مروری بر بررسی های بیوانفورماتیکی عملکرد پروتئین های ساختاری، غیرساختاری و سطح گلیکوپروتئین مهارکننده متابولیسیم پروتئین هِم توسط کرونا ویروس

[1] Corman VM, Lienau J, Witzenrath M. [Coronaviruses as the
cause of respiratory infections]. Internist (German)]. 2019;
60(11):1136-45. [DOI:10.1007/s00108-019-00671-5] [PMID]
[PMCID]
[2] Guo Q, Li M, Wang C, Wang P, Fang Z, Wu S, et al. Host and
infectivity prediction of Wuhan 2019 novel coronavirus using
deep learning algorithm. Biorxiv preprint. 2020; 1-10. [Unpublished].
[Link]
[3] Sironi M, Hasnain SE, Rosenthal B, Phan T, Luciani F, Shaw
MA, et al. SARS-COV-2 and covid-19: A genetic, epidemiological,
and evolutionary perspective. Infect Genet Evol. 2020;
84:104384. [DOI:10.1016/j.meegid.2020.104384] [PMID]
[PMCID]
[4] Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al.
A pneumonia outbreak associated with a new coronavirus
of probable bat origin. Nature. 2020; 579(7798):270-3.
[DOI:10.1038/s41586-020-2012-7] [PMID] [PMCID]
[5] Chen Y, Liu Q, Guo D. Emerging coronaviruses: Genome
structure, replication, and pathogenesis. J Med Virol. 2020;
92(4):418-23. [DOI:10.1002/jmv.25681] [PMID] [PMCID]
[6] He J, Tao H, Yan Y, Huang SY, Xiao Y. Molecular mechanism
of evolution and human infection with SARS-COV-2. Viruses.
2020; 12(4):428. [DOI:10.3390/v12040428] [PMID] [PMCID]
[7] He J, Tao H, Yan Y, Huang S, Xiao Y. Molecular mechanism of
evolution and human infection with the novel coronavirus
(2019-nCoV). Biorxiv preprint. 2020; 1-19. [Unpublished]
[DOI:10.1101/2020.02.17.952903]
[8] Mycroft-West C, Su D, Elli S, Li Y, Guimond S, Miller G, et al.
The 2019 coronavirus (SARS-COV-2) surface protein (Spike) S1
receptor binding domain undergoes conformational change
upon heparin binding. BioRxiv preprint. 2020; 1-9. [Unpublished]
[DOI:10.1101/2020.02.29.971093]
[9] Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The
proximal origin of SARS-COV-2. Nat Med. 2020; 26(4):450-2.
[DOI:10.1038/s41591-020-0820-9] [PMID] [PMCID]
[10] Liu W, Li H. Covid-19 disease: ORF8 and surface glycoprotein
inhibit heme metabolism by binding to porphyrin. Biological
and Medicinal Chemistry. 2020; 1-23. [DOI:10.26434/chemrxiv.
11938173.v3]
[11] Diao K, Han P, Pang T, Li Y, Yang Z. HRCT imaging features
in representative imported cases of 2019 novel coronavirus
pneumonia. Precision Clinical Medicine. 2020; 3(1):9-13.
[DOI:10.1093/pcmedi/pbaa004] [PMCID]
[12] Quiros Roldan E, Biasiotto G, Magro P, Zanella I. The possible
mechanisms of action of 4-aminoquinolines (chloroquine/hydroxychloroquine)
against SARS-COV-2 infection (covid-19): A
role for iron homeostasis? Pharmacol Res. 2020; 158:104904.
[DOI:10.1016/j.phrs.2020.104904] [PMID] [PMCID]
[13] Liu W, Li H. Covid-19: Attacks the 1-beta chain of hemoglobin
and captures the porphyrin to inhibit human heme
metabolism. Biological and Medicinal Chemistry. 2020; 1-28.
