| Literature DB >> 33862077 |
Sk Sarif Hassan1, Diksha Attrish2, Shinjini Ghosh3, Pabitra Pal Choudhury4, Vladimir N Uversky5, Alaa A A Aljabali6, Kenneth Lundstrom7, Bruce D Uhal8, Nima Rezaei9, Murat Seyran10, Damiano Pizzol11, Parise Adadi12, Antonio Soares13, Tarek Mohamed Abd El-Aziz14, Ramesh Kandimalla15, Murtaza M Tambuwala16, Gajendra Kumar Azad17, Samendra P Sherchan18, Wagner Baetas-da-Cruz19, Amos Lal20, Giorgio Palù21, Kazuo Takayama22, Ángel Serrano-Aroca23, Debmalya Barh24, Adam M Brufsky25.
Abstract
The current Coronavirus Disease 19 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) shows similar pathology to MERS and SARS-CoV, with a current estimated fatality rate of 1.4%. Open reading frame 10 (ORF10) is a unique SARS-CoV-2 accessory protein, which contains eleven cytotoxic T lymphocyte (CTL) epitopes each of nine amino acids in length. Twenty-two unique SARS-CoV-2 ORF10 variants have been identified based on missense mutations found in sequence databases. Some of these mutations are predicted to decrease the stability of ORF10 in silico physicochemical and structural comparative analyses were carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid (aa) homology. Though there is a high degree of ORF10 protein similarity of SARS-CoV-2 and Pangolin-CoV, there are differences of these two ORF10 proteins related to their sub-structure (loop/coil region), solubility, antigenicity and shift from strand to coil at aa position 26 (tyrosine). SARS-CoV-2 ORF10, which is apparently expressed in vivo since reactive T cell clones are found in convalescent patients should be monitored for changes which could correlate with the pathogenesis of COVID-19.Entities:
Keywords: COVID-19; Intrinsic disorder; Mutations; ORF10; Pangolin-CoV-2020; SARS-CoV-2
Year: 2021 PMID: 33862077 PMCID: PMC8051021 DOI: 10.1016/j.ijbiomac.2021.03.199
Source DB: PubMed Journal: Int J Biol Macromol ISSN: 0141-8130 Impact factor: 6.953
Twenty-four distinct ORF10 protein IDs correlated with geolocation.
| Accession | Geo_location | Collection_date |
|---|---|---|
| YP_009725255 | China | 2019-12 |
| QLJ57416 | USA: WA | 2020 |
| QIS29991 | China: Hubei, Wuhan | 2020-01-10 |
| QJR96431 | USA: CA | 2020-03-13 |
| QKU54102 | USA: Washington, King County | 2020-03-15 |
| QLA48060 | USA: NY | 2020-03-24 |
| QNG41574 | USA: Minnesota | 2020-03-25 |
| QKV08176 | USA: Washington, King County | 2020-03-26 |
| QKV37245 | Australia: Northern Territory | 2020-03-27 |
| QNI23218 | USA: Virginia | 2020-04 |
| QLG99793 | USA: CA | 2020-04-16 |
| QLY88596 | USA: GA | 2020-04-27 |
| QNC04532 | USA | 2020-04-29 |
| QNI25281 | USA: Virginia | 2020–05 |
| QLI33453 | USA | 2020-05-12 |
| QNC49349 | Pakistan | 2020-05-15 |
| QMT94417 | USA: Washington, Yakima County | 2020-05-27 |
| QMT54534 | USA: Washington, Yakima County | 2020-06-17 |
| QLG76514 | Australia: Victoria | 2020-06-20 |
| QNG42985 | USA: FL | 2020-06-23 |
| QMT97141 | USA: FL | 2020-06-30 |
| QNB17780 | Bangladesh | 2020-07-07 |
| QMU93213 | USA: Wisconsin, Dane county | 2020-07-13 |
| QNA70543 | Bangladesh | 2020-07-19 |
Fig. 1(A): Multiple sequence alignment (MSA) of 24 SARS-CoV-2 ORF10 proteins; (B): phylogeny of 24 SARS-CoV-2 ORF10 sequences.
Fig. 2(A): Mutations and their aa positions in ORF10 proteins; (B): conserved, mutated residues and molecular recognition features of ORF10 (YP_009725255) of SARS-CoV-2.
