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36 results for “intrinsically disordered proteins”
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
Open the record for dataset details and reuse information.
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.
Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (iCLIP results)
GEO Series GSE139878. Caenorhabditis elegans. 6 samples. Type: Other.
Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks
GEO Series GSE275475. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Ensembles for: Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins
<p>Flexible Meccano and Campari conformational ensembles used in the publication "<em>Computing, Analyzing, and Comparing the Radius of Gyration and Hydrodynamic Radius in Conformational Ensembles of Intrinsically Disordered Proteins</em>" by Ahmed M.C., Crehuet R., Lindorff-Larsen K.. Paper available at: https://doi.org/10.1007/978-1-0716-0524-0_21</p>
Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cells
GEO Series GSE169295. Homo sapiens. 2 samples. Type: Expression profiling by array.
Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins
GEO Series GSE139881. Caenorhabditis elegans. 24 samples. Type: Other; Expression profiling by high throughput sequencing.
Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (RNAseq and ribosome profiling)
GEO Series GSE139880. Caenorhabditis elegans. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
Targeting intrinsically disordered nuclear protein 1 (NUPR1) with single-domain antibodies alleviates triple-negative breast cancer (TNBC) progression in vivo
GEO Series GSE300149. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing
GEO Series GSE151125. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (RNAseq datasets)
GEO Series GSE139879. Caenorhabditis elegans. 6 samples. Type: Expression profiling by high throughput sequencing.
The intrinsically disordered TSSC4 protein acts as a helicase inhibitor, placeholder and multi-interaction coordinator during snRNP assembly and recycling
GEO Series GSE185418. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing; Other.
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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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.