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Intrinsically disordered protein

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https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#1
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
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...
February 6, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28223518/integrated-view-of-internal-friction-in-unfolded-proteins-from-single-molecule-fret-contact-quenching-theory-and-simulations
#2
Andrea Soranno, Andrea Holla, Fabian Dingfelder, Daniel Nettels, Dmitrii E Makarov, Benjamin Schuler
Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223358/structural-and-biochemical-analysis-of-escherichia-coli-obge-a-central-regulator-of-bacterial-persistence
#3
Sotirios Gkekas, Ranjan Kumar Singh, Alexander V Shkumatov, Joris Messens, Maarten Fauvart, Natalie Verstraeten, Jan Michiels, Wim Versées
The Obg protein family belongs to the TRAFAC (translation factor) class of P-loop GTPases and is conserved from bacteria to eukaryotes. Essential roles in many different cellular processes have been suggested for the Obg protein from Escherichia coli (ObgE), and we recently showed that it is a central regulator of bacterial persistence. Here, we report the first crystal structure of ObgE at 1.85 Å resolution in the GDP-bound state, showing the characteristic N-terminal domain and a central G domain that are common to all Obg proteins...
February 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28219316/from-disorder-to-mis-order-structural-aspects-of-pathogenic-oligomerization-in-conformational-diseases
#4
Chin Pang Benny Yiu, Yu Wai Chen
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...
February 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28214530/automaton-model-of-protein-dynamics-of-conformational-and-functional-states
#5
REVIEW
Andrei Khrennikov, Ekaterina Yurova
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory of automata to model the latter dynamics. In our model protein's behavior is modeled with the aid of two dynamical systems, ontic and epistemic, which describe evolution of conformational and functional states of proteins, respectively. The epistemic automaton is constructed from the ontic automaton on the basis of functional (observational) equivalence relation on the space of ontic states...
February 15, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28213435/genetics-of-synucleinopathies
#6
Robert L Nussbaum
Parkinson's disease (PD), diffuse Lewy body disease (DLBD), and multiple system atrophy (MSA) constitute the three major neurodegenerative disorders referred to as synucleinopathies because both genetic and pathological results implicate the α-synuclein protein in their pathogenesis. PD and DLBD are recognized as closely related diseases with substantial clinical and pathological overlap. MSA, on the other hand, has a distinctive clinical presentation and neuropathological profile. In this review, we will summarize the evidence linking α-synuclein to these three disorders...
February 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28212442/ecto-5-nucleotidase-cd73-nt5e-vitamin-d-receptor-and-fgf23-gene-polymorphisms-may-play-a-role-in-the-development-of-calcific-uremic-arteriolopathy-in-dialysis-patients-data-from-the-german-calciphylaxis-registry
#7
Hansjörg Rothe, Vincent Brandenburg, Margot Haun, Barbara Kollerits, Florian Kronenberg, Markus Ketteler, Christoph Wanner
INTRODUCTION: Calciphylaxis/calcific uremic arteriolopathy affects mainly end-stage kidney disease patients but is also associated with malignant disorders such as myeloma, melanoma and breast cancer. Genetic risk factors of calciphylaxis have never been studied before. METHODS: We investigated 10 target genes using a tagging SNP approach: the genes encoding CD73/ ecto-5'-nucleotidase (purinergic pathway), Matrix Gla protein, Fetuin A, Bone Gla protein, VKORC1 (all related to intrinsic calcification inhibition), calcium-sensing receptor, FGF23, Klotho, vitamin D receptor, stanniocalcin 1 (all related to CKD-MBD)...
2017: PloS One
https://www.readbyqxmd.com/read/28207895/the-metastasis-suppressor-kiss1-is-an-intrinsically-disordered-protein-slightly-more-extended-than-a-random-coil
#8
Alain Ibáñez de Opakua, Nekane Merino, Maider Villate, Tiago N Cordeiro, Georgina Ormaza, Marta Sánchez-Carbayo, Tammo Diercks, Pau Bernadó, Francisco J Blanco
The metastasis suppressor KISS1 is reported to be involved in the progression of several solid neoplasias, making it a promising molecular target for controlling their metastasis. The KISS1 sequence contains an N-terminal secretion signal and several dibasic sequences that are proposed to be the proteolytic cleavage sites. We present the first structural characterization of KISS1 by circular dichroism, multi-angle light scattering, small angle X-Ray scattering and NMR spectroscopy. An analysis of the KISS1 backbone NMR chemical shifts does not reveal any preferential conformation and deviation from a random coil ensemble...
