Browse
Submit Data
Databases
API
Help

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Backbone and nearly complete side-chain chemical shift assignments of the human death-associated protein 1 (DAP1).

ABSTRACT: Death-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer. Here we describe the almost complete [Formula: see text], [Formula: see text], and [Formula: see text] chemical shift assignments of the human DAP1. The limited spectral dispersion, mainly in the [Formula: see text] region, and the lack of defined secondary structure elements, predicted based on chemical shifts, identifies human DAP1 as an intrinsically disordered protein (IDP). This work lays the foundation for further structural investigations, dynamic studies, mapping of potential interaction partners or drug screening and development.

SUBMITTER: Wiedemann C

PROVIDER: S-EPMC7973646 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Backbone and nearly complete side-chain chemical shift assignments of the human death-associated protein 1 (DAP1).

Wiedemann Christoph C Voigt Johanna J Jirschitzka Jan J Häfner Sabine S Ohlenschläger Oliver O Bordusa Frank F

Biomolecular NMR assignments 20201202 1

Death-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer. Here we describe the almost complete [Formula: see text], [Formula: see text], and [Formula: see text] chemical shift assignments of the human DAP1. The limited spectral dispersion, mainly ...[more]

PMID: 33263927

Similar Datasets

Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered.

Project description:Even though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these "unknown" proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the [Formula: see text]H, [Formula: see text]C, [Formula: see text]N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.

| S-EPMC8481210 | biostudies-literature

Backbone and side-chain chemical shift assignments of p50 subunit of NF-κB transcription factor.

Project description:Nuclear Factor κB (NF-κB) is a family of five related transcription factors that recognize a κB DNA element on the promoter and enhancer regions of target genes and modulate their expression. Here we report a complete set of 1H, 13C, 15N backbone and side chain resonance assignments for the p50 DNA binding and dimerization domains of the p50 homodimer form of the NF-κB transcription factor. The chemical shift data constitute a first step towards understanding the mechanism of interaction of the p50 homodimer with DNA.

| S-EPMC7960568 | biostudies-literature

Backbone and side-chain chemical shift assignments of full-length, apo, human Pin1, a phosphoprotein regulator with interdomain allostery.

Project description:Pin1 is a human peptidyl-prolyl cis-trans isomerase important for the regulation of phosphoproteins that are implicated in many diseases including cancer and Alzheimer's. Further biophysical study of Pin1 will elucidate the importance of the two-domain system to regulate its own activity. Here, we report near-complete backbone and side-chain 1H, 13C and 15N NMR chemical shift assignments of full-length, apo Pin1 for the purpose of studying interdomain allostery and dynamics.

| S-EPMC9205186 | biostudies-literature

UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.

Project description:Chemical shifts are a readily obtainable NMR observable that can be measured with high accuracy, and because they are sensitive to conformational averages and the local molecular environment, they yield detailed information about protein structure in solution. To predict chemical shifts of protein structures, we introduced the UCBShift method that uniquely fuses a transfer prediction module, which employs sequence and structure alignments to select reference chemical shifts from an experimental database, with a machine learning model that uses carefully curated and physics-inspired features derived from X-ray crystal structures to predict backbone chemical shifts for proteins. In this work, we extend the UCBShift 1.0 method to side chain chemical shift prediction to perform whole protein analysis, which, when validated against well-defined test data shows higher accuracy and better reliability compared to the popular SHIFTX2 method. With the greater abundance of cleaned protein shift-structure data and the modularity of the general UCBShift algorithms, users can gain insight into different features important for residue-specific stabilizing interactions for protein backbone and side chain chemical shift prediction. We suggest several backward and forward applications of UCBShift 2.0 that can help validate AlphaFold structures and probe protein dynamics.

| S-EPMC11784523 | biostudies-literature

Backbone chemical shift spectral assignments of SARS coronavirus-2 non-structural protein nsp9.

Project description:As part of an International consortium aiming at the characterization by NMR of the proteins of the SARS-CoV-2 virus, we have obtained the virtually complete assignment of the backbone atoms of the non-structural protein nsp9. This small (12 kDa) protein is encoded by ORF1a, binds to RNA and seems to be essential for viral RNA synthesis. The crystal structures of the SARS-CoV-2 protein and other homologues suggest that the protein is dimeric as also confirmed by analytical ultracentrifugation and dynamic light scattering. Our data constitute the prerequisite for further NMR-based characterization, and provide the starting point for the identification of small molecule lead compounds that could interfere with RNA binding and prevent viral replication.

| S-EPMC7985572 | biostudies-literature

1H, 13C, and 15N backbone and side chain chemical shift assignments of the SARS-CoV-2 non-structural protein 7.