[DOI:10.26434/chemrxiv.11938173]
[14] Chaw SM, Tai JH, Chen SL, Hsieh CH, Chang SY, Yeh SH, et al.
The origin and underlying driving forces of the SARS-COV-2
outbreak. J Biomed Sci. 2020; 27(1):73. [DOI:10.1186/s12929-
020-00665-8] [PMID] [PMCID]
[15] Örd M, Faustova I, Loog M. The sequence at Spike S1/S2 site
enables cleavage by furin and phospho-regulation in SARSCoV2
but not in SARS-CoV1 or MERS-CoV. Sci Reports. 2020;
10(1):1-0. [DOI:10.1038/s41598-020-74101-0]
[16] Chan CM, Woo PC, Lau SK, Tse H, Chen HL, Li F, Zheng BJ,
Chen L, Huang JD, Yuen KY. Spike protein, S, of human coronavirus
HKU1: role in viral life cycle and application in antibody
detection. Experimental Biology Med. 2008; 233(12):1527-36.
[DOI:10.3181/0806-RM-197]
[17] Elrashdy F, Redwan EM, Uversky VN. Why covid-19 transmission
is more efficient and aggressive than viral transmission
in previous coronavirus epidemics? Biomolecules. 2020;
10(9):1312. [DOI:10.3390/biom10091312] [PMID] [PMCID]
[18] +++Stech O, Veits J, Weber S, Deckers D, Schröer D, Vahlenkamp
TW, et al. Acquisition of a polybasic hemagglutinin cleavage
site by a low-pathogenic avian influenza virus is not sufficient
for immediate transformation into a highly pathogenic
strain. J Virol. 2009; 83(11):5864-8. [DOI:10.1128/JVI.02649-
08] [PMID] [PMCID]
[19] Johnson BA, Graham RL, Menachery VD. Viral metagenomics,
protein structure, and reverse genetics: Key strategies
for investigating coronaviruses. Virology. 2018; 517:30-7.
[DOI:10.1016/j.virol.2017.12.009]
[20] Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses.
Nature Rev Microbiol. 2019; 17(3):181-92.
[DOI:10.1038/s41579-018-0118-9]
[21] Ranjha MI, Mooneeb Ali M. Covid 19 infodemic: An analysis
of myths and realities. Euro J Nat Soc Sci. 2020; 9(4):773-97.
[22] Huang C, Lokugamage KG, Rozovics JM, Narayanan K, Semler
BL, Makino S. SARS coronavirus nsp1 protein induces
template-dependent endonucleolytic cleavage of mRNAs:
Viral mRNAs are resistant to nsp1-induced RNA cleavage.
Plos Pathog. 2011; 7(12):e1002433. [DOI:10.1371/journal.
ppat.1002433] [PMID] [PMCID]
[23] Tanaka T, Kamitani W, DeDiego ML, Enjuanes L, Matsuura
Y. Severe acute respiratory syndrome coronavirus nsp1 facilitates
efficient propagation in cells through a specific translational
shutoff of host mRNA. J Virol. 2012; 86(20):11128-37
[DOI:10.1128/JVI.01700-12] [PMID] [PMCID]
[24] Graham RL, Sims AC, Brockway SM, Baric RS, Denison MR.
The nsp2 replicase proteins of murine hepatitis virus and
severe acute respiratory syndrome coronavirus are dispensable
for viral replication. J Virol. 2005; 79(21):13399-411.
