Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Blind testing cross-linking/mass spectrometry under the auspices of the 11^th critical assessment of methods of protein structure prediction (CASP11).

ABSTRACT: Determining the structure of a protein by any method requires various contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry (HD-CLMS) data in combination with ab initio structure prediction determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structure of up to 2.5 Å, or 3.4 Å in the context of blood serum. This paper reports the blind test on the readiness of this technology through the help of Critical Assessment of protein Structure Prediction (CASP). We identified between 201-381 unique residue pairs at an estimated 5% FDR (at link level albeit with missing site assignment precision evaluation), for four target proteins. HD-CLMS proved reliable once crystal structures were released. However, improvements in structure prediction using cross-link data were slight. We identified two reasons for this. Spread of cross-links along the protein sequence and the tightness of the spatial constraints must be improved. However, for the selected targets even ideal contact data derived from crystal structures did not allow modellers to arrive at the observed structure. Consequently, the progress of HD-CLMS in conjunction with computational modeling methods as a structure determination method, depends on advances on both arms of this hybrid approach.

SUBMITTER: Belsom A

PROVIDER: S-EPMC5354267 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)

Project description:We report the first blind test on the readiness of combining high-density cross-linking/mass spectrometry data in conjunction with ab initio structure prediction, through the help of Critical Assessment of protein Structure Prediction (CASP). This blind test was coordinated by the CASP organizers and utilized the experimental protocol developed in our lab for providing high-density cross-linking/mass spectrometry data in a matter of days. The CASP organizing committee identified and acquired suitable targets and published resulting data on the CASP web page for the community of structure predictors. We provided high-density cross-linking/mass spectrometry data for four targets in CASP11, revealing to us some of the current limitations of cross-linking. These are areas where the method must now develop. With CASP taking place biannually into the future, blind testing low-resolution structure analysis tools is a worthwhile and feasible undertaking.

2016-12-02 | PXD003643 | Pride

Suicides of Punjabi hawkers in 19th- and early 20th-century Australia.

Project description:BackgroundDuring the late nineteenth century, a considerable number of young Punjabi men sought their fortunes in the Australian colonies, working as hawkers and farm labor. While in Australia they experienced marginalization and high levels of racial vilification by the Anglo-Celtic settler community.AimsTo assess the frequency and nature of suicides of Punjabi workers in nineteenth century Australia.Materials and methodsThe paper draws on archival sources and contemporary newspaper reports.ResultsA wide range of methods of suicides were observed, with drowning the preferred method.ConclusionsThis article is the first to collate the data on the suicides and suicide attempts by young Punjabi men working in an immigration country. It can be shown that the suicide rate among Punjabi was almost six times higher than that of the host community.

| S-EPMC6657551 | biostudies-literature

Birthing parents had a lower risk of testing positive for SARS-CoV-2 in the peripartum period in Norway, 15th of February 2020 to 15th of May 2021.

Project description:Hospital infection control measures against COVID-19 may come into conflict with patients' need for support. In Norway, some hospitals have restricted access for partners of women giving birth. We investigated the incidence rate of SARS-CoV-2 among birthing parents compared to similarly aged women and men in the general population; and the additional risk posed by allowing partners in. Birthing parents often shared infection status and had a slightly lower incidence rate than the general population in the peripartum period. They should not be considered a high-risk group for SARS-CoV-2 infections.

| S-EPMC8579713 | biostudies-literature

Correction of 4th and 5th metacarpal synostosis in a skeletally mature hand using de-rotational osteotomies.

Project description:We present the successful surgical treatment and management of metacarpal synostosis in a near-skeletally mature 15-year-old patient, the significance of which is underscored by an updated review of the literature. We additionally outline a reliable surgical approach for patients with similar clinical presentations and disease severity.

| S-EPMC8725938 | biostudies-literature

Reconstruction of the cropland cover changes in eastern China between the 10th century and 13th century using historical documents.

Project description:To evaluate and improve datasets of anthropogenic land cover change used in local and global climate models, great efforts were made to reconstruct historical land use, including the LandCover 6k project which dedicated to reconstructing human land use over the past 10,000 years. In this study, we utilized historical records, including taxed-cropland and cropland measurement areas, and data on the number of households in eastern China between the 10th century and 13th century in concert with coefficient calibration, model allocation, and per capita cropland estimation to reconstruct areas of provincial cropland for 22 provinces over five time periods. Our reconstructions indicate that total cropland areas of eastern China for AD 1000, 1066, 1078, 1162, and 1215 are 34.74 × 106 ha, 49.42 × 106 ha, 51.62 × 106 ha, 35.21 × 106 ha, and 51.21 × 106 ha, respectively. And the cropland area fluctuated because of dynasty shift and went through three phases. Cropland expansion and contraction mainly occurred in the middle and lower reaches of the Yangtze and Yellow Rivers as well as the Huaihe River Basin, while in some regions far away from battlefields, including northeastern and southern China, cropland area expanded continuously throughout the study period.

| S-EPMC6131514 | biostudies-literature

ACNP 59th Annual Meeting: Poster Session II.

Project description: Not available

| S-EPMC7735200 | biostudies-literature

ACNP 59th Annual Meeting: Poster Session III.

Project description: Not available

| S-EPMC7735201 | biostudies-literature

ACNP 59th Annual Meeting: Poster Session I.

Project description: Not available

| S-EPMC7735198 | biostudies-literature

ACNP 58th Annual Meeting: Poster Session I.

Project description: Not available

| S-EPMC6957924 | biostudies-literature

Characterization of a strong covalent Th3+-Th3+ bond inside an Ih(7)-C80 fullerene cage.

Project description:The nature of the actinide-actinide bonds is of fundamental importance to understand the electronic structure of the 5f elements. It has attracted considerable theoretical attention, but little is known experimentally as the synthesis of these chemical bonds remains extremely challenging. Herein, we report a strong covalent Th-Th bond formed between two rarely accessible Th3+ ions, stabilized inside a fullerene cage nanocontainer as Th2@Ih(7)-C80. This compound is synthesized using the arc-discharge method and fully characterized using several techniques. The single-crystal X-Ray diffraction analysis determines that the two Th atoms are separated by 3.816 Å. Both experimental and quantum-chemical results show that the two Th atoms have formal charges of +3 and confirm the presence of a strong covalent Th-Th bond inside Ih(7)-C80. Moreover, density functional theory and ab initio multireference calculations suggest that the overlap between the 7s/6d hybrid thorium orbitals is so large that the bond still exists at Th-Th separations larger than 6 Å. This work demonstrates the authenticity of covalent actinide metal-metal bonds in a stable compound and deepens our fundamental understanding of f element metal bonds.

| S-EPMC8062539 | biostudies-literature