Study of proteolysis by online resources.

1. Credit Seminar
on
In silico
Proteolysis of Food
Shamim Hossain
PhD (DT)
ICAR-National Dairy Research Institute
Dairy Technology division

2. Outline
 Introduction
 Why In silico study?
 Tools
 Studies
 Conclusion
2

3. Proteolysis
3
Protease

4. 4
IN VITRO
Tests are performed
outside their normal
biological context
IN VIVO
Test on whole, living
organisms or cells
IN SILICO
Performed on computer or via computer simulation
Analysis

5. Why In-Silico??
Conventional In Silico
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6. 6
(Nongonierma et al., 2017)

7. Work Flow
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8. 8
(Anekthanakul et al., 2018)

9. Tools
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Online Protein Database
In silico Peptide Digestion Tool
Peptide Prediction Tool

10. Online Protein Database
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PepBank
BIOPEP
ProtDB
MEROPS

11. Peptide Digestion Tool
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BIOPEP
Peptide
Cutter
Peptide
Mass
BLASTProsper
Spirpep
PoPS
...&
more

12. Peptide Prediction Tool
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PeptideLocator
PeptideDB
PeptideRanker
BIOPEP
CAMP
SpirPep
mMass
DALI

13. BIOPEP
http://www.uwm.edu.pl/biochemia/index.php/en/biopep
 Sequence databases
 Proteolysis tool
 Bioactive peptides detection
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14. https://www.uniprot.org/
Resource of protein sequence & functional information
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UniProtKB
Swiss-Prot (558,590)
TrEMBL (126,780,198)

15. 15
https://www.ebi.ac.uk/merops/
 Peptidase & Inhibitor databases
 2D & 3D structure
 Sequence & sequence feature

16. https://prosper.erc.monash.edu.au/index.html
 Protein digestion
 24 different protease types
 Families:
 Aspartic
 Cysteine
 Metallo
 Serine
16

17. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=
BlastSearch&BLAST_SPEC=&LINK_LOC=blasttab&LAST_PAGE=blastp
 Basic Local Alignment Search Tool
 Finds regions of local similarity between sequences
 Calculates the statistical significance of similarity
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18. http://spirpepapp.sbi.kmutt.ac.th/SpirPep/Home
 15 enzymes
 Bioactive peptide databases (28,892 sequences)
 13 online bioactive peptide databases are accessed
 Allows backtracking of resulting peptides to their original
proteins
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19. https://www.expasy.org/
Provides access to scientific databases and software.
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Databases
UniProtKB
SWISS-MODEL
STRING
PROSITE
…and many more
Tools
PeptideCutter
PeptideMass
BLAST
PoPS
…and many more

20. https://web.expasy.org/peptide_cutter/
 Databases: SWISS-PROT and/or TrEMBL
 In silico digestion: 38 enzymes & chemicals
 Various types of output can be generated
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PeptideCutter

21. 21
PeptideMass
https://web.expasy.org/peptide_mass/
▪ Database: SWISS-PROT and/or TrEMBL
▪ 24 enzymes
▪ Computes the masses of the generated peptides
▪ Various types of proteolytic condition can be employed

22. Studies
22
DPP-IV Activity: bovine κ-casein & α- lactalbumin has highest
activity.
(Nongonierma et al., 2014)
ACE-Inhibitory Activity: Meat of pork, beef and chicken has
highest activity.
(Gu et al., 2011)
ACE-Inhibitory Activity: dietary proteins: myosin (highest)
gut endogenous proteins: mucin-5AC (highest)
(Dave et al., 2014)

23. 23
Carp protein: Anti-oxidant and ACE- Inhibitory peptides
(Darewicz et al., 2016)
Stone fish hydrolysates: ACE- Inhibitory peptides
(Auwal et al., 2018)
Oat proteins hydrolysates: ACE- Inhibitory peptides
(Cheung et al., 2009)
Milk proteins hydrolysates: Antimirobial peptides
(Dziuba et al., 2014)

24. 24
Bio-activity encountered in silico
Antihypertensive
Immunomodulating
Opioid
Antithrombotic
Antioxidative
Embriotoxic
Antiamnestic
Celiac - toxic
Opioid - antagonistic
Antibacterial &
antiviral
Chemotactic …& more
(Dziuba & Dziuba 2010)

25. Future Scope
֍In silico study in research on proteolysis
֍Large number of trial simulation in a minute
֍Bio-active peptide enriched functional foods
֍No need of protein sequencing
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26. Conclusion
֍Resource saving
֍Concise results
֍User friendly
֍Absolutely FREE ! ! !
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