The Experts below are selected from a list of 12438 Experts worldwide ranked by ideXlab platform
David M Goldenberg - One of the best experts on this subject based on the ideXlab platform.
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minimal effects of macromolecular crowding on an Intrinsically Disordered Protein a small angle neutron scattering study
Biophysical Journal, 2014Co-Authors: David M Goldenberg, Brian ArgyleAbstract:Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular Proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an Intrinsically Disordered Protein, the N Protein of bacteriophage λ. The λ N Protein was uniformly labeled with 2H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding Proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded Protein was estimated to be 30 A and was found to be remarkably insensitive to the presence of crowders, varying by <2 A for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded Proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of Disordered Proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding Proteins, which may compensate for the effects of steric exclusion.
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effects of macromolecular crowding on an Intrinsically Disordered Protein characterized by small angle neutron scattering with contrast matching
Biophysical Journal, 2011Co-Authors: Daniel Johansen, Cy M Jeffries, Boualem Hammouda, Jill Trewhella, David M GoldenbergAbstract:Small-angle neutron scattering was used to examine the effects of molecular crowding on an Intrinsically Disordered Protein, the N Protein of bacteriophage λ, in the presence of high concentrations of a small globular Protein, bovine pancreatic trypsin inhibitor (BPTI). The N Protein was labeled with deuterium, and the D2O concentration of the solvent was adjusted to eliminate the scattering contrast between the solvent and unlabeled BPTI, leaving only the scattering signal from the unfolded Protein. The scattering profile observed in the absence of BPTI closely matched that predicted for an ensemble of random conformations. With BPTI added to a concentration of 65 mg/mL, there was a clear change in the scattering profile representing an increase in the mass fractal dimension of the unfolded Protein, from 1.7 to 1.9, as expected if crowding favors more compact conformations. The crowding Protein also inhibited aggregation of the unfolded Protein. At 130 mg/mL BPTI, however, the fractal dimension was not significantly different from that measured at the lower concentration, contrary to the predictions of models that treat the unfolded conformations as convex particles. These results are reminiscent of the behavior of polymers in concentrated melts, suggesting that these synthetic mixtures may provide useful insights into the properties of unfolded Proteins under crowding conditions.
Vladimir N Uversky - One of the best experts on this subject based on the ideXlab platform.
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functional characterization of an unknown soybean Intrinsically Disordered Protein in vitro and in escherichia coli
International Journal of Biological Macromolecules, 2021Co-Authors: Fangmei Tan, Vladimir N Uversky, Nan Sun, Linsong Zhang, Shifeng Xiao, Qiulong Tan, Yun LiuAbstract:Abstract Intrinsically Disordered Proteins (IDPs) possess a wide range of biological function in all organisms, however the specific functions of most IDPs are still unknown. Soybean LOC Protein, LOC for short, is a heat-stable Protein, which is more abundant in the stress-resistant radicles. Sequence alignment and phylogenetic analysis showed that LOC is a functionally unknown Protein and conserved in Fabaceae. LOC, being enriched in most disorder-promoting residues and depleted in most order-promoting residues, was predicted to contain high levels of intrinsic disorder by several commonly used computational tools. However, it was also predicted to contain two disorder-based Protein-Protein binding sites and two short α-helical segments. The circular dichroism spectroscopic analysis showed that this Protein is mostly Disordered in water, but can form more α-helical structure in the presence of SDS and TFE. Functional in vitro studies showed that the LOC Protein is able to prevent lactate dehydrogenase inactivation by freeze-thaw at a molar ratio of 10:1. Furthermore, in vivo analyses revealed the survival rate of Escherichia coli over-expressing LOC Protein under the conditions of osmotic stress was noticeably increased in comparison with the control. These observations suggest that the Intrinsically Disordered Protein LOC might serve as a chaperone and/or cell protector.
