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77 results for “intrinsically disordered”
Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"
<p>Molecular Simulation Data Associated with the Manuscript<br> <br> "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"<br> <br> by Jie Heng, Yunfei Hu, Guillermo Pérez-Hernández, Asuka Inoue, Jiawei Zhao, Xiuyan Ma, Xiaoou Sun, Kouki Kawakami, Tatsuya Ikuta, Jienv Ding, Yujie Yang, Lujia Zhang, Sijia Peng, Xiaogang Niu, Hongwei Li, Ramon Guixà-González, Changwen Jin, Peter W. Hildebrand, Chunlai Chen & Brian K. Kobilka</p> <p>Nature Communications 2023, <a href="https://doi.org/10.1038/s41467-023-37233-1">https://doi.org/10.1038/s41467-023-37233-1</a><br> <br> The representative molecular dynamics (MD) trajectories shown in the <strong>Supplementary Fig. 8,<br> Variable contacts of the β2AR CT</strong> can be 3D visualized in the browser in the following link:</p> <ul> <li><a href="https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl"> https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl</a></li> </ul>
Intrinsically Disordered Regions Promote Protein Refoldability and Facilitate Retrieval from Biomolecular Condensates–Peptide Quantifications
<p>Many eukaryotic proteins contain intrinsically disordered regions (IDRs) that intersperse globular folded domains, in contrast with bacterial proteins which are typically highly globular. Recent years have seen great progress in identifying biological functions associated with these elusive protein sequence: in specific cases, they mediate liquid- liquid phase separation, perform molecular recognition, or act as sensors to changes in the environment. Nevertheless, only a small number of IDRs have annotated functions despite their presence in 64% of yeast proteins, stimulating some to question what ‘general purpose’ they may serve. Here, by interrogating the refoldability of two fungal proteomes (Saccharomyces cerevisiae and Neurosporra crassa), we show that IDRs render their host proteins more refoldable from the denatured state, allowing them to cohere more closely to Anfinsen’s thermodynamic hypothesis. The data provide an exceptionally clear picture of which biophysical and topological characteristics enable refoldability. Moreover, we find that almost all yeast proteins that partition into stress granules during heat shock are refoldable, a finding that holds for other condensates such as P-bodies and the nucleolus. Finally, we find that the Hsp104 unfoldase is the principal actor in mediating disassembly of heat stress granules and that the efficiency with which condensed proteins are returned to the soluble phase is also well explained by refoldability. Hence, these studies establish spontaneous refoldability as an adaptive trait that endows proteins with the capacity to reform their native soluble structures following their extraction from condensates. Altogether, our results provide an intuitive model for the function of IDRs in many multidomain proteins and clarifies their relationship to the phenomenon of biomolecular condensation.</p> <p>This dataset provides peptide quantifications (and their respective P-values) from three separate types of experiments used to support the claims in this study.</p> <p>1. Peptide quantifications from global refolding reactions, assessed with limited-proteolysis mass spectrometry (LiP-MS), carried out on two fungal organisms (S. cerevisiae [yeast] & N. crassa), at three refolding times, repeated on three separate iterations (for yeast).</p> <p>2. Peptide quantifications from LiP-MS experiments conducted on yeast extracts during heat shock or recovery from heat shock</p> <p>3. Annotations for peptides in #1 that are associated with linker regions between folded domains.</p>
Glassy dynamics and memory effects in an intrinsically disordered protein construct
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Data from: The Origin Recognition Complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man
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Data from: Oligomerization enables the selective targeting of an intrinsically disordered region by a small molecule
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Sequence/simulation data for Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence
<p>This is a DOI-linked deposition of sequence/biophysical properties pairs used in the associated paper by Lotthammer et al:</p><p>Lotthammer, J. M.<strong>*</strong>, Ginell, G. M.<strong>*</strong>, Griffith, D.<strong>*</strong>, Emenecker, R. J. & Holehouse, A. S. <br>Direct Prediction of Intrinsically Disordered Protein Conformational Properties From Sequence.<br><i><strong>Nature Methods</strong></i> (<i>in press</i>), (2023).</p><p> </p>
How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP, TP2 and ONEG?
