Molecular Immnuocomputing with Application to Alphabetical Pattern Recognition Mimics the
Characterization of ABO Blood Type
Su Dong Kim2 , Ki-Roo Shin1 & Byoung-Tak Zhang1,2*
1 School of Computer Science & Engineering,Seoul National University, Seoul, Korea
2 Interdisciplinary Program in Cognitive Science,Seoul National University, Seoul, Korea
Introduction
DNA computing
Peptide computing
vs.
Four Types of Noncovalent Bonds inPeptide Computing
Structure of Antibody with Its Antigen
Molecular Immunocomputing Mimics the Characterization of ABO Blood Type
The ABO Blood Grouping System
The Structure of Terminal Sugars in the A, B, & O Blood Antigens
(Gal; Galactose, GlcNAc; N-acetylglucosamine, Fuc; Fucose, and GalNAc; N-acetylgalactosamine)
Nucleotide Sequences of ABO Alleles Identified by PCR-SSCP
Analysis
(Ogasawara et al., 1996)
Methods
Designing the peptide sequences
Purifying the corresponding antibodiesPreparation of protein microarray chips
Four Kinds of DNA Code Operators
Operator Operation
WTransition
{C ↔ T}, {A ↔ G}
XMatched-transition{A ↔ T}, {C ↔ G}
YMismatched-transversion
{A ↔ C}, {G ↔ T}
ZBack-mutation(null mutation)
Designing the Peptide Sequences
a t c c c t tt c g g g c tt c g g g c tt c g g g c tt c g g g c tt c g g g c tt t c c c t t
1 2 3 4 5 6 78 9 1
011
12
13
14
15
16
17
18
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21
22
23
24
25
26
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31
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45
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48
49“O”- DNA template sequence:
5’- a tcc ctt tcg ggc ttc ggg ctt cgg gct tcg ggc ttc ggg ctt tcc ctt – 3’“O”- RNA transcript sequence: 3’ – ugu agg gaa agc ccg aag ccc gaa gcc cga agc ccg aag ccc gaa agg gaa – 5’“O”- peptide sequence: HOOC - *C G K R A E P K P K P S R A E P K G K -NH2
The Universal Genetic Code
Hapten-Carrier Conjugation & Immunization
Preparation of Protein Microarray Chips
(Haab et al., 2001a) (Zhu & Snyder, 2003)
Discussion
(a)
Structures of the peptide CTP3 (VEVPGSQHIDSQKKA) (a),PS1 (HQLDPAFGANSTNPD) (b), SHaPrP (104-113 ; KPKTNMKHMA) (c),and peptide with antigen binding site (d).[(a), (b), and (c): drawed by the Swiss-PdbViewer (Guex & Peitsch, 1997); (d): adapted from Lescar et al. , 1991.]
(b) (c) (d)
Classes of Capture Molecules for Protein Microarrays
Sandwich immunoassay
(Templin et al. , 2002)
Conclusion
Peptide computing Immunocomputing
Alternative toDNA computing
based onMathematical model
Biomolecule → Computation Computation → Biomolecule
= Molecular Immunocomputing (?)
Acknowledgments
This research was supported in part by the Ministry of Education& Human Resources Development under the BK21-IT Program,The Ministry of Commerce, Industry and Energy through the MECproject, and the NRL Program from Korean Ministry of Science &Technology.The ICT at Seoul National University provided research facilitiesfor this study.