homology search of defensins among different species ht05 fall research training project of mbb...
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Homology search of Defensins among different
species
HT05 Fall Research Training Project of MBB Program
XIA Han
The Purpose of My Project
Database of Defensins 10~40 amino acids length OS: Plant, Invertebrate and Vertebrate Literatures related to this sequences
Search for conversed sequence patterns Connect sequence’s features with structur
e
What is DEFENSIN?
Antimicrobial Peptide (AMP) Germline-encoded Widespread Cysteine-rich Wide antimicrobial spectrum
Structural Features
4~8 cysteine (mostly) 2~4 disulfide bridges Lineal or cyclic molecule Cationic Amphipathic
Tang, Y. Q. et al. Science 286, 498-502 (1999)
Construction of Database
Stage 1: Search for sequences
Protocol for search
Literature Search
Database Search
Data Refine and Validation
Database Search
AMSDb
Antimicrobial Sequences Database
http://www.bbcm.units.it/~tossi/amsdb.html APD
Antimicrobial Peptide Database http://aps.unmc.edu/AP/main.php
NCBI
Data Refinement and Validation
Refinement Strategy 10~40 amino acids 2~4 disulfide bridges
Validation Strategy Consistent with corresponding entry in NCBI
Construction of Database
Stage 2: Accession of Data
Classification : Based on Taxonomy
Format : FASTA
Additional information : References of Sequences
Summary of Database
Plant MusselArachni
-daInsect
Vertebr
-ateTotal
AMSDb
The Number
of Sequences
9 3 2 8 23 44
APD 5 1 0 2 23 31
BLAST 235
Final Data Set
11 3 4 22 77 117
Sequence Alignment
ClustalX Multiple alignment && Profile alignment Alignment based on evolutionary tree More interactive More Protein Weight Matrices
BLOSUM (Henikoff) PAM (Dayhoff) GONNET
Test Runs
Parameters Default settings GONNET series as Protein Weight Matrices
Pairwise alignment: GONNET 250 Multiple Alignment: GONNET series
However……
Profile Alignment
Important Parameters End Gap Separation : On Residue Specific Penalties and Hydrophilic
Gap Penalties : On New Gaps before Alignment and Reset All
Gaps before Alignment : Off BLOSUM series as Protein Weight Matrices
Pairwise alignment: BLOSUM 30 Multiple Alignment: BLOSUM series
Profile Alignment
Profile Alignment in a designed order : 1. Profile alignment multiple-aligned insect sequences with multi
ple-aligned Arachnida sequences, get P1.aln (26 sequences) ; 2. P1.aln with multiple-aligned Mussel sequences, get P2.aln (29
sequences) 3. P2.aln with multiple-aligned vertebrate sequences, get P3.aln
(106 sequences)
4. P2.aln with multiple-aligned plant sequences, get P4.aln (40 s
equences)
Structural Alignment
Secondary Structural Prediction JPRED(http://www.compbio.dundee.ac.uk/~www-jpred/
)
Sequence-based Structural Alignment BLAST MSDlite(http://www.ebi.ac.uk/msd-srv/msdlite
/index.html)
Acknowledgements:
My Supervisor : Anders Backlund Everyone in Department of Pharmacognosy Margareta Krabble Mikael Thollesson My Supporting, lovely Classmates!
References
1. Bulet, P., Stocklin, R. & Menin, L. Anti-microbial peptides: from invertebrates to vertebrates. Immunol Rev 198, 169-84 (2004).
2. Tang, Y. Q. et al. A cyclic antimicrobial peptide produced in primate leukocytes by the ligation of two truncated alpha-defensins. Science 286, 498-502 (1999).
3. Gueguen, Y. et al. Characterization of a defensin from the oyster crassostrea gigas: Recombinant production, folding, solution structure, antimicrobial activities and gene expression. J Biol Chem (2005).
4. Hoffmann, J. A., Kafatos, F. C., Janeway, C. A. & Ezekowitz, R. A. Phylogenetic perspectives in innate immunity. Science 284, 1313-8 (1999).
5. Mygind, P. H. et al. Plectasin is a peptide antibiotic with therapeutic potential from a saprophytic fungus. Nature 437, 975-80 (2005).