aya presentation of discussion seminar .ppt

aya presentation of discussion seminar .ppt

1. Aya Samir Mohamed
3-D structure prediction and
analysis of the NS4B protein
of Zika virus

2. Supervisors:
Prof. Dr.
Prof. Dr .

3. Zika virus moved outside of Africa and Asia in 2007 and 2013 with outbreaks in Yap
Island and French Polynesia, respectively. The first cases in the Americas were
detected in Brazil in May 2015. The virus circulating in Brazil is an Asian genotype, 
possibly imported during the World Cup of 2014. As of this writing Zika virus has
spread to 23 countries in the Americas.

4. ZIKV Infection

5. NS4B Protein
Zika virus is a positive sense, single-strand ribonucleic acid (RNA)
virus with a genome size of approximately 10.8 kb
(NS4B): Induces the formation of ER-derived membrane vesicles where the
viral replication takes place
NS4B protein of ZIKV of 251 amino acids was retrieved from UniProt
Knowledgebase (UniProtKB) and used in this study.

6. Protein structure prediction
•proteomic tool for understanding phenomena in modern molecular and cell
biology
•has important applications in biotechnology and medicine.

•One of these applications is the prediction of three dimensional structures of
virus’ proteins, hence elucidating their functions.
•This will aid in drug design, and integrative understanding of viral processes.

7. Protein structure
predication

8. Aim of work
 3-D structure prediction of NS4B protein by using Servers
according to CASP
Prediction and analysis of motifs and PTMS of NS4B protein
Correlation of Structural and Functional Prediction

9. Proposed Plan

11. •Analysis of NS4B protein includes the prediction of:
conserved regions, domains.
signatures and motifs.
 post-translational modification sites.
 Correlation of Structural and Functional Prediction

13. Structure-Based Virtual Screening MOE program
 Protein Preparation Schemes for SBVS
 Binding Site Identification
 Compound Database Preparation
 Molecular Docking
 Improving Pose/Compound Selection After Docking (Post processing)
 Binding Energy and Binding Affinity Calculations

14. Results and Discussion

15. Multiple Sequence Alignment

16. phylogenetic analysis

17. Domain separation
only one domain (1-191) with Cutoff 0.66, E value 1.3e-60, Score 111.604 , length 216 , Z –
Score 4.032.

18.  Secondary structure and solvent accessibility prediction

19. SS- Prediction and solvent accessibility
Helical Transmembrane regions
(36 – 54 length 19 )
(91 – 107 length 17 )
(109 – 127 length 20 )
(170 – 189 length 17 )
(220 – 238 length 19 ) Helix
( 38 – 60 length 23 )
( 91 – 100 ) length 10
( 106 – 123 L 18 )
( 127 – 144 L 18 )
( 165 – 185 L 21 )
( 189 – 203 L 15 )
( 218 – 227 L 10 )
( 231 – 244 L 14 )
Intermediate
( 168 – 168 L 1 )
( 145 – 145 L 1 )
( 137 – 137 L 1 )
( 30 – 30 L 1 )

20. Buried
( 230 – 241 L 12 )
( 228 – 228 L 1 )
( 225 – 226 L 2 )
( 218 – 223 L 6 )
( 216 – 216 L 1 )
( 213 – 214 L 2 )
( 205 – 206 L 2 )
( 194 – 202 L 9 )
( 190 – 192 L 3 )
( 187 – 188 L 2 )
( 165 – 165 L 1 )
( 161 – 161 L 1 )
( 159 – 159 L 1 )
( 156 – 156 L1 )
( 150 – 154 L 5 )
( 146 – 148 L 2 )
( 138 – 143 L 6 )
( 134 – 135 L 2 )
( 130 – 131 L 2 )
( 105 – 126 L 22 )
( 90 – 100 L 2 )
( 82 – 88 L 7 )
( 78 – 79 L 2 )
( 64 – 65 L 2 )
( 62 – 62 L 1 )
( 55 – 57 L 3 )
( 38 – 53 L 16 )
( 35 – 36 L 2 )
( 33 - 33 L 1 )
( 28 – 29 L 2 )
( 11 – 12 L 2 )
( 8 – 8 L 1 )
( 4 – 5 L 2 )

21. Exposed
( 0 – 3 L 4 )
( 6 – 7 L 2)
( 9 – 10 L 2 )
( 13 – 14 L 2 )
( 16 – 27 L 12 )
( 34 – 34 L 1 )
( 58 – 61 L 4 )
( 63 – 63 L 1 )
( 66 – 67 L 2 )
( 71 – 72 L 2 )
( 77 – 77 L 1 )
( 80 – 81 L 2 )
( 89 – 89 L 1 )
( 101 – 102 L 2 )
( 104 – 104 L 1 )
( 127 – 127 L 1 )
( 129 – 129 L 1 )
( 133 – 133 L 1 )
( 136 – 136 L 1 )
( 144 – 144 L 1 )
( 149 – 149 L 1 )
( 155 – 155 L 1 )
( 157 – 158 L 2 )
( 160 – 160 L 1 )
( 162 – 164 – L 3 )
( 186 – 186 L 1 )
( 189 – 189 L 1 )
( 193 – 193 L 1 )
( 203 – 204 L 2 )
( 207 – 212 L 6 )
( 215 – 215 L 1 )
( 217 – 217 L 1 )
(229 – 229 L 1 )

22. Protein binding regions
(8–8 L 1 )
( 20 – 20 L 1 )
( 22 – 22 L 1 )
( 24 – 24 L 1 )
( 26 – 29 L 4 )
( 247 – 251 L 5 0
( 212 – 213 L 2 )
( 162 – 162 L 1 )
( 136 – 136 L 1 )
( 102 – 102 L 1 )

23.  3-D Structure Prediction:
•First: Construction of initial model using target-template alignment
•Second: Reduced-level structure assembly and refinement simulations:
•Third: Model evaluation and selection

24. Table 1: Evaluation of 3-D structure model from selected servers for p7 protein structure prediction

25. Table 2. Motif analysis using motif finder server.
 
Motif number
 
Family
 
Match Position
 
Independent
E-value
PF01349 Flavi_NS4B 1 - 241
 
2.4e - 78
PF05968 Bacillus_papR 66 – 82 0.92
 

26. Initial and refined models :
I – Tasser server

27. Lomets server

29. Galaxy web .

30. .

31. Quark
Initial model

32. I – Tasser

33. LOMETS

34. SWISSMODEL

35. Quark

36. Phyre2

37. TM align I – Tasser

38. LOMETS

39. Swissmodel

40. Quark

41. Phyre2

42. Galaxy web

43. 3DOM

44. SMART

46. 4. Conclusion
•In this work, Different bioinformatics servers were used to predict and analyze NS4B ZIKV protein
Such as (I-TASSER, Phyre2, QUARK, GalaxyWEB, Swiss-Model and LOMETS metaserver).
•Only one domain (1-191) was predicted and a fairly best model had been obtained from I-TASSER server after
refinement and energy minimization according to best value of C-score, RMSD, TM-score and QMEAN Z-score.

•NS4B OF ZIKV has two Post-translational modification site prediction: flavi_NS4B and Bacillus papR which is
small and poorly conserved amonf the flavi-viruse . It contains multiple hydrophobic potential membrane spanning
redgions { cite : PUB00000118 } . NS4B Protein may fornm membrane components of the viral replication complex
and could be involved in membrane localization of NS3 and NS5 . { Interpro : IPR 000208 } { cite : PUB00000118 }
using SCOP, NO hit matched protein sequence and was classified as small proteins superfamily. From CATH

47. THANK
YOU