[DOI:10.1128/JVI.79.21.13399-13411.2005] [PMID] [PMCID]
[25] Gadlage MJ, Graham RL, Denison MR. Murine coronaviruses
encoding nsp2 at different genomic loci have altered
replication, protein expression, and localization. J Virol. 2008;
82(23):11964-9. [DOI:10.1128/JVI.01126-07] [PMID] [PMCID]
Piri-Gharaghie T, et al. A Review of Bio-informatics Studies on the Function of Structural and Non-structural Proteins and the Level of Glycoprotein Inhibiting Heme Metabolism . JSMJ. 2022; 21(2):176-193
192
June, July 2022. Volume 21. Number 2
[26] Lei J, Kusov Y, Hilgenfeld R. Nsp3 of coronaviruses: Structures
and functions of a large multi-domain protein. Antiviral
Res. 2018; 149:58-74. [DOI:10.1016/j.antiviral.2017.11.001]
[PMID] [PMCID]
[27] Serrano P, Johnson MA, Chatterjee A, Neuman BW, Joseph
JS, Buchmeier MJ, et al. Nuclear magnetic resonance structure
of the nucleic acid-binding domain of severe acute respiratory
syndrome coronavirus nonstructural protein 3. J Virol. 2009;
83(24):12998-3008. [DOI:10.1128/JVI.01253-09] [PMID] [PMCID]
[28] Beachboard DC, Anderson-Daniels JM, Denison MR. Mutations
across murine hepatitis virus nsp4 alter virus fitness
and membrane modifications. J Virol. 2015; 89(4):2080-9.
[DOI:10.1128/JVI.02776-14] [PMID] [PMCID]
[29] Gadlage MJ, Sparks JS, Beachboard DC, Cox RG, Doyle JD,
Stobart CC, et al. Murine hepatitis virus nonstructural protein
4 regulates virus-induced membrane modifications and
replication complex function. J Virol. 2010; 84(1):280-90.
[DOI:10.1128/JVI.01772-09] [PMID] [PMCID]
[30] Stobart CC, Sexton NR, Munjal H, Lu X, Molland KL, Tomar
S, et al. Chimeric exchange of coronavirus nsp5 proteases
(3CLpro) identifies common and divergent regulatory determinants
of protease activity. J Virol. 2013; 87(23):12611-8.
[DOI:10.1128/JVI.02050-13] [PMID] [PMCID]
[31] Zhu X, Wang D, Zhou J, Pan T, Chen J, Yang Y, et al. Porcine deltacoronavirus
nsp5 antagonizes type i interferon signaling by
cleaving STAT2. J Virol. 2017; 91(10):e00003-17. [DOI:10.1128/
JVI.00003-17] [PMID] [PMCID]
[32] Angelini MM, Akhlaghpour M, Neuman BW, Buchmeier MJ.
Severe acute respiratory syndrome coronavirus nonstructural
proteins 3, 4, and 6 induce double-membrane vesicles. mBio.
2013; 4(4):e00524-13. [DOI:10.1128/mBio.00524-13] [PMID]
[PMCID]
[33] Cottam EM, Whelband MC, Wileman T. Coronavirus NSP6
restricts autophagosome expansion. Autophagy. 2014;
10(8):1426-41. [DOI:10.4161/auto.29309] [PMID] [PMCID]
[34] Kirchdoerfer RN, Ward AB. Structure of the SARS-CoV nsp12
polymerase bound to nsp7 and nsp8 co-factors. Nat Commun.
2019; 10(1):2342. [DOI:10.1038/s41467-019-10280-3] [PMID]
[PMCID]
[35] Zhai Y, Sun F, Li X, Pang H, Xu X, Bartlam M, et al. Insights
into SARS-CoV transcription and replication from the structure
of the nsp7-nsp8 hexadecamer. Nat Struct Mol Biol. 2005;
12(11):980-6. [DOI:10.1038/nsmb999] [PMID] [PMCID]
[36] te Velthuis AJ, van den Worm SH, Snijder EJ. The SARS-coronavirus
nsp7+nsp8 complex is a unique multimeric RNA polymerase
capable of both de novo initiation and primer extension.
