Acid-base disturbances are commonly found in critically ill patients and are often associated with fatal complications. The basis of a successful treatment is a thorough understanding of the causes of these disorders. The "classical methods" to explain acid-base disorders--pH, base excess and bicarbonate concentration--mostly do not provide a causal correlation to the underlying pathology. An unusual case of a combined respiratory-metabolic disorder with hyperlactatemia and hypercapnia is presented. An acidosis masked by hypochloremic and hypoalbuminemic alkalosis was identified with the help of Stewart's concept and finally permitted a successful therapy. The modern Stewart concept provides enhanced information, enabling an exact diagnosis and causal therapy even in complex cases.

A Multiprotein Binding Interface in an Intrinsically Disordered Region of the Tumor Suppressor Protein Interferon Regulatory Factor-1*

PubMed Central

Narayan, Vikram; Halada, Petr; Hernychová, Lenka; Chong, Yuh Ping; Žáková, Jitka; Hupp, Ted R.; Vojtesek, Borivoj; Ball, Kathryn L.

2011-01-01

The interferon-regulated transcription factor and tumor suppressor protein IRF-1 is predicted to be largely disordered outside of the DNA-binding domain. One of the advantages of intrinsically disordered protein domains is thought to be their ability to take part in multiple, specific but low affinity protein interactions; however, relatively few IRF-1-interacting proteins have been described. The recent identification of a functional binding interface for the E3-ubiquitin ligase CHIP within the major disordered domain of IRF-1 led us to ask whether this region might be employed more widely by regulators of IRF-1 function. Here we describe the use of peptide aptamer-based affinity chromatography coupled with mass spectrometry to define a multiprotein binding interface on IRF-1 (Mf2 domain; amino acids 106–140) and to identify Mf2-binding proteins from A375 cells. Based on their function as known transcriptional regulators, a selection of the Mf2 domain-binding proteins (NPM1, TRIM28, and YB-1) have been validated using in vitro and cell-based assays. Interestingly, although NPM1, TRIM28, and YB-1 all bind to the Mf2 domain, they have differing amino acid specificities, demonstrating the degree of combinatorial diversity and specificity available through linear interaction motifs. PMID:21245151

Sotos syndrome: An interesting disorder with gigantism.

PubMed

Nalini, A; Biswas, Arundhati

2008-07-01

We report the case of a 16-year-old boy diagnosed to have Sotos syndrome, with rare association of bilateral primary optic atrophy and epilepsy. He presented with accelerated linear growth, facial gestalt, distinctive facial features, seizures and progressive diminution of vision in both eyes. He had features of gigantism from early childhood. An MRI showed that brain and endocrine functions were normal. This case is of interest, as we have to be aware of this not so rare disorder. In addition to the classic features, there were two unusual associations with Sotos syndrome in the patient.

Slipping rib syndrome in childhood.

PubMed

Mooney, D P; Shorter, N A

1997-07-01

Slipping rib syndrome is an unusual cause of lower chest and upper abdominal pain in children not mentioned in major pediatric surgical texts. The syndrome occurs when the medial fibrous attachments of the eighth, ninth, or tenth ribs are inadequate or ruptured, allowing their cartilage tip to slip superiorly and impinge on the intervening intercostal nerve. This may cause a variety of somatic and visceral complaints. Although the diagnosis may be made based on history and physical examination, lack of recognition of this disorder frequently leads to extensive diagnostic evaluations before definitive therapy. The authors report on four children who have this disorder.

Familial pseudoxanthoma elasticum associated with multiple comedones.

PubMed

Maarouf, Melody; Sharon, Victoria R; Sivamani, Raja K; Prakash, Neha; Bipin, T H; Davis, Tracy; Shi, Vivian Y

2017-09-15

Pseudoxanthoma elasticum (PXE) is an autosomal recessive disorder characterized by atypical elastic fibers that causes connective tissue abnormalities of the skin, eyes, and heart, among other organs. The disorder is rare, with a classic presentation of yellow-orange cobblestone-like papules on flexural areas, lax skin, ocular degeneration, and moribund vasculature in multiple organs. There is wide variability in the presentation of the affected organs [1]. We present two sisters with classic cutaneous findings of PXE with the additional unusual findings of numerous open comedones on the neck. To our knowledge, this is the first report of numerous open comedones in familial PXE.

Coeliac Disease With Rheumatoid Arthritis: An Unusual Association.

PubMed

Warjri, Synrang Batngen; Ete, Tony; Beyong, Taso; Barman, Bhupen; Lynrah, Kyrshanlang G; Nobin, Hage; Perme, Obang

2015-02-01

Coeliac disease has a significant association with many autoimmune disorders. It shares many common genetic and immunological features with other autoimmune diseases. Gluten, a gut-derived antigen, is the driver of the autoimmunity seen in coeliac disease. The altered intestinal permeability found in coeliac patients, coupled with a genetic predisposition and altered immunological response, may result in a systemic immune response that is directed against sites other than the gut. Gut-derived antigens may have a role in the pathogenesis of other autoimmune disorders including rheumatoid arthritis. Here we report a case of adult coeliac disease associated with rheumatoid arthritis.

Sotos syndrome: An interesting disorder with gigantism

PubMed Central

Nalini, A.; Biswas, Arundhati

2008-01-01

We report the case of a 16-year-old boy diagnosed to have Sotos syndrome, with rare association of bilateral primary optic atrophy and epilepsy. He presented with accelerated linear growth, facial gestalt, distinctive facial features, seizures and progressive diminution of vision in both eyes. He had features of gigantism from early childhood. An MRI showed that brain and endocrine functions were normal. This case is of interest, as we have to be aware of this not so rare disorder. In addition to the classic features, there were two unusual associations with Sotos syndrome in the patient. PMID:19893668

Circadian Rhythm Sleep-Wake Disorders.

PubMed

Pavlova, Milena

2017-08-01

The endogenous circadian rhythms are one of the cardinal processes that control sleep. They are self-sustaining biological rhythms with a periodicity of approximately 24 hours that may be entrained by external zeitgebers (German for time givers), such as light, exercise, and meal times. This article discusses the physiology of the circadian rhythms, their relationship to neurologic disease, and the presentation and treatment of circadian rhythm sleep-wake disorders. Classic examples of circadian rhythms include cortisol and melatonin secretion, body temperature, and urine volume. More recently, the impact of circadian rhythm on several neurologic disorders has been investigated, such as the timing of occurrence of epileptic seizures as well as neurobehavioral functioning in dementia. Further updates include a more in-depth understanding of the symptoms, consequences, and treatment of circadian sleep-wake disorders, which may occur because of extrinsic misalignment with clock time or because of intrinsic dysfunction of the brain. An example of extrinsic misalignment occurs with jet lag during transmeridian travel or with intrinsic circadian rhythm sleep-wake disorders such as advanced or delayed sleep-wake phase disorders. In advanced sleep-wake phase disorder, which is most common in elderly individuals, sleep onset and morning arousal are undesirably early, leading to impaired evening function with excessive sleepiness and sleep-maintenance insomnia with early morning awakening. By contrast, delayed sleep-wake phase disorder is characterized by an inability to initiate sleep before the early morning hours, with subsequent delayed rise time, leading to clinical symptoms of severe sleep-onset insomnia coupled with excessive daytime sleepiness in the morning hours, as patients are unable to "sleep in" to attain sufficient sleep quantity. Irregular sleep-wake rhythm disorder is misentrainment with patches of brief sleep and wakefulness spread throughout the day, leading to unstable sleep and waking behavioral patterns and an entirely idiosyncratic sleep-wake schedule. Familiarity with these major circadian rhythm sleep-wake disorder phenotypes and their overlap with other neurologic disorders is essential for the neurologist so that clinicians may intervene and improve patient functioning and quality of life.