2017: PloS One
https://www.readbyqxmd.com/read/28197405/on-the-helix-propensity-in-generalized-born-solvent-descriptions-of-modeling-the-dark-proteome
#9
Mark A Olson
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...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28196895/intrinsically-disordered-proteins-drive-enamel-formation-via-an-evolutionarily-conserved-self-assembly-motif
#10
Tomas Wald, Frantisek Spoutil, Adriana Osickova, Michaela Prochazkova, Oldrich Benada, Petr Kasparek, Ladislav Bumba, Ophir D Klein, Radislav Sedlacek, Peter Sebo, Jan Prochazka, Radim Osicka
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...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192291/understanding-disordered-and-unfolded-proteins-using-single-molecule-fret-and-polymer-theory
#11
Hagen Hofmann
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...
November 17, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28190398/transforming-cytosolic-proteins-into-insoluble-and-membrane-toxic-forms-by-genetic-pathological-or-environmental-factors
#12
Jianxing Song
An increasing spectrum of diseases other than neurodegenerative diseases is characteristic of aggregation of specific proteins, while aggregation of a large number of non-specific proteins are associated with aging down to Escherichia coli. Triggered by disease-causing mutations and aging-associated damages, many well-folded cytosolic proteins become "completely insoluble" in vivo. As facilitated by our discovery in 2005 that "completely insoluble" proteins could be solubilized in unsalted water, we have deciphered that disease- and aging-associated factors act to eliminate the native folds of human VAPB-MSP and SOD1, as well as E...
February 9, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28187186/structural-coalescence-underlies-the-aggregation-propensity-of-a-%C3%AE-barrel-protein-motif
#13
Carla R Angelani, Julio J Caramelo, Lucrecia M Curto, José M Delfino
A clear understanding of the structural foundations underlying protein aggregation is an elusive goal of central biomedical importance. A step toward this aim is exemplified by the β-barrel motif represented by the intestinal fatty acid binding protein (IFABP) and two abridged all-β sheet forms (Δ98Δ and Δ78Δ). At odds with the established notion that a perturbation of the native fold should necessarily favor a buildup of intermediate forms with an enhanced tendency to aggregate, the intrinsic stability (ΔG°H2O) of these proteins does not bear a straightforward correlation with their trifluoroethanol (TFE)-induced aggregation propensity...
2017: PloS One
https://www.readbyqxmd.com/read/28179137/the-impact-of-different-mutations-at-arg54-on-structure-chaperone-like-activity-and-oligomerization-state-of-human-%C3%AE-a-crystallin-the-pathomechanism-underlying-congenital-cataract-causing-mutations-r54l-r54p-and-r54c
#14
Kazem Khoshaman, Reza Yousefi, Ali Mohammad Tamaddon, Samira Sadat Abolmaali, Ahmad Oryan, Ali Akbar Moosavi-Movahedi, Boris I Kurganov
A major part of cataractogenic mutations in human αA-Crystallin (αA-Cry) occurs at Arg residues. While Arg54 is highly conserved within different species, the cataractogenic mutations R54L, R54P and R54C have been recently identified in CRYAA gene, encoding human αA-Cry. The detailed structural and functional aspects, stability and amyloidogenic properties of αA-Cry were determined upon the above-mentioned missense mutations, using various spectroscopic techniques, gel electrophoresis, electron microscopy, size exclusion HPLC analyses, and chaperone-like activity assay...
February 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28177918/caspase-9-structure-mechanisms-and-clinical-application
#15
Ping Li, Libin Zhou, Ting Zhao, Xiongxiong Liu, Pengcheng Zhang, Yan Liu, Xiaogang Zheng, Qiang Li
As the most intensively studied initiator caspase, caspase-9 is a key player in the intrinsic or mitochondrial pathway which is involved in various stimuli, including chemotherapies, stress agents and radiation. Caspase-9 is activated on the apoptosome complex to remain catalytic status and is thought of involving homo-dimerization monomeric zymogens. Failing to activate caspase-9 has profound physiological and pathophysiological outcomes, leading to degenerative and developmental disorders even cancer. To govern the apoptotic commitment process appropriately, plenty of proteins and small molecules involved in regulating caspase-9...