Nucleic Acids Res. 2012; 40(4):1737-47. [DOI:10.1093/
nar/gkr893] [PMID] [PMCID]
[37] Egloff MP, Ferron F, Campanacci V, Longhi S, Rancurel C, Dutartre
H, et al. The severe acute respiratory syndrome-coronavirus
replicative protein nsp9 is a single-stranded RNA-binding
subunit unique in the RNA virus world. Proc Natl Acad Sci U
S A. 2004; 101(11):3792-6. [DOI:10.1073/pnas.0307877101]
[PMID] [PMCID]
[38] Zeng Z, Deng F, Shi K, Ye G, Wang G, Fang L, et al. Dimerization
of coronavirus nsp9 with diverse modes enhances its
nucleic acid binding affinity. J Virol. 2018; 92(17):e00692-18.
[DOI:10.1128/JVI.00692-18] [PMID] [PMCID]
[39] Bouvet M, Lugari A, Posthuma CC, Zevenhoven JC, Bernard
S, Betzi S, et al. Coronavirus Nsp10, a critical co-factor for activation
of multiple replicative enzymes. J Biol Chem. 2014;
289(37):25783-96. [DOI:10.1074/jbc.M114.577353] [PMID]
[PMCID]
[40] Ma Y, Wu L, Shaw N, Gao Y, Wang J, Sun Y, et al. Structural
basis and functional analysis of the SARS coronavirus nsp14-
nsp10 complex. Proc Natl Acad Sci USA. 2015; 112(30):9436-
41. [DOI:10.1073/pnas.1508686112] [PMID] [PMCID]
[41] Fang SG, Shen H, Wang J, Tay FP, Liu DX. Proteolytic processing
of polyproteins 1a and 1ab between non-structural
proteins 10 and 11/12 of coronavirus infectious bronchitis
virus is dispensable for viral replication in cultured cells. Virology.
2008; 379(2):175-80. [DOI:10.1016/j.virol.2008.06.038]
[PMID] [PMCID]
[42] Ahn DG, Choi JK, Taylor DR, Oh JW. Biochemical characterization
of a recombinant SARS coronavirus nsp12 RNA-dependent
RNA polymerase capable of copying viral RNA templates.
Arch Virol. 2012; 157(11):2095-104. [DOI:10.1007/s00705-
012-1404-x] [PMID] [PMCID]
[43] te Velthuis AJ, Arnold JJ, Cameron CE, van den Worm SH,
Snijder EJ. The RNA polymerase activity of SARS-coronavirus
nsp12 is primer dependent. Nucleic Acids Res. 2010;
38(1):203-14. [DOI:10.1093/nar/gkp904] [PMID] [PMCID]
[44] Adedeji AO, Lazarus H. Biochemical characterization of middle
east respiratory syndrome coronavirus helicase. mSphere.
2016; 1(5):e00235-16. [DOI:10.1128/mSphere.00235-16]
[PMID] [PMCID]
[45] Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, et
al. Infidelity of SARS-CoV Nsp14-exonuclease mutant virus
replication is revealed by complete genome sequencing.
PLoS Pathog. 2010; 6(5):e1000896. [DOI:10.1371/journal.
ppat.1000896] [PMID] [PMCID]
[46] Jia Z, Yan L, Ren Z, Wu L, Wang J, Guo J, et al. Delicate structural
coordination of the severe acute respiratory syndrome coronavirus
Nsp13 upon ATP hydrolysis. Nucleic Acids Res. 2019;
47(12):6538-50. [DOI:10.1093/nar/gkz409] [PMID] [PMCID]
[47] Bouvet M, Imbert I, Subissi L, Gluais L, Canard B, Decroly E.
RNA 3'-end mismatch excision by the severe acute respiratory
syndrome coronavirus nonstructural protein nsp10/nsp14
exoribonuclease complex. Proc Natl Acad Sci USA. 2012 Jun
12;109(24):9372-7. [DOI:10.1073/pnas.1201130109] [PMID]
[PMCID]
[48] Minskaia E, Hertzig T, Gorbalenya AE, Campanacci V, Cambillau
C, Canard B, et al. Discovery of an RNA virus 3'->5'
exoribonuclease that is critically involved in coronavirus RNA
synthesis. Proc Natl Acad Sci USA. 2006; 103(13):5108-13.