Erysipelothrix rhusiopathiae endocarditis and presumed osteomyelitis

PubMed Central

Romney, Marc; Cheung, Stephen; Montessori, Valentina

2001-01-01

Erysipelothrix rhusiopathiae is known to cause infections in humans following exposure to decaying organic matter or animals colonized with the organism, such as swine and fish. Invasive infections with this organism are unusual and are manifested primarily as infective endocarditis. The present report is believed to be the first to report a case of E rhusiopathiae endocarditis and presumptive osteomyelitis. E rhusiopathiae appears to have intrinsic resistance to vancomycin. Because vancomycin is often used empirically for the treatment of endocarditis, rapid differentiation of E rhusiopathiae from other Gram-positive organisms is critical. In patients with endocarditis caused by a Gram-positive bacillus and epidemiological risk factors for E rhusiopathiae exposure, empirical treatment with vancomycin should be reconsidered. PMID:18159347

Erysipelothrix rhusiopathiae endocarditis and presumed osteomyelitis.

PubMed

Romney, M; Cheung, S; Montessori, V

2001-07-01

Erysipelothrix rhusiopathiae is known to cause infections in humans following exposure to decaying organic matter or animals colonized with the organism, such as swine and fish. Invasive infections with this organism are unusual and are manifested primarily as infective endocarditis. The present report is believed to be the first to report a case of E rhusiopathiae endocarditis and presumptive osteomyelitis. E rhusiopathiae appears to have intrinsic resistance to vancomycin. Because vancomycin is often used empirically for the treatment of endocarditis, rapid differentiation of E rhusiopathiae from other Gram-positive organisms is critical. In patients with endocarditis caused by a Gram-positive bacillus and epidemiological risk factors for E rhusiopathiae exposure, empirical treatment with vancomycin should be reconsidered.

Negative and Zero Thermal Expansion NiTi Superelastic Shape Memory Alloy by Microstructure Engineering

NASA Astrophysics Data System (ADS)

Sun, Qingping; Yu, Chao; Kang, Guozheng

2018-03-01

We report recent progress in tailoring the thermal expansion (TE) of nanocrystalline (NC) NiTi by microstructure hierarchical design and control without composition change. Fabrication and characterization methods are outlined and preliminary results of both experiment and mechanism-based modeling are presented to understand and get insight into the unusual TE phenomena. The important roles of the intrinsic thermal expansion anisotropy of B19' lattice and the suppression of phase transition by the extrinsic fabricated microstructure (cold rolling and annealing, grain size, defects, textures and volume fractions of nanoscaled B2 and B19' lattices) in the overall macroscopic TE behaviors of the superelastic NC NiTi polycrystal SMAs are emphasized.

Genealogy of an ancient protein family: the Sirtuins, a family of disordered members.

PubMed

Costantini, Susan; Sharma, Ankush; Raucci, Raffaele; Costantini, Maria; Autiero, Ida; Colonna, Giovanni

2013-03-05

Sirtuins genes are widely distributed by evolution and have been found in eubacteria, archaea and eukaryotes. While prokaryotic and archeal species usually have one or two sirtuin homologs, in humans as well as in eukaryotes we found multiple versions and in mammals this family is comprised of seven different homologous proteins being all NAD-dependent de-acylases. 3D structures of human SIRT2, SIRT3, and SIRT5 revealed the overall conformation of the conserved core domain but they were unable to give a structural information about the presence of very flexible and dynamically disordered regions, the role of which is still structurally and functionally unclear. Recently, we modeled the 3D-structure of human SIRT1, the most studied member of this family, that unexpectedly emerged as a member of the intrinsically disordered proteins with its long disordered terminal arms. Despite clear similarities in catalytic cores between the human sirtuins little is known of the general structural characteristics of these proteins. The presence of disorder in human SIRT1 and the propensity of these proteins in promoting molecular interactions make it important to understand the underlying mechanisms of molecular recognition that reasonably should involve terminal segments. The mechanism of recognition, in turn, is a prerequisite for the understanding of any functional activity. Aim of this work is to understand what structural properties are shared among members of this family in humans as well as in other organisms. We have studied the distribution of the structural features of N- and C-terminal segments of sirtuins in all known organisms to draw their evolutionary histories by taking into account average length of terminal segments, amino acid composition, intrinsic disorder, presence of charged stretches, presence of putative phosphorylation sites, flexibility, and GC content of genes. Finally, we have carried out a comprehensive analysis of the putative phosphorylation sites in human sirtuins confirming those sites already known experimentally for human SIRT1 and 2 as well as extending their topology to all the family to get feedback of their physiological functions and cellular localization. Our results highlight that the terminal segments of the majority of sirtuins possess a number of structural features and chemical and physical properties that strongly support their involvement in activities of recognition and interaction with other protein molecules. We also suggest how a multisite phosphorylation provides a possible mechanism by which flexible and intrinsically disordered segments of a sirtuin supported by the presence of positively or negatively charged stretches might enhance the strength and specificity of interaction with a particular molecular partner.

Effects of functional group mass variance on vibrational properties and thermal transport in graphene

DOE PAGES

Lindsay, L.; Kuang, Y.

2017-03-13

Intrinsic thermal resistivity critically depends on features of phonon dispersions dictated by harmonic interatomic forces and masses. We present the effects of functional group mass variance on vibrational properties and thermal conductivity (κ ) of functionalized graphene from first principles calculations. We also use graphane, a buckled graphene backbone with covalently bonded Hydrogen atoms on both sides, as the base material and vary the mass of the Hydrogen atoms to simulate the effect of mass variance from other functional groups. We find non-monotonic behavior of κ with increasing mass of the functional group and an unusual cross-over from acoustic-dominated tomore » optic-dominated thermal transport behavior. We connect this cross-over to changes in the phonon dispersion with varying mass which suppress acoustic phonon velocities, but also give unusually high velocity optic modes. Further, we show that out-of-plane acoustic vibrations contribute significantly more to thermal transport than in-plane acoustic modes despite breaking of a reflection symmetry based scattering selection rule responsible for their large contributions in graphene. Our work demonstrates the potential for manipulation and engineering of thermal transport properties in two dimensional materials toward targeted applications.« less

Effects of functional group mass variance on vibrational properties and thermal transport in graphene

NASA Astrophysics Data System (ADS)

Lindsay, L.; Kuang, Y.