Twenty-two ORF10 proteins, their corresponding mutations, and predicted effects with chemical property changes.
| Accession ID | Mutations | Type of mutations | PROVEAN score | Effect of mutations on structure | RI | Polarity changes | Charge |
|---|---|---|---|---|---|---|---|
| QNI23218.1 | G2D | Deleterious | −7 | Decrease | 7 | NP to P | Neutral to acidic |
| QIS29991.1 | V6I | Neutral | −1 | Decrease | 7 | NP to NP | Neutral to neutral |
| QLI33453.1 | Y14C | Deleterious | −9 | Decrease | 2 | P to P | Neutral to neutral |
| QNC04532.1 | R20I | Deleterious | −8 | Decrease | 3 | NP to NP | Basic (strongly) to neutral |
| QLA48060.1 | R20K | Deleterious | −3 | Decrease | 8 | NP to P | Basic (strongly) to basic |
| QMT97141.1 | S23F | Deleterious | −6 | Increase | 2 | P to NP | Neutral to neutral |
| QMU93213.1 | R24C | Deleterious | −8 | Decrease | 7 | P to P | Basic (strongly) to neutral |
| QMT54534.1 | R24L | Deleterious | −7 | Decrease | 9 | P to NP | Basic (strongly) to neutral |
| QKU54102.1 | Y26H | Deleterious | −5 | Decrease | 8 | P to P | Neutral to basic (weakly) |
| QNI25281.1 | V30A | Deleterious | −4 | Decrease | 9 | NP to NP | Neutral to neutral |
| QNC49349.1 | V30L | Deleterious | −3 | Decrease | 4 | NP to NP | Neutral to neutral |
| QNA70543.1 | L37F | Deleterious | −4 | Decrease | 7 | NP to NP | Neutral to neutral |
| QKV37245.1 | T38I | Deleterious | −6 | Decrease | 5 | P to NP | Neutral to neutral |
| QKV08176.1 | L37P | Deleterious | −7 | Decrease | 8 | NP to NP | Neutral to neutral |
| QNB17780.1 | F35S | Deleterious | −8 | Decrease | 9 | NP to P | Neutral to neutral |
| QMT94417.1 | D31Y | Deleterious | −9 | Decrease | 6 | P to P | Acidic to neutral |
| QLY88596.1 | A28V | Deleterious | −4 | Decrease | 5 | NP to NP | Neutral to neutral |
| QLG76514.1 | N22T | Deleterious | −6 | Decrease | 1 | P to P | Neutral to neutral |
| QLG99793.1 | I13M | Deleterious | −3 | Decrease | 8 | NP to NP | Neutral to neutral |
| QNG42985.1 | P10S | Deleterious | −8 | Decrease | 8 | NP to P | Neutral to neutral |
| QLJ57416.1 | A8V | Deleterious | −4 | Increase | 3 | NP to NP | Neutral to neutral |
| QNG41574.1 | I4L | Neutral | −2 | Increase | 1 | NP to NP | Neutral to neutral |
PROVEAN score: If the PROVEAN score is equal to or below a predefined threshold (e.g., −2.5), the protein variant is predicted to have a “deleterious” effect. If the PROVEAN score is above the threshold, the variant is predicted to have a “neutral” effect.
RI: Reliability Index ranges from 0 to 9.
Fig. 3Alignment of two ORF10 sequences (37 out of 38 identical residues) of Pangolin-CoV.
Fig. 4(A) Comparison of the intrinsic disorder profile of the reference ORF10 protein from SARS-CoV-2 (YP_009725255) from the NC_045512 SARS-CoV-2 genome (China, Wuhan) (black curve) with ORF10 proteins from the Pangolin-CoV (QIG55954.1) and SARS-CoV TW-HP1 (UniProt ID: Q6SRY8).
(B) Predisposition of intrinsic disease of SARS-CoV-2 ORF10 single variants relative to SARS-CoV-2 (YP 009725255) ORF10 protein of the NC_045512 SARS-CoV-2 genome (China, Wuhan) (black curve). The analysis is conducted using the PONDR-VSL2 algorithm [34], one of the more accurate standalone disorder predictors [[35], [36], [37]]. A thin line (score = 0.5) is the threshold separating order from disorder. Residues with the predicted disorder scores ≥0.5 are considered as disordered, residues with the disorder scores ranging between 0.25 and 0.5 are flexible, whereas disorder scores below 0.25 correspond to ordered residues.
Fig. 5(A): Basic properties of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV; (B): peptide and solvent accessibility properties of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV.
Fig. 6(A): Physicochemical properties and hydropathy of ORF10 of SARS-CoV-2 and Pangolin-CoV; (B): enzymes and numbers of associated cleavages and their positions.
Fig. 7Disordered loops and hotloops of ORF10 of SARS-CoV-2 and Pangolin-CoV.
Fig. 8In 12 HLA subtypes, 11 distinct epitopes were described and analyzed in the SARS-CoV-2 ORF10 for binding affinity using PICKPOCKET. Using the IDEB tool, the IDEB value was estimated. Eleven epitopes of the Wuhan SARS-CoV-2 ORF10 series (marked in orange). Red/blue scores indicate an increase/decline of the score for nine epitopes. The immunogenicity attribute remains unchanged with significant green values.