Project description:The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project covid19-nmr, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein nsp7. The 83 amino acid nsp7 protein is an essential cofactor in the RNA-dependent RNA polymerase. The polymerase activity and processivity of nsp12 are greatly enhanced by binding 1 copy of nsp7 and 2 copies of nsp8 to form a 160 kD complex. A separate hexadecameric complex of nsp7 and nsp8 (8 copies of each) forms a large ring-like structure. Thus, nsp7 is an important component of several large protein complexes that are required for replication of the large and complex coronavirus genome. We here report the near-complete NMR backbone and sidechain resonance assignment (1H,13C,15N) of isolated nsp7 from SARS-CoV-2 in solution. Further, we derive the secondary structure and compare it to the previously reported assignments and structure of the SARS-CoV nsp7.

| S-EPMC7678775 | biostudies-literature

Backbone and side chain resonance assignments for a structured domain within Atg32.

Project description:Autophagy is a catabolic cellular process that targets cytosolic material, including mitochondria, to the vacuole or lysosomes for degradation. The selective degradation of mitochondria by autophagy is termed mitophagy. Dysfunctional mitophagy, which leads to the accumulation of damaged mitochondria, has been implicated in Parkinson's disease, cancer, cardiac disease and metabolic disease. In Saccharomyces cerevisiae, mitophagy is initiated by the autophagy receptor Atg32, an outer mitochondrial membrane protein. A lack of structural information for Atg32 has hindered our understanding of the molecular mechanisms of mitophagy initiation. To gain new structural insight into Atg32, we have identified the location of a structured domain within the cytosolic region of Atg32 and completed the backbone and side chain resonance assignments for this domain.

| S-EPMC5693731 | biostudies-literature

Backbone and ILV side chain methyl group assignments of the integral human membrane protein VDAC-1.

Project description:The voltage dependent anion channel (VDAC) forms a channel for metabolites and nutrients in the outer membrane of mitochondria, and it is also involved in apoptotic pathways. Here, we report sequence-specific NMR assignments for the isoform 1 of human VDAC reconstituted in lauryldimethylamine oxide (LDAO) detergent micelles. The assignments were deposited in the BMRB data base with accession number 16381.

| S-EPMC2896003 | biostudies-literature

Backbone chemical shift assignments and secondary structure analysis of the U1 protein from the Bas-Congo virus.

Project description:The Bas-Congo virus (BASV) is the first rhabdovirus associated with a human outbreak of acute hemorrhagic fever. The single-stranded, negative-sense RNA genome of BASV contains the five core genes present in all rhabdoviral genomes plus an additional three genes, annotated U1, U2, and U3, with weak (<21%) sequence similarity only to a handful of genes observed in a few other rhabdoviral genomes. The function of the rhabdoviral U proteins is unknown, but, they are hypothesized to play a role in viral infection or replication. To better understand this unique family of proteins, a construct containing residues 27-203 of the 216-residue U1 protein (BASV-U1*) was prepared. By collecting data in 0.5 M urea it was possible to eliminate transient association enough to enable the assignment of most of the observable 1HN, 1Hα, 15N, 13Cα, 13Cβ, and 13C´ chemical shifts for BASV-U1* that will provide a foundation to study its solution properties. The analyses of these chemical shifts along with 15N-edited NOESY data enabled the identification of the elements of secondary structure present in BASV-U1*.

| S-EPMC8457264 | biostudies-literature

Backbone and side-chain NMR assignments for the C-terminal domain of mammalian Vps28.

Project description:Vps28 is one of four cytosolic proteins comprising the endosomal sorting complex required for transport I (ESCRT-I). ESCRT-I is involved in sorting ubiquitinated proteins to multivesicular bodies as well as in mediating budding of retroviruses. Here, we report the backbone and side-chain assignments of the mammalian C-terminal domain of Vps28 (mVps28(CTD)), which is involved in interactions with other ESCRT components. We also compare the predicted secondary structures of mVps28(CTD) with those of the published X-ray crystal structures of Saccharomyces cerevisiae and Xenopus laevis Vps28(CTD). These NMR resonance assignments will facilitate chemical shift mapping and structural determination of mammalian Vps28 interactions with other components of the endosomal sorting machinery that sorts ubiquitinated proteins for lysosomal degradation.

| S-EPMC4470380 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data