2017-03-01

Intrinsic thermal resistivity critically depends on features of phonon dispersions dictated by harmonic interatomic forces and masses. Here we present the effects of functional group mass variance on vibrational properties and thermal conductivity (κ ) of functionalized graphene from first-principles calculations. We use graphane, a buckled graphene backbone with covalently bonded hydrogen atoms on both sides, as the base material and vary the mass of the hydrogen atoms to simulate the effect of mass variance from other functional groups. We find nonmonotonic behavior of κ with increasing mass of the functional group and an unusual crossover from acoustic-dominated to optic-dominated thermal transport behavior. We connect this crossover to changes in the phonon dispersion with varying mass which suppress acoustic phonon velocities, but also give unusually high velocity optic modes. Further, we show that out-of-plane acoustic vibrations contribute significantly more to thermal transport than in-plane acoustic modes despite breaking of a reflection-symmetry-based scattering selection rule responsible for their large contributions in graphene. This work demonstrates the potential for manipulation and engineering of thermal transport properties in two-dimensional materials toward targeted applications.

Effects of functional group mass variance on vibrational properties and thermal transport in graphene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lindsay, L.; Kuang, Y.

Intrinsic thermal resistivity critically depends on features of phonon dispersions dictated by harmonic interatomic forces and masses. We present the effects of functional group mass variance on vibrational properties and thermal conductivity (κ ) of functionalized graphene from first principles calculations. We also use graphane, a buckled graphene backbone with covalently bonded Hydrogen atoms on both sides, as the base material and vary the mass of the Hydrogen atoms to simulate the effect of mass variance from other functional groups. We find non-monotonic behavior of κ with increasing mass of the functional group and an unusual cross-over from acoustic-dominated tomore » optic-dominated thermal transport behavior. We connect this cross-over to changes in the phonon dispersion with varying mass which suppress acoustic phonon velocities, but also give unusually high velocity optic modes. Further, we show that out-of-plane acoustic vibrations contribute significantly more to thermal transport than in-plane acoustic modes despite breaking of a reflection symmetry based scattering selection rule responsible for their large contributions in graphene. Our work demonstrates the potential for manipulation and engineering of thermal transport properties in two dimensional materials toward targeted applications.« less

Evaluation of laser speckle contrast imaging as an intrinsic method to monitor blood brain barrier integrity

PubMed Central

Dufour, Suzie; Atchia, Yaaseen; Gad, Raanan; Ringuette, Dene; Sigal, Iliya; Levi, Ofer

2013-01-01

The integrity of the blood brain barrier (BBB) can contribute to the development of many brain disorders. We evaluate laser speckle contrast imaging (LSCI) as an intrinsic modality for monitoring BBB disruptions through simultaneous fluorescence and LSCI with vertical cavity surface emitting lasers (VCSELs). We demonstrated that drug-induced BBB opening was associated with a relative change of the arterial and venous blood velocities. Cross-sectional flow velocity ratio (veins/arteries) decreased significantly in rats treated with BBB-opening drugs, ≤0.81 of initial values. PMID:24156049

Double disordered YBCO coated conductors of industrial scale: high currents in high magnetic field

NASA Astrophysics Data System (ADS)

Abraimov, D.; Ballarino, A.; Barth, C.; Bottura, L.; Dietrich, R.; Francis, A.; Jaroszynski, J.; Majkic, G. S.; McCallister, J.; Polyanskii, A.; Rossi, L.; Rutt, A.; Santos, M.; Schlenga, K.; Selvamanickam, V.; Senatore, C.; Usoskin, A.; Viouchkov, Y. L.

2015-11-01

A significant increase of critical current in high magnetic field, up to 31 T, was recorded in long tapes manufactured by employing a double-disorder route. In a double-disordered high-temperature superconductor (HTS), a superimposing of intrinsic and extrinsic disorder takes place in a way that (i) the intrinsic disorder is caused by local stoichiometry deviations that lead to defects of crystallinity that serve as pining centers in the YBa2Cu3O x-δ matrix and (ii) the extrinsic disorder is introduced via embedded atoms or particles of foreign material (e.g. barium zirconate), which create a set of lattice defects. We analyzed possible technological reasons for this current gain. The properties of these tapes over a wider field-temperature range as well as field anisotropy were also studied. Record values of critical current as high as 309 A at 31 T, 500 A at 18 Tm and 1200 A at 5 T were found in 4 mm wide tape at 4.2 K and B perpendicular to tape surface. HTS layers were processed in medium-scale equipment that allows a maximum batch length of 250 m while 22 m long batches were provided for investigation. Abnormally high ratios (up to 10) of critical current density measured at 4.2 K, 19 T to critical current density measured at 77 K, self-field were observed in tapes with the highest in-field critical current. Anisotropy of the critical current as well as angular dependences of n and α values were investigated. The temperature dependence of critical current is presented for temperatures between 4.2 and 40 K. Prospects for the suppression of the dog-bone effect by Cu plating and upscale of processing chain to >500 m piece length are discussed.

Expanding the proteome: disordered and alternatively-folded proteins

PubMed Central

Dyson, H. Jane

2011-01-01

Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well-structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question “why would a particular domain need to be unstructured?” are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but of partially structured and highly dynamic members of the disorder-order continuum. PMID:21729349

[Ulnar nerve tunnel syndrome of the elbow and an occupational disorder. Analysis of socio-professional and physical parameters].

PubMed

Pellieux, S; Fouquet, B; Lasfargues, G

2001-05-01

The ulnar nerve tunnel syndrome at the elbow is the second frequently tunnel syndrome, registered as an occupational disorder. The musculoskeletal troubles of the upper limb are now a public health challenge. These disorders allow manifold risk factors related to the work state, extrinsic to the patient, and related to individual factors, or intrinsic. In the same venture, 25 patients with a UNTS, declared as an occupational disorder, have been compared to 48 individuals (T). Intrinsic (physical and psychological) and extrinsic parameters have been evaluated by a questionnaire, physical examination completed by an investigation in the venture. The Nottingham Health Profile was performed by all the individuals. All the cases of UNTS were observed after an increase of the production and a change in the work organization. Only 50% of the declared UNTS have a typical topography of the pain. No UNTS patient had neurological objective motor and sensitive deficit. 52% of the UNTS patients had diffused physical disorders comparatively to 17% of the T population. Stress events were observed more frequently in the UNTS population than in the T population: in the living area, in respectively 96% and 52% of the cases, at the work place in 12% and 2%. 50% of the UNTS population was distress comparatively to 17% of the T population. The NHP score was significantly higher in the UNTS population than the T population. These data confirm the mutual influences of individual factors, physical and psychological, and of workplace factors in the occurrence of painful disorders related to an occupational activity. The therapeutic approach of these patients must be done with a physical, psychological and social evaluation.

