Homology search of Defensins among different species
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Transcript of Homology search of Defensins among different species
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Homology search of Defensins among different
species
HT05 Fall Research Training Project of MBB Program
XIA Han
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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
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What is DEFENSIN?
Antimicrobial Peptide (AMP) Germline-encoded Widespread Cysteine-rich Wide antimicrobial spectrum
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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)
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Construction of Database
Stage 1: Search for sequences
Protocol for search
Literature Search
Database Search
Data Refine and Validation
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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
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Data Refinement and Validation
Refinement Strategy 10~40 amino acids 2~4 disulfide bridges
Validation Strategy Consistent with corresponding entry in NCBI
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Construction of Database
Stage 2: Accession of Data
Classification : Based on Taxonomy
Format : FASTA
Additional information : References of Sequences
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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
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Sequence Alignment
ClustalX Multiple alignment && Profile alignment Alignment based on evolutionary tree More interactive More Protein Weight Matrices
BLOSUM (Henikoff) PAM (Dayhoff) GONNET
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Test Runs
Parameters Default settings GONNET series as Protein Weight Matrices
Pairwise alignment: GONNET 250 Multiple Alignment: GONNET series
However……
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Test Runs Results
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Test Runs Results
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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
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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)
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Profile Alignment Result: P2.aln
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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)
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Profile Alignment Result: P2.aln
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Superposition : 1L4V and 1ICA
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Acknowledgements:
My Supervisor : Anders Backlund Everyone in Department of Pharmacognosy Margareta Krabble Mikael Thollesson My Supporting, lovely Classmates!
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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).
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Tack sä mycket!
God Jul och
Gott Nytt Är!