[DOI:10.1073/pnas.0508200103] [PMID] [PMCID]
[49] Bhardwaj K, Sun J, Holzenburg A, Guarino LA, Kao CC. RNA
recognition and cleavage by the SARS coronavirus endoribonuclease.
J Mol Biol. 2006; 361(2):243-56. [DOI:10.1016/j.
jmb.2006.06.021] [PMID] [PMCID]
Piri-Gharaghie T, et al. A Review of Bio-informatics Studies on the Function of Structural and Non-structural Proteins and the Level of Glycoprotein Inhibiting Heme Metabolism . JSMJ. 2022; 21(2):176-193
193
June, July 2022. Volume 21. Number 2
[50] Zhang L, Li L, Yan L, Ming Z, Jia Z, Lou Z, Rao Z. Structural
and biochemical characterization of endoribonuclease Nsp15
encoded by Middle East respiratory syndrome coronavirus. J
Virol. 2018; 92(22):e00893-18. [DOI:10.1128/JVI.00893-18]
[PMID] [PMCID]
[51] Chen Y, Su C, Ke M, Jin X, Xu L, Zhang Z, et al. Biochemical
and structural insights into the mechanisms of SARS coronavirus
RNA ribose 2'-O-methylation by nsp16/nsp10 protein
complex. Plos Pathog. 2011; 7(10):e1002294. [DOI:10.1371/
journal.ppat.1002294] [PMID] [PMCID]
[52] Decroly E, Debarnot C, Ferron F, Bouvet M, Coutard B, Imbert
I, et al. Crystal structure and functional analysis of the SARScoronavirus
RNA cap 2'-O-methyltransferase nsp10/nsp16
complex. PLos Pathog. 2011; 7(5):e1002059. [DOI:10.1371/
journal.ppat.1002059] [PMID] [PMCID]
[53] Shi P, Su Y, Li R, Liang Z, Dong S, Huang J. PEDV nsp16 negatively
regulates innate immunity to promote viral proliferation. Virus
Res. 2019; 265:57-66. [DOI:10.1016/j.virusres.2019.03.005]
[54] Singhal T. A review of coronavirus disease-2019 (covid-19).
Indian J Pediatr. 2020 Apr;87(4):281-86. [DOI:10.1007/s12098-
020-03263-6] [PMID] [PMCID]
[55] Zamorano Cuervo N, Grandvaux N. ACE2: Evidence of role as
entry receptor for SARS-CoV-2 and implications in comorbidities.
Elife. 2020; 9:e61390. [DOI:10.7554/eLife.61390] [PMID]
[PMCID]
[56] Lam TT, Jia N, Zhang YW, Shum MH, Jiang JF, Zhu HC, et al.
Identifying SARS-CoV-2-related coronaviruses in Malayan
pangolins. Nature. 2020; 583(7815):282-85. [DOI:10.1038/
s41586-020-2169-0] [PMID]
[57] Islam MR, Hoque MN, Rahman MS, Alam ASMRU, Akther
M, Puspo JA, et al. Genome-wide analysis of SARS-CoV-2 virus
strains circulating worldwide implicates heterogeneity. Sci
Rep. 2020; 10(1):14004. [DOI:10.1038/s41598-020-70812-6]
[PMID] [PMCID]
[58] Piri Gharaghie T, Beiranvand S, Doosti A, Ghadiri AH, Haji Mohammadi
S. A review of the epidemiology and clinical signs of
SARS-COV-2. New Cell Mol Biotechnol J. 2020; 11(41):103-20.
[Doi:20.1001.1.22285458.1399.11.41.4.8]
Piri-Gharaghie T, et al. A Review of Bio-informatics Studies on the Function of