Alterations of Intrinsic Brain Connectivity Patterns in Depression and Bipolar Disorders: A Critical Assessment of Magnetoencephalography-Based Evidence

PubMed Central

Alamian, Golnoush; Hincapié, Ana-Sofía; Combrisson, Etienne; Thiery, Thomas; Martel, Véronique; Althukov, Dmitrii; Jerbi, Karim

2017-01-01

Despite being the object of a thriving field of clinical research, the investigation of intrinsic brain network alterations in psychiatric illnesses is still in its early days. Because the pathological alterations are predominantly probed using functional magnetic resonance imaging (fMRI), many questions about the electrophysiological bases of resting-state alterations in psychiatric disorders, particularly among mood disorder patients, remain unanswered. Alongside important research using electroencephalography (EEG), the specific recent contributions and future promise of magnetoencephalography (MEG) in this field are not fully recognized and valued. Here, we provide a critical review of recent findings from MEG resting-state connectivity within major depressive disorder (MDD) and bipolar disorder (BD). The clinical MEG resting-state results are compared with those previously reported with fMRI and EEG. Taken together, MEG appears to be a promising but still critically underexploited technique to unravel the neurophysiological mechanisms that mediate abnormal (both hyper- and hypo-) connectivity patterns involved in MDD and BD. In particular, a major strength of MEG is its ability to provide source-space estimations of neuromagnetic long-range rhythmic synchronization at various frequencies (i.e., oscillatory coupling). The reviewed literature highlights the relevance of probing local and interregional rhythmic synchronization to explore the pathophysiological underpinnings of each disorder. However, before we can fully take advantage of MEG connectivity analyses in psychiatry, several limitations inherent to MEG connectivity analyses need to be understood and taken into account. Thus, we also discuss current methodological challenges and outline paths for future research. MEG resting-state studies provide an important window onto perturbed spontaneous oscillatory brain networks and hence supply an important complement to fMRI-based resting-state measurements in psychiatric populations. PMID:28367127

Biophysical characterization of the structural change of Nopp140, an intrinsically disordered protein, in the interaction with CK2α

DOE Office of Scientific and Technical Information (OSTI.GOV)

Na, Jung-Hyun; Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792; Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760

2016-08-19

Nucleolar phosphoprotein 140 (Nopp140) is a nucleolar protein, more than 80% of which is disordered. Previous studies have shown that the C-terminal region of Nopp140 (residues 568–596) interacts with protein kinase CK2α, and inhibits the catalytic activity of CK2. Although the region of Nopp140 responsible for the interaction with CK2α was identified, the structural features and the effect of this interaction on the structure of Nopp140 have not been defined due to the difficulty of structural characterization of disordered protein. In this study, the disordered feature of Nopp140 and the effect of CK2α on the structure of Nopp140 were examinedmore » using single-molecule fluorescence resonance energy transfer (smFRET) and electron paramagnetic resonance (EPR). The interaction with CK2α was increased conformational rigidity of the CK2α-interacting region of Nopp140 (Nopp140C), suggesting that the disordered and flexible conformation of Nopp140C became more rigid conformation as it binds to CK2α. In addition, site specific spin labeling and EPR analysis confirmed that the residues 574–589 of Nopp140 are critical for binding to CK2α. Similar technical approaches can be applied to analyze the conformational changes in other IDPs during their interactions with binding partners. - Highlights: • Nopp140 is intrinsically disordered protein (IDP). • Conformation of Nopp140 became more rigid conformation due to interaction with CK2α. • smFRET and EPR could be applied to analyze the structural changes of IDPs.« less

Magnetic Alignment of Block Copolymer Microdomains by Intrinsic Chain Anisotropy.

PubMed

Rokhlenko, Yekaterina; Gopinadhan, Manesh; Osuji, Chinedum O; Zhang, Kai; O'Hern, Corey S; Larson, Steven R; Gopalan, Padma; Majewski, Paweł W; Yager, Kevin G

2015-12-18

We examine the role of intrinsic chain susceptibility anisotropy in magnetic field directed self-assembly of a block copolymer using in situ x-ray scattering. Alignment of a lamellar mesophase is observed on cooling across the disorder-order transition with the resulting orientational order inversely proportional to the cooling rate. We discuss the origin of the susceptibility anisotropy, Δχ, that drives alignment and calculate its magnitude using coarse-grained molecular dynamics to sample conformations of surface-tethered chains, finding Δχ≈2×10^{-8}. From field-dependent scattering data, we estimate that grains of ≈1.2  μm are present during alignment. These results demonstrate that intrinsic anisotropy is sufficient to support strong field-induced mesophase alignment and suggest a versatile strategy for field control of orientational order in block copolymers.

The Impact of O-Glycan Chemistry on the Stability of Intrinsically Disordered Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beckham, Gregg T; Prates, Erica T; Crowley, Michael F

2018-03-02

Protein glycosylation is a diverse post-translational modification that serves myriad biological functions. O-linked glycans in particular vary widely in extent and chemistry in eukaryotes, with secreted proteins from fungi and yeast commonly exhibiting O-mannosylation in intrinsically disordered regions of proteins, likely for proteolysis protection, among other functions. However, it is not well understood why mannose is often the preferred glycan, and more generally, if the neighboring protein sequence and glycan have coevolved to protect against proteolysis in glycosylated intrinsically disordered proteins (IDPs). Here, we synthesized variants of a model IDP, specifically a natively O-mannosylated linker from a fungal enzyme, withmore » a-O-linked mannose, glucose, and galactose moieties, along with a non-glycosylated linker. Upon exposure to thermolysin, O-mannosylation, by far, provides the highest extent of proteolysis protection. To explain this observation, extensive molecular dynamics simulations were conducted, revealing that the axial configuration of the C2-hydroxyl group (2-OH) of a-mannose adjacent to the glycan-peptide bond strongly influences the conformational features of the linker. Specifically, a-mannose restricts the torsions of the IDP main chain more than other glycans whose equatorial 2-OH groups exhibit interactions that favor perpendicular glycan-protein backbone orientation. We suggest that IDP stiffening due to O-mannosylation impairs protease action, with contributions from protein-glycan interactions, protein flexibility, and protein stability. Our results further imply that resistance to proteolysis is an important driving force for evolutionary selection of a-mannose in eukaryotic IDPs, and more broadly, that glycan motifs for proteolysis protection likely coevolve with the protein sequence to which they attach.« less

Human cytomegalovirus phosphoproteins are hypophosphorylated and intrinsically disordered.

PubMed

Rieder, Franz J J; Kastner, Marie-Theres; Hartl, Markus; Puchinger, Martin G; Schneider, Martina; Majdic, Otto; Britt, William J; Djinović-Carugo, Kristina; Steininger, Christoph

2017-03-01

Protein phosphorylation has important regulatory functions in cell homeostasis and is tightly regulated by kinases and phosphatases. The tegument of human cytomegalovirus (CMV) contains not only several proteins reported to be extensively phosphorylated but also cellular protein phosphatases (PP1 and PP2A). To investigate this apparent inconsistency, we evaluated the phosphorylation status of the tegument proteins pUL32 and pp65 by enzymatic dephosphorylation and MS. Enzymatic dephosphorylation with bacterial λ phosphatase, but not with PP1, shifted the pUL32-specific signal on reducing SDS-PAGE from ~150 to ~148 kDa, a mass still much larger than the ~118 kDa obtained from our diffusion studies and from the calculated protein mass of ~113 kDa. Remarkably, inhibition of phosphatases through treatment with the phosphatase inhibitors calyculin A and okadaic acid resulted in a shift to ~190 or ~180 kDa, respectively, indicating that a considerable number of potential phosphorylated residues on pUL32 are not phosphorylated under normal conditions. MS revealed a general state of hypophosphorylation of CMV phosphoproteins with only 17 phosphorylated residues detected on pUL32 and 19 on pp65, respectively. Moreover, bioinformatics analysis shows that the C-terminal two-thirds of pUL32 are intrinsically disordered and that most phosphorylations map to this region. In conclusion, we show that important CMV tegument proteins are indeed phosphorylated, though to a lesser extent than previously reported, and the difference in mobility on SDS-PAGE and calculated mass of pUL32 may not be attributed to phosphorylation but more likely due to the partially intrinsically disordered nature of pUL32.

