Journal of proteins and proteomics最新文献

The emergence of novel coronavirus SARS-CoV-2 is responsible for causing coronavirus disease-19 (COVID-19) imposing serious threat to global public health. Infection of SARS-CoV-2 to the host cell is characterized by direct translation of positive single stranded (+ ss) RNA to form large polyprotein polymerase 1ab (pp1ab), which acts as precursor for a number of nonstructural and structural proteins that play vital roles in replication of viral genome and biosynthesis of new virus particles. The maintenance of viral protein homeostasis is essential for continuation of viral life cycle in the host cell. To test whether the protein homeostasis of SARS-CoV-2 can be disrupted by inducing specific protein aggregation, we made an effort to examine whether the viral proteome contains any aggregation prone regions (APRs) that can be explored for inducing toxic protein aggregation specifically in viral proteins and without affecting the host cell. This curiosity leads to the identification of several (> 70) potential APRs in SARS-CoV-2 proteome. The length of the APRs ranges from 5 to 25 amino acid residues. Nearly 70% of total APRs investigated are relatively smaller and found to be in the range of 5-10 amino acids. The maximum number of ARPs (> 50) was observed in pp1ab. On the other hand, the structural proteins such as, spike (S), nucleoprotein (N), membrane (M) and envelope (E) proteins also possess APRs in their primary structures which altogether constitute 30% of the total APRs identified. Our findings may provide new windows of opportunities to design specific peptide-based, anti-SARS-CoV-2 therapeutic molecules against COVID-19.

There are three types of proteins in coronaviruses: nonstructural, structural, and accessory proteins. Coronavirus proteins are essential for viral replication and for the binding and invasion of hosts and the regulation of host cell metabolism and immunity. This study investigated the amino acid sequence similarity and identity percentages of 10 proteins in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were the 1ab polyprotein, spike protein, orf3a, the envelope protein, the membrane protein, orf6, orf7a, orf7b, orf8, and the nucleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the percentages of protein similarity and identity in the three viruses. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins were both greater than 95%, while the identity and similarity percentages of SARS-CoV-2 and SARS-CoV were both greater than 38%. The proteins of SARS-CoV-2 and BatCoV RaTG13 have high identity and similarity compared to those of SARS-CoV-2 and SARS-CoV.

Graphic abstract: The proteins of the SARS-CoV-2 are most identical and similar to those of BatCoV RaTG13 than to the proteins of SARS-CoV.

Supplementary information: The online version contains supplementary material available at 10.1007/s42485-021-00060-3.

In the ongoing COVID-19 pandemic, the global fraternity of researchers has been assiduously investigating pharmacological interventions against the SARS-CoV2. This novel virus is known to gain entry through the ACE 2 receptor of pulmonary epithelial cells lining the respiratory tract. Many of its initial symptoms (e.g. difficulty breathing) resemble acute high altitude illnesses, particularly HAPE. Based on these overt symptoms, a number of high altitude researchers have speculated on repurposing of drugs used to treat acute altitude illnesses (especially HAPE). However, eminent high altitude researchers with medical expertise as well as some studies on the deeper causes underlying the overt symptoms have found that such repurposing maybe counter-productive. Other factors, (e.g. contra-indications of these drugs), make their use in COVID-19 patients hazardous. The fit-for-repurposing options maybe experimental prophylactic interventions (e.g. silymarin, curcumin) which have proven anti-oxidant and anti-inflammatory effects. Another line of thought focuses on proteomics-based investigations of such patients. However, apart from the logistical and safety issues, a targeted proteomics approach based on prior sound molecular investigations is a more logical approach instead of mere shotgun proteomics. In this commentary, we shed light on such issues associated with COVID-19.