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An efficient visualization tool for the analysis of protein mutation matrices

A visualization tool for protein mutation matrices, aiding in the analysis of evolving sequences for applications in protein engineering and design. Utilizes physico-chemical properties and matrix scaling for quick pattern elucidation.

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An efficient visualization tool for the analysis of protein mutation matrices

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  1. An efficient visualization tool for the analysis of protein mutation matrices Maria Pamela C. David, Carlo M. Lapid and Vincent Ricardo M. Daria Computational Science Research Center University of the Philippines, Diliman

  2. Outline • Visualization • A crash course on protein structure, function and engineering • Protein mutation matrices • Generation • Data • Visualization • Applications of visualization

  3. Visualization

  4. Visualization

  5. Visualization

  6. Visualization • “Our species relies on vision over all other senses” (about half of the human brain is devoted directly or indirectly to vision) • “We learn about 11% audibly and 83% visually” • ~50% of our brain gets involved in visual processing • Other perceptual channels can be used : - They work in parallel as long as they don’t conflict - In a conflict, the visual channel will dominate

  7. Crash course on protein structure and engineering

  8. Protein mutations?

  9. Protein mutation/substitution matrices • Analysis of evolving sequences/sequences with high variability • Would have applications in artificial protein design

  10. W S T D R A K I Y E G L E R G D T G K G Matrix generation

  11. Hydrophilicity Size and Polarizability Charge and polarity D → G R → E T → I S → L S → K W → R T → D Matrix generation W S T D R A K I Y E G L E R G D T G K G Physico-chemical properties • Note: • Alignment should be good • Primer-derived sequences should be removed

  12. Sample mutation matrix Replacement residues, increasing hydrophilicity Replaced residues, increasing hydrophilicity

  13. Image equivalent Lower hydrophilicity Higher hydrophilicity

  14. Tool 1: Matrix scaling W L F I M V Y P A T C Q G K S H N E R D

  15. Tool 2: Matrix comparison Find mutations exclusive to either matrix W L F I M V Y P A T C Q G K S H N E R D W L F I M V Y P A T C Q G K S H N E R D Matrix 1 Matrix 2

  16. Tool 2: Matrix comparison W L F I M V Y P A T C Q G K S H N E R D Matrix 2 only Matrix 1 only

  17. Complementarity Determining Region FRamework Application 1: antibody engineering

  18. Application 1: antibody engineering W L F I M V Y P A T C Q G K S H N E R D W L F I M V Y P A T C Q G K S H N E R D FR mutations CDR mutations

  19. D T I D K R Application 1: antibody engineering W S T D R A K I Y E G L E R G D T G K G Engineered antibody

  20. Application 2: vaccine design

  21. Application 2: vaccine design Lower hydrophilicity Higher hydrophilicity

  22. Application 3: biosensor design

  23. Smaller residues Larger residues Application 3: biosensor design

  24. Other advantages of visualization

  25. Conclusion • Visualization plays a key role in analysis • Quicker elucidation of patterns • Find those that were not immediately obvious • Key applications of protein mutation matrix visualization • Evolution studies • Protein engineering • Image manipulation and analysis techniques may be applied to images

  26. Current activities + future targets • Matrix generation tool development • Prototype hosted at the CSRC site • Migrate from Matlab to open source software (i.e. Scilab/Octave + PERL/Tcl/Tk) • Offer full matrix generation + visualization package online

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