Partner-Mediated Polymorphism of an Intrinsically Disordered Protein.

PubMed

Bignon, Christophe; Troilo, Francesca; Gianni, Stefano; Longhi, Sonia

2017-11-29

Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (N TAIL ) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, N TAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the N TAIL /hsp70 complex. Using mutational studies combined with a protein complementation assay based on green fluorescent protein reconstitution, we have investigated both N TAIL /XD and N TAIL /hsp70 interactions. Although the same N TAIL region binds the two partners, the binding mechanisms are different. Hsp70 binding is much more tolerant of MoRE substitutions than XD, and the majority of substitutions lead to an increased N TAIL /hsp70 interaction strength. Furthermore, while an increased and a decreased α-helicity of the MoRE lead to enhanced and reduced interaction strength with XD, respectively, the impact on hsp70 binding is negligible, suggesting that the MoRE does not adopt an α-helical conformation once bound to hsp70. Here, by showing that the α-helical conformation sampled by the free form of the MoRE does not systematically commit it to adopt an α-helical conformation in the bound form, we provide an example of partner-mediated polymorphism of an IDP and of the relative insensitiveness of the bound structure to the pre-recognition state. The present results therefore contribute to shed light on the molecular mechanisms by which IDPs recognize different partners. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetic recognition of the retinoblastoma tumor suppressor by a specific protein target.

PubMed

Chemes, Lucía B; Sánchez, Ignacio E; de Prat-Gay, Gonzalo

2011-09-16

The retinoblastoma tumor suppressor (Rb) plays a key role in cell cycle control and is linked to various types of human cancer. Rb binds to the LxCxE motif, present in a number of cellular and viral proteins such as AdE1A, SV40 large T-antigen and human papillomavirus (HPV) E7, all instrumental in revealing fundamental mechanisms of tumor suppression, cell cycle control and gene expression. A detailed kinetic study of RbAB binding to the HPV E7 oncoprotein shows that an LxCxE-containing E7 fragment binds through a fast two-state reaction strongly favored by electrostatic interactions. Conversely, full-length E7 binds through a multistep process involving a pre-equilibrium between E7 conformers, a fast electrostatically driven association step guided by the LxCxE motif and a slow conformational rearrangement. This kinetic complexity arises from the conformational plasticity and intrinsically disordered nature of E7 and from multiple interaction surfaces present in both proteins. Affinity differences between E7N domains from high- and low-risk types are explained by their dissociation rates. In fact, since Rb is at the center of a large protein interaction network, fast and tight recognition provides an advantage for disruption by the viral proteins, where the balance of physiological and pathological interactions is dictated by kinetic ligand competition. The localization of the LxCxE motif within an intrinsically disordered domain provides the fast, diffusion-controlled interaction that allows viral proteins to outcompete physiological targets. We describe the interaction mechanism of Rb with a protein ligand, at the same time an LxCxE-containing model target, and a paradigmatic intrinsically disordered viral oncoprotein. Copyright © 2011 Elsevier Ltd. All rights reserved.

Munchausen Syndrome and the Wide Spectrum of Factitious Disorders.

PubMed

Tatu, Laurent; Aybek, Selma; Bogousslavsky, Julien

2018-01-01

Since its initial description in 1851, Munchausen syndrome has been widely used interchangeably with factitious disorder. Nevertheless, this syndrome is only one form of factitious disorder that is both severe and chronic. The syndrome was named after Karl Friedrich Hieronymus, Baron von Münchhausen (1720-1797), a German nobleman who became famous as a narrator of false and exaggerated exploits. His name was progressively corrupted to Munchausen. Factitious disorders and Munchausen syndrome remain a great diagnosis challenge for physicians. All medical specialities are concerned by these disorders. The diagnosis process involves a first step to exclude an unusual presentation of a common medical condition. The second step consists of excluding somatoform disorders and malingering. Unfortunately, the boundaries between factitious disorder, somatization, and malingering are often unclear. In 1977, the term "Munchausen's syndrome by proxy" was coined to define a situation where a person produces false symptoms in another one, especially a child. This term was extended to similar interactions between human and pets. Because varied conditions have been included in the definition of this syndrome, there is ongoing debate about alternative names. © 2018 S. Karger AG, Basel.

Ruminations on Hildegard of Bingen (1098-1179) and autism.

PubMed

Ranft, Patricia

2014-05-01

The article brings together contemporary research on autism spectrum disorder and historical sources concerning the medical condition of a 12th century nun, Hildegard of Bingen, to test two hypotheses: first, that Hildegard manifested disabilities that meet the criteria for autism spectrum disorder and, second, that medieval monasticism was unwittingly well-suited to treat Hildegard's condition. Abundant Hildegardian sources document traces of autism spectrum disorder behaviour in Hildegard's unusual childhood and the composite picture that emerges, when these individual traits are gathered together, is consistent with an autism spectrum disorder diagnosis. The role monasticism played in helping Hildegard overcome these behaviours is documented and aspects that monasticism shares with modern autism spectrum disorder treatment programs are identified. By recognizing the presence of autism spectrum disorder traits in a major cultural leader of another era and by identifying the type of life she lived while those traits were minimized, we gain insight into the history of autism, medieval monastic life and effective elements of autism spectrum disorder treatment. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective.

PubMed

Maxwell, Peter I; Popelier, Paul L A

2017-11-05

Accurate description of the intrinsic preferences of amino acids is important to consider when developing a biomolecular force field. In this study, we use a modern energy partitioning approach called Interacting Quantum Atoms to inspect the cause of the φ and ψ torsional preferences of three dipeptides (Gly, Val, and Ile). Repeating energy trends at each of the molecular, functional group, and atomic levels are observed across both (1) the three amino acids and (2) the φ/ψ scans in Ramachandran plots. At the molecular level, it is surprisingly electrostatic destabilization that causes the high-energy regions in the Ramachandran plot, not molecular steric hindrance (related to the intra-atomic energy). At the functional group and atomic levels, the importance of key peptide atoms (O i -1 , C i , N i , N i +1 ) and some sidechain hydrogen atoms (H γ ) are identified as responsible for the destabilization seen in the energetically disfavored Ramachandran regions. Consistently, the O i -1 atoms are particularly important for the explanation of dipeptide intrinsic behavior, where electrostatic and steric destabilization unusually complement one another. The findings suggest that, at least for these dipeptides, it is the peptide group atoms that dominate the intrinsic behavior, more so than the sidechain atoms. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Aberrant topology of striatum's connectivity is associated with the number of episodes in depression.

