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3/29/2015 1
 Introduction
 Aims and Objective
 Significance
 Materials and Methods
 Protein Sequence of Livestock Species
 Prote...
 Protein Structure Prediction
 Protein Mutation Comparison
 Conservation Scenario of cow β-casein in 41
species
 Ident...
Caseins are the major protein fraction and their function is to
transport calcium phosphate in milk.
β-casein is a fractio...
Literature review on milk proteins with a particular
attention to recent findings on milk protein genetic
variants.
To stu...
β-casein milk protein was studied in 41 species.
12 closely related species to cow were examined in
detail.
Critical resid...
3/29/2015 8
 β-casein protein sequence of livestock
species have 222-224 base pairs length.
Artiodactyla
3/29/2015 9
Sequence length
for β-casein protein
varies between
188-302 base pair
in 41 species.
Species of order
Diprotodontia have
m...
 Cow has 12 NaturalVariants A1, A2, A3, B, C, D, E, F,
G, H1, H2 and I.
3/29/2015 11
Glycosylation
Phosphorylation
Post
Translational
Modifications
3/29/2015 12
 2D Protein Structure
>Cow
MKVLILACLVALALARELEELNVPGEIVESLSSS
EESITRINKKIEKFQSEEQQQTEDEL
 3D Protein Structure
3/29/2015...
2D Protein Structure 3D Protein Structure
3/29/2015 14
3D Protein Structure2D Protein Structure
3/29/2015 15
2D Protein Structure 3D Protein Structure
3/29/2015 16
2D Protein Structure 3D Protein Structure
3/29/2015 17
 To check residue variations in β-casein of 41
species logo was generated using skylign.
3/29/2015 18
Multiple sequence
alignment of β casein
protein of 41 species
NaturalVariants,
Glycosylation sites and
Phosphorylation sit...
3/29/2015 20
Multiple sequence alignment of β-casein protein sequence in 41 species.
3/29/2015 21
3/29/2015 22
Pairwise
Alignment
Check Identity
% of β-casein
of cow with that
of other species
Identify closely
species to cow
on the b...
3/29/2015 24
Exons number was retrieved for
gene structure analysis
Species of order
Artiodactyla
have 9 exons
except sheep
with 7 exon...
3/29/2015 26
3/29/2015 27
Milk quality of Cow
and Buffalo is closely
similar because of
mostly conserved
variations in those
species.
Phosphorylated...
The relationship between polymorphic variants of β-casein and the
composition of milk can be studied in further research
D...
 Worthy Director, CIIT SWL, Dr. Abdul
Waheed.
 Head of Department of BioSciences, Dr.
Shazia Mannan.
 Supervisor, Ms. S...
 Caroli A.M., Chessa S. and Erhardt G.J.: Milk protein polymorphisms in cattle: effect on
animal breeding and human nutri...
Insilico comparative analysis of critical residues of CSN gene in 41 mammals: predicting health implications of milk cont...
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Insilico comparative analysis of critical residues of CSN gene in 41 mammals: predicting health implications of milk containing β-casein in live stock.

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1.Introduction
2.Aims and Objective
3.Significance
4.Materials and Methods
5.Protein Sequence of Livestock Species
6.Protein Sequence of Orthologous Species
7.Natural Variants
8.Post Translational Modifications
9.Protein Structure Prediction
10.Protein Mutation Comparison
11.Conservation Scenario of cow β-casein in 41 species
12.Identification of closely related species to cow
13.Gene Structure Analysis
14.Identification Of Novel Mutational Sites, Protein Quality And Composition
15.Conclusion
16.Recommendation

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Insilico comparative analysis of critical residues of CSN gene in 41 mammals: predicting health implications of milk containing β-casein in live stock.