February 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28176659/intrinsically-disordered-domains-amyloids-and-protein-liquid-phases-evolving-concepts-and-open-questions
#16
Miguel Ángel Mompeán, Douglas Vinson Laurents
Enzymes and structural proteins dominated thinking about protein structure and function for most of the twentieth century. In recent decades, however, we have begun to appreciate the significant physiological and pathological roles of nonglobular proteins. Amyloids first gained infamy from their implications in a score of human mortal diseases. However, they have recently been discovered to play vital physiological roles, such as memory consolidation in humans. This raises an important question: Can we inhibit pathological amyloids without affecting functional amyloids? Intrinsically disordered proteins (IDPs), many of which are prone to form amyloids, perform many essential functions, yet their importance has only been recognized in the last quarter century...
February 6, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28176657/emerging-methods-for-structural-analysis-of-protein-aggregation
#17
Eshan Khan, Amit Kumar
Protein misfolding and aggregation is a key attribute of different neurodegenerative diseases. Misfolded and aggregated proteins are intrinsically disordered and rule out structure based drug design. The comprehensive characterization of misfolded proteins and associated aggregation pathway is prerequisite to develop therapeutics for neurodegenerative diseases caused due to the protein aggregation. Visible protein aggregates used to be the final stage during aggregation mechanism. The structural analysis of intermediate steps in such protein aggregates will help us to discern the conformational role and subsequently involved pathways...
February 6, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28167231/nicotine-slows-down-oligomerisation-of-%C3%AE-synuclein-and-ameliorates-cytotoxicity-in-a-yeast-model-of-parkinson-s-disease
#18
Jay Kardani, Ratnika Sethi, Ipsita Roy
Several retrospective epidemiological reports have indicated an inverse correlation between smoking and development of Parkinson's disease (PD). This has mostly been attributed to the neuroprotective role of nicotine in stimulating nicotinic acetylcholine receptors and dopaminergic neurons which are damaged in PD. One of the characteristic features of PD is the intraneuronal deposition of globular inclusions of the intrinsically disordered protein α-synuclein as Lewy bodies. Using in vitro and the well-validated yeast cell models, we show that nicotine also exerts a beneficial effect on aggregation of α-synuclein...
February 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28166455/structural-and-mechanistic-insights-into-nuclear-transport-and-delivery-of-the-critical-pluripotency-factor-oct4-to-dna
#19
Takahide Okuyama, Ryosuke Yamagishi, Jiro Shimada, Masaaki Ikeda, Yayoi Maruoka, Hiroki Kaneko
Oct4 is a master regulator of the induction and maintenance of cellular pluripotency, and has crucial roles in early stages of differentiation. It is the only factor that cannot be substituted by other members of the same protein family to induce pluripotency. However, although Oct4 nuclear transport and delivery to target DNA are critical events for reprogramming to pluripotency, little is known about the molecular mechanism. Oct4 is imported to the nucleus by the classical nuclear transport mechanism, which requires importin α as an adaptor to bind the nuclear localization signal (NLS)...
February 6, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28159831/prion-like-protein-aggregates-and-type-2-diabetes
#20
Abhisek Mukherjee, Claudio Soto
Type 2 diabetes (T2D) is a highly prevalent metabolic disease characterized by chronic insulin resistance and β-cell dysfunction and loss, leading to impaired insulin release and hyperglycemia. Although the mechanism responsible for β-cell dysfunction and death is not completely understood, recent findings suggest that the accumulation of misfolded aggregates of the islet amyloid polypeptide (IAPP) in the islets of Langerhans may play an important role in pancreatic damage. Misfolding and aggregation of diverse proteins and their accumulation as amyloid in different organs is the hallmark feature in a group of chronic, degenerative diseases termed protein misfolding disorders (PMDs)...
February 3, 2017: Cold Spring Harbor Perspectives in Medicine
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