PubMed

Meng, Chun; Brandl, Felix; Tahmasian, Masoud; Shao, Junming; Manoliu, Andrei; Scherr, Martin; Schwerthöffer, Dirk; Bäuml, Josef; Förstl, Hans; Zimmer, Claus; Wohlschläger, Afra M; Riedl, Valentin; Sorg, Christian

2014-02-01

In major depressive disorder, depressive episodes reoccur in ∼60% of cases; however, neural mechanisms of depressive relapse are poorly understood. Depressive episodes are characterized by aberrant topology of the brain's intrinsic functional connectivity network, and the number of episodes is one of the most important predictors for depressive relapse. In this study we hypothesized that specific changes of the topology of intrinsic connectivity interact with the course of episodes in recurrent depressive disorder. To address this hypothesis, we investigated which changes of connectivity topology are associated with the number of episodes in patients, independently of current symptoms and disease duration. Fifty subjects were recruited including 25 depressive patients (two to 10 episodes) and 25 gender- and age-matched control subjects. Resting-state functional magnetic resonance imaging, Harvard-Oxford brain atlas, wavelet-transformation of atlas-shaped regional time-series, and their pairwise Pearson's correlation were used to define individual connectivity matrices. Matrices were analysed by graph-based methods, resulting in outcome measures that were used as surrogates of intrinsic network topology. Topological scores were subsequently compared across groups, and, for patients only, related with the number of depressive episodes and current symptoms by partial correlation analysis. Concerning the whole brain connectivity network of patients, small-world topology was preserved but global efficiency was reduced and global betweenness-centrality increased. Aberrant nodal efficiency and centrality of regional connectivity was found in the dorsal striatum, inferior frontal and orbitofrontal cortex as well as in the occipital and somatosensory cortex. Inferior frontal changes were associated with current symptoms, whereas aberrant right putamen network topology was associated with the number of episodes. Results were controlled for effects of total grey matter volume, medication, and total disease duration. This finding provides first evidence that in major depressive disorder aberrant topology of the right putamen's intrinsic connectivity pattern is associated with the course of depressive episodes, independently of current symptoms, medication status and disease duration. Data suggest that the reorganization of striatal connectivity may interact with the course of episodes in depression thereby contributing to depressive relapse risk.

[Münchhausen syndrome by proxy].

PubMed

Le Heuzey, M-F; Mouren, M-C

2008-01-01

Münchhausen syndrome by proxy is a factitious disorder, a disease produced or simulated by a parent, the mother in most cases. Clinical presentation is miscellaneous (factitious bleeding, epilepsy, apnea are frequent) and unusual. Physicians participate in the abuse by their therapeutic and diagnostical measures. It is very important to think about this diagnostic in any ambiguous situation in order to evaluate and protect the child.

Airway Autoimmune Inflammatory Response (AAIR) Syndrome: An Asthma-Autoimmune Overlap Disorder?

PubMed

Spencer, Chantal Y; Millman, Jennifer; Veiga, Keila; Vicencio, Alfin G

2018-02-15

Asthma encompasses numerous phenotypes that may require alternate approaches to diagnosis and therapy, particularly for patients whose symptoms remain poorly controlled despite escalating treatment. We describe 3 patients with apparent asthma who demonstrated unusual findings on cryobiopsy by flexible bronchoscopy and responded to therapy directed against autoimmune disease. Copyright © 2018 by the American Academy of Pediatrics.

Did Michelangelo (1475-1564) have high-functioning autism?

PubMed

Arshad, Muhammad; Fitzgerald, Michael

2004-05-01

In this paper evidence is presented that Michelangelo met the criteria for Asperger's disorder, or high-functioning autism. The evidence relates to his single-minded work routine, unusual lifestyle, limited interests, poor social and communication skills, and issues of life control. Depression and various medical conditions, including gout, renal colic and renal stones, did not stop his obsessive working habits.

Aerophagia and belching after herpes simplex encephalitis.

PubMed

Scheid, Rainer; Teich, Niels; Schroeter, Matthias L

2008-03-01

The etiology of abnormal belching is not known. Currently, it is being subsumed under "functional gastroduodenal disorders." Here, we report the unusual case history of a patient who developed aerophagia and consecutive excessive belching in association with herpes simplex encephalitis. The case report adds to the limited information about potential organic geneses of belching. Implications for possible medical therapies are discussed.

Munchausen syndrome: Playing sick or sick player

PubMed Central

Prakash, Jyoti; Das, R. C.; Srivastava, K.; Patra, P.; Khan, S. A.; Shashikumar, R.

2014-01-01

Munchausen syndrome is rare factitious disorder which entails frequent hospitalization, pathological lying and intentional production of symptoms for sick role. Management requires collateral history taking, sound clinical approach, exclusion of organicity and addressing psychological issues. A case which presented with unusual symptoms of similar dimension is discussed here. The case brings out finer nuances in evaluation and management of this entity. PMID:25535450

Hemophilia Care in the Pediatric Age

PubMed Central

Bertamino, Marta; Riccardi, Francesca; Banov, Laura; Svahn, Johanna; Molinari, Angelo Claudio

2017-01-01

Hemophilia is the most common of the severe bleeding disorders and if not properly managed since early infancy can lead to chronic disease and lifelong disabilities. However, it enjoys the most efficacious and safe treatment among the most prevalent monogenic disorders. Hemophilia should be considered in the neonatal period in the case of unusual bleeding or in the case of positive family history. Later, hemophilia should be suspected mainly in males because of abnormal bruising/bleeding or unusual bleeding following invasive procedures—for example, tonsillectomy or circumcision. Prophylactic treatment that is started early with clotting-factor concentrates has been shown to prevent hemophilic arthropathy and is, therefore, the gold standard of care for hemophilia A and B in most countries with adequate resources. Central venous access catheters and arterovenous fistulas play an important role in the management of hemophilia children requiring repeated and/or urgent administration of coagulation factor concentrates. During childhood and adolescence, personalized treatment strategies that suit the patient and his lifestyle are essential to ensure optimal outcomes. Physical activity is important and can contribute to better coordination, endurance, flexibility and strength. The present article focuses also on questions frequently posed to pediatric hematologists like vaccinations, day-care/school access and dental care. PMID:28534860

Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

PubMed

Lindström, Ida; Dogan, Jakob

2017-08-15

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.

Recognition and treatment of neuropsychiatric disturbances in Parkinson's disease.

PubMed

Akbar, Umer; Friedman, Joseph H

2015-01-01

The non-motor symptoms of Parkinson's disease (PD) have been attracting increasing attention due to their ubiquitous nature and their often devastating effects on the quality of life. Behavioral problems in PD include dementia, depression, apathy, fatigue, anxiety, psychosis, akathisia, personality change, sleep disorders and impulse control disorders. Some of these are intrinsic to the neuropathology while others occur as an interplay between pathology, psychology and pharmacology. While few data exist for guiding therapy, enough is known to guide therapy in a rational manner.

Superconductivity in disordered thin films: giant mesoscopic fluctuations.

PubMed

Skvortsov, M A; Feigel'man, M V

2005-07-29

We discuss the intrinsic inhomogeneities of superconductive properties of uniformly disordered thin films with a large dimensionless conductance g. It is shown that mesoscopic fluctuations, which usually contain a small factor 1/g, are crucially enhanced near the critical conductance g(cF) > 1 where superconductivity is destroyed at T = 0 due to Coulomb suppression of the Cooper attraction. This leads to strong spatial fluctuations of the local transition temperature and thus to the percolative nature of the thermal superconductive transition.