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not an exception to the rule the functional significance of Intrinsically Disordered Protein regions in enzymes
Molecular BioSystems, 2017Co-Authors: Shelly Deforte, Vladimir N UverskyAbstract:Intrinsically Disordered Protein regions (IDPRs) are remarkably common and have unique and important biological functions. Enzymes have long been considered an exception to the rule of Protein intrinsic disorder due to the structural requirements for catalysis. Although functionally significant IDPRs have been described in several enzymes, there has been no study quantifying the extent of this phenomenon. We have conducted a multilevel computational analysis of missing regions in X-ray crystal structures in the PDB and predicted disorder in 66 representative proteomes. We found that the fraction of predicted disorder was higher in non-enzymes than enzymes, because non-enzymes were more likely to be fully Disordered. However, we also found that transferases, hydrolases and enzymes with multiple assigned functional classifications were similar to non-enzymes in terms of the length of the longest continuous stretch of predicted disorder. Both eukaryotic enzymes and non-enzymes had a greater disorder content than was seen in bacteria. Disorder at the proteome level appears to emerge in response to organismic and functional complexity, and enzymes are not an exception to this rule.
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functional roles of transiently and Intrinsically Disordered regions within Proteins
FEBS Journal, 2015Co-Authors: Vladimir N UverskyAbstract:Proteins are structurally heterogeneous and comprise folded regions with variable conformational stabilities and Intrinsically Disordered Protein regions that do not have well-folded structures. Even small, well-folded single-domain Proteins are structurally heterogeneous and contain multiple foldon units with different conformational stability. Although the ability of many Intrinsically Disordered Protein regions to undergo at least partial folding at interaction with specific binding partners is a well-established fact, recent studies have revealed that functions of some ordered Proteins rely on the decrease in the amount of their ordered structure and require local or even global functional unfolding. This functional unfolding is induced by transient alterations in Protein environment or by modification of Protein structure and can be reversed as soon as the environment is restored or the modification is removed. Therefore, the important features of these conditionally Disordered Protein regions (or unfoldons) are the induced nature and the transient character of their disorder. In other words, structurally any Protein can be described as a modular assembly of foldons, inducible foldons, semi-foldons, nonfoldons and unfoldons. Obviously, differently ordered/Disordered Proteins and Protein regions can possess very different functional repertoires. This review represents some of the key functions of transiently and Intrinsically Disordered Protein regions.
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actinidia drm1 an Intrinsically Disordered Protein whose mrna expression is inversely correlated with spring budbreak in kiwifruit
PLOS ONE, 2013Co-Authors: Marion Wood, Vladimir N Uversky, Georgina M Rae, Eric F Walton, Bin Xue, Roger P HellensAbstract:Intrinsically Disordered Proteins (IDPs) are a relatively recently defined class of Proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such Proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and Protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and Protein levels. It is predicted to be an Intrinsically Disordered Protein with two distinct highly conserved domains. Several Actinidia DRM1 homologues, which align into two distinct Actinidia-specific families, Type I and Type II, have been identified. No candidates for the Arabidopsis DRM1-Homologue (AtDRM2) an additional family member, has been identified in Actinidia.
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rational drug design via Intrinsically Disordered Protein
Trends in Biotechnology, 2006Co-Authors: Yugong Cheng, Christopher J Oldfield, Tanguy Legall, James P Mueller, Ya Yue J Van, Pedro Romero, Marc S Cortese, Vladimir N Uversky, Keith A DunkerAbstract:Despite substantial increases in research funding by the pharmaceutical industry, drug discovery rates seem to have reached a plateau or perhaps are even declining, suggesting the need for new strategies. Protein–Protein interactions have long been thought to provide interesting drug discovery targets, but the development of small molecules that modulate such interactions has so far achieved a low success rate. In contrast to this historic trend, a few recent successes raise hopes for routinely identifying druggable Protein–Protein interactions. In this Opinion article, we point out the importance of coupled binding and folding for Protein–Protein signalling interactions generally, and from this and associated observations, we develop a new strategy for identifying Protein–Protein interactions that would be particularly promising targets for modulation by small molecules. This novel strategy, based on Intrinsically Disordered Protein, has the potential to increase significantly the discovery rate for new molecule entities.
Sanjay Kumar - One of the best experts on this subject based on the ideXlab platform.