<p>Simulation trajectory dataset to accompany publication:</p> <p>Reid, L.M., Guzzetti, I., Svensson, T., Carlsson, A-C., Su, W., Leek, T., von Sydow, L., Czechtizky, W., Miljak, M., Verma, C., De Maria, L., Essex, J.W., Chem. Sci., 2022, DOI: 10.1039/d1sc03496k</p> <p> </p>
Conformational ensembles used in "Assessment of forward models for the hydrodynamic radius of intrinsically disordered proteins. Pesce et al. 2022"
<p>Ensemble of intrinsically disordered proteins used in: <em>"Assessment of forward models for the hydrodynamic radius of intrinsically disordered proteins. Pesce et al. 2022"</em>.</p> <p>Ensembles are produced with Flexible-meccano and Langevin simulations with CALVADOS for:</p> <ul> <li>Hst5</li> <li>RS</li> <li>DSS1</li> <li>Sic1</li> <li>ProTa</li> <li>NHE6cmdd</li> <li>A1</li> <li>aSyn</li> <li>ANAC046</li> <li>GHR-ICD</li> <li>Tau</li> </ul>
Salt Induced Transitions in Structural Ensemble of Intrinsically Disordered Proteins
<p>Simulation data and the corrosponding analysis script for the work "<strong>Salt Induced Transitions in Conformational Ensemble of Intrinsically Disordered Proteins</strong> " by <em>Hiranmay Maity, Lipika Baidya </em>and<em> Govardhan reddy</em> are deposited here. </p> <p>Analysis Scripts:</p> <p>The scripts for analysing the simulation data are in analysis_script.zip. The folder contains:</p> <ul> <li> <p>autocorrelation.c : code for calculating end_to_end distance autocorrelation function with time in C.</p> </li> <li> <p>average_property.cpp: code for calculating average property such as radius of gyration (R<sub>g</sub>) from trajectory files in C++.</p> </li> <li> <p>calculate_saxs_kratky.c: code for calculating scattering profile (SAXS and Kratky) from simulation data in C.</p> </li> <li> <p>compute_contact_map.cpp: code for calculating contact map in C.</p> </li> <li> <p>probablity_distribution.c: code for calculating probablity distribution of Rg in C.</p> </li> <li> <p>structure_factor.c: code for calculating structure factor in C.</p> </li> </ul>
Strategy of selection and optimization of single domain antibodies targeting the PHF6 linear peptide within the Tau intrinsically disordered protein
<p>Dataset pertaining to Strategy of selection and optimization of single domain antibodies targeting the PHF6 linear peptide within the Tau intrinsically disordered protein</p>
Data from: The intrinsically disordered N-terminus of the voltage-dependent anion channel
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Assessing SIRAH's Capability to Simulate Intrinsically Disordered Proteins and Peptides
<p>This dataset contains the structures, topologies, and trajectory files of coarse-grained molecular dynamics simulations of five Intrinsically Disordered Proteins (IDPs). We explored the dynamics of α-synuclein (randomly generated conformers), p31-43(PDB is: 6QAX), PaaA2 antitoxin (PDB id:3ZBE), Amyloid-beta 1-40 (PDB id: 2FLM), and Insulin C-peptide (PDB id: 1T0C) using the SIRAH force field running with the Gromacs 18.4 under the conditions reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. Briefly, simulations were performed in triplicate for 5 μs at 300 K and 1 atm in the NPT ensemble. We used a time-step of 20 fs, a direct cutoff for non-bonded interactions of 1.2 nm, and Particle Mesh Ewald summation for long-range electrostatics. For α-synuclein and p31-43, initial conformations were obtained from models built on arbitrary conformations and heated up to 340 K. For PaaA2 antitoxin, Amyloid-beta 1-40, and Proinsulin C-peptide, three different NMR conformers were arbitrarily selected. </p> <p>The information is divided into five tar files containing each system's data (only protein coordinates are reported). Additionally, the Sirah Tools' tcl script with macros for selections and analyses is also included. Please visit http://www.sirahff.com for step-by-step tutorials on running and analyzing CG simulations with SIRAH. </p> <p>To take a quick look at the trajectories:</p> <p>1- Untar the tar file of interest </p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd "your_protein".psf "your_protein".xtc -e sirah_vmdtk.tcl</p> <p><br> Note that using the tcl script you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.</p> <p>This dataset contains simulations associated to a manuscript with the same title and by the same authors.</p> <p>For questions, kindly contact Florencia Klein (fklein@pasteur.edu.uy), Exequiel Barrera (ebarrera@pasteur.edu.uy), or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Input files and scripts for Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered proteins using a software GROMACS patched with PLUMED
<p>Here we share the necessary files and scripts to run Hamiltonian replica-exchange molecular dynamics simulations of intrinsically disordered protein studied in the preprint uploaded to bioRxiv (doi: https://doi.org/10.1101/2020.06.16.155374). It requires software GROMACS patched with PLUMED.</p>
Data from: Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μ s of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies "blobs" of 5-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β -bridging between Val66 and Val94 (on either side of the linker) with specific side-chain interactions between Met66 and Met95.The protein backbone in the vicinity of Met95 is then free to form β -bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.
SpatPPI: a geometric deep learning model for predicting protein-protein interactions involving intrinsically disordered regions
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Data from: Functional advantages of conserved intrinsic disorder in RNA-binding proteins
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Data from: Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
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Data from: A collection of intrinsic disorder characterizations from eukaryotic proteomes
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An Intrinsic Disorder Region Controlling Condensation of a Circadian Clock Component and Rhythmic Transcription in the Liver [RNA-seq]
GEO Series GSE202605. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Arabidopsis heat stress-induced proteins are enriched in electrostatically charged amino acids and intrinsically disordered regions
GEO Series GSE116592. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.