non-structural protein 1 is a protein in sars-cov-2 virus( coronavirus),which block host cell ribosomes from producing essential proteins. in my article and this power point I investigated the effects of this protein both in human translation system and intermediate carrier animals . I though the difference between these two groups comes from different attachments of this protein to its host cell ribosomes.

1. NSP1 inhibition effects on Human
40S ribosomes
compared to intermediate carrier animals
Authors :
Afagh Bapirzadeh (1,2)ˏ Mitra Salehi (1)ˏ Zarrin Minuchehr (2)ˏ Bijan Bambai (2)
Affiliation :
(1) Islamic Azad University, Tehran branch,Heravy Sq.,South makran St.,P.O. BOX:1651153311
(2 ) National Institute of Genetic Engineering and Biotechnology, Shahrake pajohesh,Tehran-Karaj
Highway,Tehran,Iran,P.O. BOX:1497716316
Corresponding author’s email :
Bambai2biotech@gmail.com
NSP1
NSP1
NSP1
NSP1
1

2. How did we get to this point
• In December 2019,Wuhan China was a start point of the most
serious world Pandemic from one member of coronaviridea
family ,SARS-CoV-2.
• According to World Health Organization (WHO) statement on
March 2020,coronavirus disease was considered a pandemic
• Islamic Republic of IRANs Health Ministry and government
stablished committee to deal with coronavirus disease ,one of the
prominent center of such these researches is :
Iran National Institute of Genetic Engineering and
Biotechnology(NIGEB)
to work on various aspects of this virus 2

3. Getting to know NSP1
Nsp1 is a 20 Kd protein and another
name of it is leader protein
It is found on cytoplasm of
infected cells
It plays a crucial role in
inhibition of 40s ribosomal
function
It is a product of ORF1 cleavage at
N-terminal by Plpro protease ,only
in some types of CoV
Nsp1 has no nucleotide similarity in
tBLASTn and BLASTn Databases
3

4. NSP1 interactions with human 40s ribosome complex
PyMOL2 software
PDB file:7k5i
4

5. NSP1 –in red
Ball and stick view
18Sr RNA interaction point with NSP1
18Sr RNA-in cyan
Solid topography view
Pictures provided by Chimera X1.4 Software 5

6. Position of NSP1 in between 18sr RNA
Video is provided with ChimeraX version 1.4 software 6

7. 18srRNA interaction points with
NSP1
18srRNA interaction
points with NSP1
18srRNA interaction points in
normal situations
G-600 C-622/U-630
G-601 G-6/C-621
A-604 C-603/C-639
A-605 C-603/C-638/G-598/Lys-
22(S9)
G-606 NON
U-607 Arg-143(S3)
C-624 G-623/G-617/U-631
G-625 Asn-63(S23)/C-615/G-617
U-630 G-600
U-631 G-623/A-629/C-624
18srRNA interaction points at NSP1 presence in comparison
with normal conditions
18srRNA interactions (Cyan) with NSP1 (Red)
7

8. Camelus dromedarius Manis pentadactyla Manis javanica Saimiri boliviensis
Mus musculus
Human 18srRNA
Camelus dromedarius
Manis pentadactyla
Manis Javanica
Saimiri Boliviensis
TCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGCGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC
Bos taurus Gorilla gorilla
18srRNA sequence
alignment comparison
TCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGCGCCAGCAGCCGCGGTAATTCCAGCTC
TCCATTGGAGGGCAAGTCTGGCGCCAGCAGCCGCGGTAATTCCAGCTC
Human 18srRNA
Mus Musculus
Bos Taurus
Gorilla Gorilla
8
691
585
594
542
590
739
633
642
590
638
691
639
638
638
691
591
590
590

9. NSP1 -18srRNA polar and non-polar interactions
Video provided with PyMOL Software
9

10. Position of NSP1 with S2
Pictures and video provided by Chimera X1.4 Software
NSP1
(red)
S2
(purple)
10

11. Protein S2 interactions with NSP1
NSP1
amino acids
Protein S2
amino acids
Asn-178 Val-106
Gln-158 Val-147,
Glu-146,
Phe-124
Met-174 Val-106
Trp-161 Phe-124,
Thr-122,
Pro-111
Phe-157 Phe124,
Ile-109-
S2 internal interactions in normal conditions
S2(Purple)interactions with NSP1(Red) 11

12. • LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIR
• LKDEVLKIMPVQKQTRAGQQTRLKAFVATGDDKG-----------------
• LKDEVLKIMTVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIR
• LKDDVLKIMPVQKQTRAGQRTRFKAFVAIGHYNGHVGLGX--SKEVATAIR
Human S2
Camelus dromedaries
Mandrillus Leucophaeus
(isoform X1)
Manis Javanica
Ribosomal S2 sequence
alignment comparison
• LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIR
• LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIR
• LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIR
• LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIR
Human S2
Gorilla Gorilla
Mus Musculus
Bos Taurus
Camelus dromedaries Mandrillus leucophaeus Manis javanica
Gorilla gorilla Mus musculus Bos taurus
12
101
14
101
145
152
48
152
196
101
101
101
101
152
152
152
152

13. NSP1-S2 polar and non-polar contacts
Video provided with PyMOL Software
13

14. NSP1-S3 positions
Pictures and video provided by Chimera X1.4 Software
NSP1(red)
S3(green)
14

15. S3 from 40s ribosomes(Green) interactions with NSP1 (Red)
S3 internal interactions in normal conditions.PDB file:5oA3
NSP1
amino acids
Protein S3
amino acids
Asp-152 Arg-116,117
Asp-156 Arg-143
Asn-160 Arg-143
Glu-159 Arg-143
Leu-149 Leu-113,
Arg-117
Glu-155 Val-115,
Ala-114,
Arg-116
Thr-151 Arg-117
Gly-150 Arg-117,
Leu-113
Protein S3 interactions with NSP1
15

16. Ribosomal S3 sequence
alignment comparison
• QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
• ---------------------------------------------------MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
• ---------------------------------------------------MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
Human S3
Manis pentadactyla
(isoform X3)
Manis javanica
(isoform X2)
Manis pentadactyla Manis javanica
• QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
• QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
• QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
• QAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHS
Human S3
Ochotona princeps
Rhinolophus ferrumequinum
Camelus dromedarius
Ochotona princeps Rhinolophus ferrumequinum Camelus dromedarius
16
101
1
1
160
34
34
101
101
101
65
160
160
160
124

17. NSP1-S3 polar and non-polar interactions
Video provided with PyMOL Software
17

18. NSP1-S30 positions
Pictures and video provided by Chimera X1.4 Software
S30(blue)
NSP1(red)
18

19. S30 (Blue) interactions with NSP1(Red)
• S30 has only 2 interactions with NSP1
• Lys52 from S30 interact with Arg-175 and Glu-176 of
NSP1
• Interestingly in sequence alignment ,S30 sequence of
Human was only 59 amino acids long
• In comparison to other species (cows,rabitts,mouse and
etc…)Human S30 has become smaller in size
S30 Protein interactions with NSP1
19

20. Ribosomal S30 sequence
alignment comparison
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GQAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
Human S30
Camelus ferus
Camelus dromedaries
Manis pentadactyla
Manis javanica
Rhinolophus ferrumequinum
Myotis brandtii
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNAN-
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
GRAKRRMQYNRRFVNVVPTFGKKKGPNANS
Human S30
Mus musculus
Cricetulus griseus
Bos Taurus
Pan paniscus
Camelus ferus Camelus dromedaries Manis pentadactyla Manis javanica Rhinolophus ferrumequinum Myotis brandtii
Mus musculus Cricetulus griseus Bos taurus Pan paniscus
0
133
148
133
133
133
133
59
163
178
163
163
163
163
20
0
133
132
133
133
59
163
161
163
163

21. NSP1-S30 polar and non-polar interactions
Video provided with PyMOL Software
21

22. NSP1 Interacting Ribosomal Proteins(S2,S3 and S30) Natural Roles In Translation Process
Ribosomal
proteins
S2 protein
Involved in the formation of the translation initiation complex, where
it might contact the messenger RNA and several other components of
ribosome
S3 protein
Participates in the rearrangements of the small subunits structure
occurring at the binding of initiation factors elF1,elF1A(mRNA entry
site)
S30 protein Belongs to the ribosomal S30e family and is a component of 40s
cytoplasmic ribosomes which display antimicrobial activity
18srRNA
Is the active center of the protein synthesis in 40S ribosomal subunit.
It Could also be an ideal indicator for measuring the synthesis of
protein
22

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