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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3.  Introduction
 Aims and Objective
 Significance
 Materials and Methods
 Protein Sequence of Livestock Species
 Protein Sequence of Orthologous Species
 NaturalVariants
 PostTranslational Modifications
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4.  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
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5. 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.
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6. 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.
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7. 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
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9.  β-casein protein sequence of livestock
species have 222-224 base pairs length.
Artiodactyla
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10. 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.
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11.  Cow has 12 NaturalVariants A1, A2, A3, B, C, D, E, F,
G, H1, H2 and I.
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12. Glycosylation
Phosphorylation
Post
Translational
Modifications
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13.  2D Protein Structure
>Cow
MKVLILACLVALALARELEELNVPGEIVESLSSS
EESITRINKKIEKFQSEEQQQTEDEL
 3D Protein Structure
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Template Search
BLAST
Model Building
Model Refinement

14. 2D Protein Structure 3D Protein Structure
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15. 3D Protein Structure2D Protein Structure
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16. 2D Protein Structure 3D Protein Structure
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17. 2D Protein Structure 3D Protein Structure
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18.  To check residue variations in β-casein of 41
species logo was generated using skylign.
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19. 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
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Multiple sequence alignment of β-casein protein sequence in 41 species.

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23. Pairwise
Alignment
Check Identity
% of β-casein
of cow with that
of other species
Identify closely
species to cow
on the basis of
identity %
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25. 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.
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28. 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.
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29. 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.
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30.  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.
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31.  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.
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