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self assembling micelles based on an Intrinsically Disordered Protein domain
Journal of the American Chemical Society, 2019Co-Authors: Sarah H Klass, Sanjay Kumar, Matthew J Smith, Tahoe A Fiala, Jess P Lee, Anthony O Omole, Bonggyoon Han, Kenneth H Downing, Matthew B FrancisAbstract:The self-assembly of micellar structures from diblock polymers that contain hydrophilic and hydrophobic domains has been of great interest for the encapsulation of drugs and other hydrophobic molecules. While most commercially used surfactants are derived from hydrocarbon sources, there have been recent efforts to replace these with biodegradable, nontoxic, biologically synthesized alternatives. Previous examples have primarily examined naturally occurring self-assembling Proteins, such as silk and elastin-like sequences. Herein, we describe a new series of fusion Proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing Protein tag. The sequences of the Proteins are based on a human Intrinsically Disordered Protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CM...
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Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain
2019Co-Authors: Sarah H. Klass, Sanjay Kumar, Matthew J Smith, Tahoe A Fiala, Jess P Lee, Anthony O Omole, Bonggyoon Han, Kenneth H Downing, Matthew B FrancisAbstract:The self-assembly of micellar structures from diblock polymers that contain hydrophilic and hydrophobic domains has been of great interest for the encapsulation of drugs and other hydrophobic molecules. While most commercially used surfactants are derived from hydrocarbon sources, there have been recent efforts to replace these with biodegradable, nontoxic, biologically synthesized alternatives. Previous examples have primarily examined naturally occurring self-assembling Proteins, such as silk and elastin-like sequences. Herein, we describe a new series of fusion Proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing Protein tag. The sequences of the Proteins are based on a human Intrinsically Disordered Protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values in the low micromolar range, 3 orders of magnitude lower than the CMC of commonly used surfactant sodium dodecyl sulfate (SDS). The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications. Furthermore, the inherent flexibility in the design of these Protein sequences enables the encoding of additional functionalities for many future applications. Overall, this work represents a new biomolecular alternative to traditional surfactants that are based on nonrenewable and poorly biodegradable hydrocarbon sources
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Stimuli-sensitive Intrinsically Disordered Protein brushes
Nature Communications, 2014Co-Authors: Nithya Srinivasan, Maniraj Bhagawati, Badriprasad Ananthanarayanan, Sanjay KumarAbstract:Polymer brush surface coatings are important biomaterials for the reduction of biomolecule and cell adhesion. Here, the authors use a recombinantly expressed, Intrinsically Disordered Protein to form a stimuli-responsive and enzyme-active polymer brush surface. Grafting polymers onto surfaces at high density to yield polymer brush coatings is a widely employed strategy to reduce biofouling and interfacial friction. These brushes almost universally feature synthetic polymers, which are often heterogeneous and do not readily allow incorporation of chemical functionalities at precise sites along the constituent chains. To complement these synthetic systems, we introduce a biomimetic, recombinant Intrinsically Disordered Protein that can assemble into an environment-sensitive brush. This macromolecule adopts an extended conformation and can be grafted to solid supports to form oriented Protein brushes that swell and collapse dramatically with changes in solution pH and ionic strength. We illustrate the value of sequence specificity by using proteases with mutually orthogonal recognition sites to modulate brush height in situ to predictable values. This study demonstrates that stimuli-responsive brushes can be fabricated from Proteins and introduces them as a new class of smart biomaterial building blocks.
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stimuli sensitive Intrinsically Disordered Protein brushes
Nature Communications, 2014Co-Authors: Nithya Srinivasan, Maniraj Bhagawati, Badriprasad Ananthanarayanan, Sanjay KumarAbstract:Grafting polymers onto surfaces at high density to yield polymer brush coatings is a widely employed strategy to reduce biofouling and interfacial friction. These brushes almost universally feature synthetic polymers, which are often heterogeneous and do not readily allow incorporation of chemical functionalities at precise sites along the constituent chains. To complement these synthetic systems, we introduce a biomimetic, recombinant Intrinsically Disordered Protein that can assemble into an environment-sensitive brush. This macromolecule adopts an extended conformation and can be grafted to solid supports to form oriented Protein brushes that swell and collapse dramatically with changes in solution pH and ionic strength. We illustrate the value of sequence specificity by using proteases with mutually orthogonal recognition sites to modulate brush height in situ to predictable values. This study demonstrates that stimuli-responsive brushes can be fabricated from Proteins and introduces them as a new class of smart biomaterial building blocks.
Douglas J. Tobias - One of the best experts on this subject based on the ideXlab platform.