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Jianfeng, E-mail: hjf@bit.edu.cn; Dai, Jin, E-mail: daijing491@gmail.com; Li, Jing, E-mail: jinglichina@139.com

The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regimemore » where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.« less

Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Warren, Christopher; Matsui, Tsutomu; Karp, Jerome M.

Here, nucleoplasmin (Npm) is a highly conserved histone chaperone responsible for the maternal storage and zygotic release of histones H2A/H2B. Npm contains a pentameric N-terminal core domain and an intrinsically disordered C-terminal tail domain. Though intrinsically disordered regions are common among histone chaperones, their roles in histone binding and chaperoning remain unclear. Using an NMR-based approach, here we demonstrate that the Xenopus laevis Npm tail domain controls the binding of histones at its largest acidic stretch (A2) via direct competition with both the C-terminal basic stretch and basic nuclear localization signal. NMR and small-angle X-ray scattering (SAXS) structural analyses allowedmore » us to construct models of both the tail domain and the pentameric complex. Functional analyses demonstrate that these competitive intramolecular interactions negatively regulate Npm histone chaperone activity in vitro. Together these data establish a potentially generalizable mechanism of histone chaperone regulation via dynamic and specific intramolecular shielding of histone interaction sites.« less

Phosphorylation of an intrinsically disordered segment in Ets1 shifts conformational sampling toward binding-competent substates.

PubMed

Bui, Jennifer M; Gsponer, Jörg

2014-08-05

Functions of many proteins are affected by posttranslational modifications of intrinsically disordered (ID) regions, yet little is known about the underlying molecular mechanisms. By combining molecular dynamics simulations and protein docking, we demonstrate that the addition of phosphates to an ID segment adjacent to the PNT domain of Ets1 directs conformational sampling toward substates that are most compatible with high-affinity binding of the TAZ1 domain of its coactivator CBP. The phosphate charges disrupt salt bridges and thereby open a hydrophobic cleft and expose hydrophobic residues at the ID N terminus. The structure of the PNT-TAZ1 complex that we determined shows that PNT binds to TAZ1 via these hydrophobic regions in a similar manner to how it interacts with other partners. Our calculations reveal a dual effect of phosphorylation in that it changes the dynamics of PNT so that it becomes more compatible for TAZ1 binding and increases complementarity with this binding partner. Copyright © 2014 Elsevier Ltd. All rights reserved.

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

NASA Astrophysics Data System (ADS)

Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

2017-06-01

Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release

DOE PAGES

Warren, Christopher; Matsui, Tsutomu; Karp, Jerome M.; ...

2017-12-20

Here, nucleoplasmin (Npm) is a highly conserved histone chaperone responsible for the maternal storage and zygotic release of histones H2A/H2B. Npm contains a pentameric N-terminal core domain and an intrinsically disordered C-terminal tail domain. Though intrinsically disordered regions are common among histone chaperones, their roles in histone binding and chaperoning remain unclear. Using an NMR-based approach, here we demonstrate that the Xenopus laevis Npm tail domain controls the binding of histones at its largest acidic stretch (A2) via direct competition with both the C-terminal basic stretch and basic nuclear localization signal. NMR and small-angle X-ray scattering (SAXS) structural analyses allowedmore » us to construct models of both the tail domain and the pentameric complex. Functional analyses demonstrate that these competitive intramolecular interactions negatively regulate Npm histone chaperone activity in vitro. Together these data establish a potentially generalizable mechanism of histone chaperone regulation via dynamic and specific intramolecular shielding of histone interaction sites.« less

Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21

PubMed Central

Wang, Yuefeng; Fisher, John C.; Mathew, Rose; Ou, Li; Otieno, Steve; Sublett, Jack; Xiao, Limin; Chen, Jianhan; Roussel, Martine F.; Kriwacki, Richard W.

2011-01-01

Traditionally, well-defined three-dimensional structure was thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently exhibit “binding diversity” by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and herein report that the cyclin-dependent kinase (Cdk) inhibitor, p21Cip1, adaptively binds to and inhibits the various Cdk/cyclin complexes that regulate eukaryotic cell division. Based on results from NMR spectroscopy, and biochemical and cellular assays, we show that structural adaptability of a helical sub-domain within p21 termed LH enables two other sub-domains termed D1 and D2 to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk/cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes. PMID:21358637

Aspects of structural landscape of human islet amyloid polypeptide

NASA Astrophysics Data System (ADS)

He, Jianfeng; Dai, Jin; Li, Jing; Peng, Xubiao; Niemi, Antti J.

2015-01-01

The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones.

PubMed

Barik, Sailen

2018-01-01

The two classical immunophilin families, found essentially in all living cells, are: cyclophilin (CYN) and FK506-binding protein (FKBP). We previously reported a novel class of immunophilins that are natural chimera of these two, which we named dual-family immunophilin (DFI). The DFIs were found in either of two conformations: CYN-linker-FKBP (CFBP) or FKBP-3TPR-CYN (FCBP). While the 3TPR domain can serve as a flexible linker between the FKBP and CYN modules in the FCBP-type DFI, the linker sequences in the CFBP-type DFIs are relatively short, diverse in sequence, and contain no discernible motif or signature. Here, I present several lines of computational evidence that, regardless of their primary structure, these CFBP linkers are intrinsically disordered. This report provides the first molecular foundation for the model that the CFBP linker acts as an unstructured, flexible loop, allowing the two flanking chaperone modules function independently while linked in cis , likely to assist in the folding of multisubunit client complexes.

Leptin receptor signaling in T cells is required for Th17 differentiation.

PubMed

Reis, Bernardo S; Lee, Kihyun; Fanok, Melania H; Mascaraque, Cristina; Amoury, Manal; Cohn, Lillian B; Rogoz, Aneta; Dallner, Olof S; Moraes-Vieira, Pedro M; Domingos, Ana I; Mucida, Daniel

2015-06-01

The hormone leptin plays a key role in energy homeostasis, and the absence of either leptin or its receptor (LepR) leads to severe obesity and metabolic disorders. To avoid indirect effects and to address the cell-intrinsic role of leptin signaling in the immune system, we conditionally targeted LepR in T cells. In contrast with pleiotropic immune disorders reported in obese mice with leptin or LepR deficiency, we found that LepR deficiency in CD4(+) T cells resulted in a selective defect in both autoimmune and protective Th17 responses. Reduced capacity for differentiation toward a Th17 phenotype by lepr-deficient T cells was attributed to reduced activation of the STAT3 and its downstream targets. This study establishes cell-intrinsic roles for LepR signaling in the immune system and suggests that leptin signaling during T cell differentiation plays a crucial role in T cell peripheral effector function. Copyright © 2015 by The American Association of Immunologists, Inc.

An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Daisy  W.; Borek, Dominika; Luthra, Priya

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNP NTD complex, solved to 3.7 Å resolution, reveals how NPBP peptidemore » occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.« less

Intrinsic motivation as a mediator of relationships between symptoms and functioning among individuals with schizophrenia spectrum disorders in a diverse urban community.