  1. 1. 3/29/2015 1
  2. 2.  Introduction  Aims and Objective  Significance  Materials and Methods  Protein Sequence of Livestock Species  Protein Sequence of Orthologous Species  NaturalVariants  PostTranslational Modifications 3/29/2015 3
  3. 3.  Protein Structure Prediction  Protein Mutation Comparison  Conservation Scenario of cow β-casein in 41 species  Identification of closely related species to cow  Gene Structure Analysis  Identification Of Novel Mutational Sites, Protein Quality And Composition  Conclusion  Recommendation 3/29/2015 4
  4. 4. Caseins are the major protein fraction and their function is to transport calcium phosphate in milk. β-casein is a fraction which forms up to 45 % of bovine caseins in milk. Milk protein variants are also a useful tool for breed characterization, diversity, and phylogenetic studies. 3/29/2015 5
  5. 5. Literature review on milk proteins with a particular attention to recent findings on milk protein genetic variants. To study the effects of different protein variants on milk yield and composition. To understand the biological significance of the PostTranslational Modifications and genetic variations. 3/29/2015 6
  6. 6. β-casein milk protein was studied in 41 species. 12 closely related species to cow were examined in detail. Critical residues were predicted which can play vital role in improving milk quality. 1 3 2 3/29/2015 7
  7. 7. 3/29/2015 8
  8. 8.  β-casein protein sequence of livestock species have 222-224 base pairs length. Artiodactyla 3/29/2015 9
  9. 9. Sequence length for β-casein protein varies between 188-302 base pair in 41 species. Species of order Diprotodontia have maximum sequence length. Species of same order consisted of relatively closer sequence length. 3/29/2015 10
  10. 10.  Cow has 12 NaturalVariants A1, A2, A3, B, C, D, E, F, G, H1, H2 and I. 3/29/2015 11
  11. 11. Glycosylation Phosphorylation Post Translational Modifications 3/29/2015 12
  12. 12.  2D Protein Structure >Cow MKVLILACLVALALARELEELNVPGEIVESLSSS EESITRINKKIEKFQSEEQQQTEDEL  3D Protein Structure 3/29/2015 13 Template Search BLAST Model Building Model Refinement
  13. 13. 2D Protein Structure 3D Protein Structure 3/29/2015 14
  14. 14. 3D Protein Structure2D Protein Structure 3/29/2015 15
  15. 15. 2D Protein Structure 3D Protein Structure 3/29/2015 16
  16. 16. 2D Protein Structure 3D Protein Structure 3/29/2015 17
  17. 17.  To check residue variations in β-casein of 41 species logo was generated using skylign. 3/29/2015 18
  18. 18. Multiple sequence alignment of β casein protein of 41 species NaturalVariants, Glycosylation sites and Phosphorylation sites have been observed Species of each order contains mostly conserved Phosphorylation sites within the same order No glycosylation site was found in livestock species 3/29/2015 19
  19. 19. 3/29/2015 20 Multiple sequence alignment of β-casein protein sequence in 41 species.
  20. 20. 3/29/2015 21
  21. 21. 3/29/2015 22
  22. 22. Pairwise Alignment Check Identity % of β-casein of cow with that of other species Identify closely species to cow on the basis of identity % 3/29/2015 23
  23. 23. 3/29/2015 24
  24. 24. Exons number was retrieved for gene structure analysis Species of order Artiodactyla have 9 exons except sheep with 7 exons. Primates’ species possess 6-7 exons. Species as dog, mouse, rat, horse, donkey, rabbit and pika have 9 exons. 3/29/2015 25
  25. 25. 3/29/2015 26
  26. 26. 3/29/2015 27
  27. 27. Milk quality of Cow and Buffalo is closely similar because of mostly conserved variations in those species. Phosphorylated sites play important role in milk quality. Highlighted Post translational modifications can be introduced in other species than cow to enhance their milk quality and milk composition. 3/29/2015 28
  28. 28. The relationship between polymorphic variants of β-casein and the composition of milk can be studied in further research Dolphin can be considered as an important species for future work on milk quality and milk composition due to 70% identity of β-casein milk protein of dolphin with that of cow and conserved Phosphorylation sites with primates species. Microbat can be considered for further research because Phosphorylation sites predicted in microbat are conserved in order Artiodactyla. 3/29/2015 29
  29. 29.  Worthy Director, CIIT SWL, Dr. Abdul Waheed.  Head of Department of BioSciences, Dr. Shazia Mannan.  Supervisor, Ms. Samina Kausar.  Co-supervisor, Mr. MuhammadAsif  All faculty members. 3/29/2015 30
  30. 30.  Caroli A.M., Chessa S. and Erhardt G.J.: Milk protein polymorphisms in cattle: effect on animal breeding and human nutrition. Dairy Science. 2009, 92: 5335–52.  Jensen HB, Holland JW, Poulsen NA and Larsen LB: Milk protein variants and isoforms identified in bovine milk representing extremes in coagulation properties. Dairy Sci. 2012, 95:2891–2903.  Ceriotti, G., D. Marletta, A. Caroli, and G. Erhardt.: Milk protein loci in taurine (Bos taurus) and zebu (Bos indicus) populations bred in hot climate. Anim. Breed. Genet. 2004a, 121:404–415.  Blom, N., Gammeltoft, S. and Brunak, S: Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. Molecular Biology. 1999, 294(5): 1351-1362.  Jensen HB, Holland JW, Poulsen NA and Larsen LB: Milk protein variants and isoforms identified in bovine milk representing extremes in coagulation properties. Dairy Sci. 2012, 95:2891–2903. 3/29/2015 31

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