Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.

DisProt is the major repository of manually curated data for intrinsically disordered proteins collected from the literature. Although lacking a stable three-dimensional structure under physiological conditions, intrinsically disordered proteins carry out a plethora of biological functions, some of them directly arising from their flexible nature. A growing number of scientific studies have been published during the last few decades to shed light on their unstructured state, their binding modes, and their functions. DisProt makes use of a team of expert biocurators to provide up-to-date annotations of intrinsically disordered proteins from the literature, making them available to the scientific community. Here we present a comprehensive description on how to use DisProt in different contexts and provide a detailed explanation of how to explore and interpret manually curated annotations of intrinsically disordered proteins. We describe how to search DisProt annotations, both using the web interface and the API for programmatic access. Finally, we explain how to visualize and interpret a DisProt entry, the SARS-CoV-2 Nucleoprotein, characterized by the presence of unstructured N-terminal and C-terminal regions and a flexible linker. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Performing a search in DisProt Support Protocol 1: Downloading options Support Protocol 2: Programmatic access with DisProt REST API Basic Protocol 2: Exploring the DisProt Ontology page Basic Protocol 3: Visualizing and interpreting DisProt entries-the SARS-CoV-2 Nucleoprotein use case.

The impact of COVID-19 on the living and survival conditions of internally displaced persons in Burkina Faso.

In recent years, as in other parts of the Sahel, the threat of terrorism has escalated in Burkina Faso. In 2019, this country hosted the fourth highest number of new conflict-related internal displaced persons (IDPs) in the world. These people have to cope simultaneously with the full spectrum of environmental, social and health-related stresses in the long, medium and short term, respectively. We seek to compare the living conditions of IDPs before and during the lockdown implemented by the authorities (between 27 March and 5 May 2020) to contain the spread of the virus. Interviews were conducted with 106 IDPs in Kongoussi (Central-Northern region). Although no respondent reported having been directly affected by the virus, 84.9% of the IDPs surveyed had no income-generating activities during the lockdown and the remaining 15.1% who continued to work reported that their activities had been greatly scaled-down. For a large majority of them, their living conditions, already described as difficult under 'normal' circumstances (insufficient food, insignificant financial assistance, or difficult access to health care), further deteriorated. In addition, IDPs were unable to leave the camps or regions where they were located to search for better living conditions or to return home. Lastly, 96.2% of respondents believed that the COVID-19 pandemic would have a negative impact on their future. These IDPs, like many in the sub-region and around the world, therefore require urgent assistance from the authorities and humanitarian NGOs, as the slightest new stress is likely to considerably worsen their already vulnerable state.

SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion.

The SARS-CoV-2 pandemic is maintained by the emergence of successive variants, highlighting the flexibility of the protein sequences of the virus. We show that experimentally determined intrinsically disordered regions (IDRs) are abundant in the SARS-CoV-2 viral proteins, making up to 28% of disorder content for the S1 subunit of spike and up to 51% for the nucleoprotein, with the vast majority of mutations occurring in the 13 major variants mapped to these IDRs. Strikingly, antigenic sites are enriched in IDRs, in the receptor-binding domain (RBD) and in the N-terminal domain (NTD), suggesting a key role of structural flexibility in the antigenicity of the SARS-CoV-2 protein surface. Mutations occurring in the S1 subunit and nucleoprotein (N) IDRs are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies. Overall, this suggests the presence of variable regions on S1 and N protein surfaces, which confer sequence and antigenic flexibility to the virus without altering its protein functions.

Higher risk of COVID-19 infection among internally displaced persons (IDPs) in Myanmar under the military coup.

Access to healthcare has been difficult for over a thousand internally displaced people (IPDs) living in camps even before the COVID-19 pandemic surge in Myanmar. Amidst the pandemic crisis, the coup d'etat state power on February 1, 2021, and arbitrary detained all elected officials. Subsequently, over a hundred thousand civilians were displaced from their homes due to the intensified conflict between the military, ethnic armed groups, and people's defence force (PDF). The military attacks on IDP camps, deliberately blockings all humanitarian aid to IDPs, including medical packages and food pack supplies more vulnerable to contracting an infection. Many of IDPs suffer from infectious diseases such as malaria and dengue fever. Some tested COVID-19 positive due to their precarious living conditions, lack of protective resources supplies and lack of access to healthcare. Urgent international community response is needed to halt the military inhumanity action against the people of Myanmar to curb the pandemic outbreak among the IDPs in Myanmar. Access to primary healthcare services is a fundamental human right. No one should be ignored in vaccination in the fight against the global health pandemic because no one will be safe until everyone is safe.

The highly flexible disordered regions of the SARS-CoV-2 nucleocapsid N protein within the 1-248 residue construct: sequence-specific resonance assignments through NMR.

The nucleocapsid protein N from SARS-CoV-2 is one of the most highly expressed proteins by the virus and plays a number of important roles in the transcription and assembly of the virion within the infected host cell. It is expected to be characterized by a highly dynamic and heterogeneous structure as can be inferred by bioinformatics analyses as well as from the data available for the homologous protein from SARS-CoV. The two globular domains of the protein (NTD and CTD) have been investigated while no high-resolution information is available yet for the flexible regions of the protein. We focus here on the 1-248 construct which comprises two disordered fragments (IDR1 and IDR2) in addition to the N-terminal globular domain (NTD) and report the sequence-specific assignment of the two disordered regions, a step forward towards the complete characterization of the whole protein.

Is Nigeria prepared and ready to respond to the COVID-19 pandemic in its conflict-affected northeastern states?

Northeastern Nigeria has over the decade suffered from the Boko Haram insurgency and is still in the process of recovery from the complex humanitarian crisis that has displaced and subjected millions of vulnerable children, women and elderly population to poverty, disease outbreaks, hunger and malnutrition. Yet, the conflict-affected states in Northeastern Nigeria is not far away from being the worse-hit by the COVID-19 pandemic if urgent public health preventive measures are not taken to contain the spread of the deadly and highly infectious virus. The question arises, "what is Nigeria doing to tackle the burden of a COVID-19 spread and an ongoing humanitarian crisis?