PubMed

Yamada, Ann-Marie; Lee, Karen K; Dinh, Tam Q; Barrio, Concepción; Brekke, John S

2010-01-01

This study investigated intrinsic motivation as a mediator of the relationship between clinical symptoms and functioning. The mediation model was tested with a sample of 166 adults with schizophrenia spectrum disorders attending psychosocial rehabilitation programs in a diverse urban community. Ethnic minority status was examined as a moderator of the mediation model. Motivation was measured using items reflecting intrapsychic drive. Symptoms were assessed with the expanded Brief Psychiatric Rating Scale and functioning with the Role Functioning Scale. Motivation was a significant mediator of the relationship between functioning and all symptom scores; fully mediating the relationship between functioning and negative, disorganized, and global symptoms, and partially mediating the relationship between positive symptoms and functioning. Motivation scores between ethnic minority and nonminority individuals differed significantly (p < 0.05), but no moderation effect was indicated. The strong mediation effect schizophrenia of motivation on the symptoms-functioning relationship supports future work to translate findings into effective recovery-oriented services.

Intrinsic Motivation as a Mediator of Relationships Between Symptoms and Functioning Among Individuals With Schizophrenia Spectrum Disorders in a Diverse Urban Community

PubMed Central

Yamada, Ann-Marie; Lee, Karen K.; Dinh, Tam Q.; Barrio, Concepción; Brekke, John S.

2010-01-01

This study investigated intrinsic motivation as a mediator of the relationship between clinical symptoms and functioning. The mediation model was tested with a sample of 166 adults with schizophrenia spectrum disorders attending psychosocial rehabilitation programs in a diverse urban community. Ethnic minority status was examined as a moderator of the mediation model. Motivation was measured using items reflecting intrapsychic drive. Symptoms were assessed with the expanded Brief Psychiatric Rating Scale and functioning with the Role Functioning Scale. Motivation was a significant mediator of the relationship between functioning and all symptom scores; fully mediating the relationship between functioning and negative, disorganized, and global symptoms, and partially mediating the relationship between positive symptoms and functioning. Motivation scores between ethnic minority and nonminority individuals differed significantly (p < 0.05), but no moderation effect was indicated. The strong mediation effect schizophrenia of motivation on the symptoms-functioning relationship supports future work to translate findings into effective recovery-oriented services. PMID:20061866

An intrinsically disordered peptide from Ebola virus VP35 controls viral RNA synthesis by modulating nucleoprotein-RNA interactions

DOE PAGES

Leung, Daisy  W.; Borek, Dominika; Luthra, Priya; ...

2015-04-01

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNP NTD complex, solved to 3.7 Å resolution, reveals how NPBP peptidemore » occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.« less

An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.

PubMed

Leung, Daisy W; Borek, Dominika; Luthra, Priya; Binning, Jennifer M; Anantpadma, Manu; Liu, Gai; Harvey, Ian B; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; Shabman, Reed S; Chiu, Wah; Davey, Robert A; Otwinowski, Zbyszek; Basler, Christopher F; Amarasinghe, Gaya K

2015-04-21

During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex.

PubMed

Ketterer, Philip; Ananth, Adithya N; Laman Trip, Diederik S; Mishra, Ankur; Bertosin, Eva; Ganji, Mahipal; van der Torre, Jaco; Onck, Patrick; Dietz, Hendrik; Dekker, Cees

2018-03-02

The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Autism

PubMed Central

Levy, Susan E; Mandell, David S; Schultz, Robert T

2010-01-01

Autism spectrum disorders are characterised by severe deficits in socialisation, communication, and repetitive or unusual behaviours. Increases over time in the frequency of these disorders (to present rates of about 60 cases per 10 000 children) might be attributable to factors such as new administrative classifications, policy and practice changes, and increased awareness. Surveillance and screening strategies for early identification could enable early treatment and improved outcomes. Autism spectrum disorders are highly genetic and multifactorial, with many risk factors acting together. Genes that affect synaptic maturation are implicated, resulting in neurobiological theories focusing on connectivity and neural effects of gene expression. Several treatments might address core and comorbid symptoms. However, not all treatments have been adequately studied. Improved strategies for early identification with phenotypic characteristics and biological markers (eg, electrophysiological changes) might hopefully improve effectiveness of treatment. Further knowledge about early identification, neurobiology of autism, effective treatments, and the effect of this disorder on families is needed. PMID:19819542

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brahlek, Matthew; Koirala, Nikesh; Salehi, Maryam

Topological insulators (TI) are a phase of matter that host unusual metallic states on their surfaces. Unlike the states that exist on the surface of conventional materials, these so-called topological surfaces states (TSS) are protected against disorder-related localization effects by time reversal symmetry through strong spin-orbit coupling. By combining transport measurements, angle-resolved photo-emission spectroscopy and scanning tunneling microscopy, we show that there exists a critical level of disorder beyond which the TI Bi 2Se 3 loses its ability to protect the metallic TSS and transitions to a fully insulating state. The absence of the metallic surface channels dictates that theremore » is a change in material’s topological character, implying that disorder can lead to a topological phase transition even without breaking the time reversal symmetry. This observation challenges the conventional notion of topologically-protected surface states, and will provoke new studies as to the fundamental nature of topological phase of matter in the presence of disorder.« less

Autism.

PubMed

Levy, Susan E; Mandell, David S; Schultz, Robert T

2009-11-07

Autism spectrum disorders are characterised by severe deficits in socialisation, communication, and repetitive or unusual behaviours. Increases over time in the frequency of these disorders (to present rates of about 60 cases per 10,000 children) might be attributable to factors such as new administrative classifications, policy and practice changes, and increased awareness. Surveillance and screening strategies for early identification could enable early treatment and improved outcomes. Autism spectrum disorders are highly genetic and multifactorial, with many risk factors acting together. Genes that affect synaptic maturation are implicated, resulting in neurobiological theories focusing on connectivity and neural effects of gene expression. Several treatments might address core and comorbid symptoms. However, not all treatments have been adequately studied. Improved strategies for early identification with phenotypic characteristics and biological markers (eg, electrophysiological changes) might hopefully improve effectiveness of treatment. Further knowledge about early identification, neurobiology of autism, effective treatments, and the effect of this disorder on families is needed.

Acute hepatic decompensation precipitated by pregnancy-related catabolic stress: a rare mimic of acute liver failure.

PubMed

Sinclair, Marie; Ket, Shara; Testro, Adam; Gow, Paul J; Angus, Peter W

2014-02-01

Abnormal liver function tests are common in pregnancy; however, liver failure is rare. Pregnancy is a catabolic state that can precipitate illness in patients with underlying metabolic disorders. A 19-year-old woman presented at 14 weeks of gestation with an alanine transaminase of 2,252 international units/L (less than 30), an international normalized ratio of 6.9 (0.9-1.2), and an ammonia of 58 micromole/L (11-51 micromole/L). No cause was identified on routine investigations including liver biopsy. Biochemical and clinical deterioration prompted investigation for a metabolic disorder. Urinary orotic acid was elevated, consistent with the urea cycle disorder type 1 citrullinemia. Appropriate management (arginine supplementation and dietary protein restriction) led to rapid improvement and later delivery of a healthy neonate. This is an unusual presentation that reminds us of the importance of considering metabolic disorders during the catabolic stress of pregnancy.