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molecular dynamics simulations of a powder model of the Intrinsically Disordered Protein tau
Journal of Physical Chemistry B, 2015Co-Authors: Yann Fichou, Guiseppe Zaccai, Martini Weik, Matthias Heyden, Douglas J. TobiasAbstract:The tau Protein, whose aggregates are involved in Alzheimer’s disease, is an Intrinsically Disordered Protein (IDP) that regulates microtubule activity in neurons. An IDP lacks a single, well-defined structure and, rather, constantly exchanges among multiple conformations. In order to study IDP dynamics, the combination of experimental techniques, such as neutron scattering, and computational techniques, such as molecular dynamics (MD) simulations, is a powerful approach. Amorphous hydrated powder samples have been very useful for studying Protein internal dynamics experimentally, e.g., using neutron scattering. Thus, there is demand for realistic in silico models of hydrated Protein powders. Here we present an MD simulation analysis of a powder hydrated at 0.4 g water/g Protein of the IDP tau in the temperature range 20–300 K. By comparing with neutron scattering data, we identify the Protein–water interface as the predominant feature determining IDP dynamics. The so-called Protein dynamical transition i...
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Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau.
Journal of Physical Chemistry B, 2015Co-Authors: Yann Fichou, Guiseppe Zaccai, Martini Weik, Matthias Heyden, Douglas J. TobiasAbstract:The tau Protein, whose aggregates are involved in Alzheimer's disease, is an Intrinsically Disordered Protein (IDP) that regulates microtubule activity in neurons. An IDP lacks a single, well-defined structure and, rather, constantly exchanges among multiple conformations. In order to study IDP dynamics, the combination of experimental techniques, such as neutron scattering, and computational techniques, such as molecular dynamics (MD) simulations, is a powerful approach. Amorphous hydrated powder samples have been very useful for studying Protein internal dynamics experimentally, e.g., using neutron scattering. Thus, there is demand for realistic in silico models of hydrated Protein powders. Here we present an MD simulation analysis of a powder hydrated at 0.4 g water/g Protein of the IDP tau in the temperature range 20-300 K. By comparing with neutron scattering data, we identify the Protein-water interface as the predominant feature determining IDP dynamics. The so-called Protein dynamical transition is shown to be attenuated, but not suppressed, in the parts of the Protein that are not exposed to the solvent. In addition, we find similarities in the mean-squared displacements of the core of a globular Protein and "dry" clusters formed by the IDP in hydrated powders. Thus, the ps to ns dynamics of Proteins in hydrated powders originate mainly from those residues in contact with solvent. We propose that by measuring the dynamics of Protein assemblies, such as aggregates, one might assess qualitatively their state of hydration.
Brian Argyle - One of the best experts on this subject based on the ideXlab platform.
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minimal effects of macromolecular crowding on an Intrinsically Disordered Protein a small angle neutron scattering study
Biophysical Journal, 2014Co-Authors: David M Goldenberg, Brian ArgyleAbstract:Small-angle neutron scattering was used to study the effects of macromolecular crowding by two globular Proteins, i.e., bovine pancreatic trypsin inhibitor and equine metmyoglobin, on the conformational ensemble of an Intrinsically Disordered Protein, the N Protein of bacteriophage λ. The λ N Protein was uniformly labeled with 2H, and the concentrations of D2O in the samples were adjusted to match the neutron scattering contrast of the unlabeled crowding Proteins, thereby masking their contribution to the scattering profiles. Scattering from the deuterated λ N was recorded for samples containing up to 0.12 g/mL bovine pancreatic trypsin inhibitor or 0.2 g/mL metmyoglobin. The radius of gyration of the uncrowded Protein was estimated to be 30 A and was found to be remarkably insensitive to the presence of crowders, varying by <2 A for the highest crowder concentrations. The scattering profiles were also used to estimate the fractal dimension of λ N, which was found to be ∼1.8 in the absence or presence of crowders, indicative of a well-solvated and expanded random coil under all of the conditions examined. These results are contrary to the predictions of theoretical treatments and previous experimental studies demonstrating compaction of unfolded Proteins by crowding with polymers such as dextran and Ficoll. A computational simulation suggests that some previous treatments may have overestimated the effective volumes of Disordered Proteins and the variation of these volumes within an ensemble. The apparent insensitivity of λ N to crowding may also be due in part to weak attractive interactions with the crowding Proteins, which may compensate for the effects of steric exclusion.
