PROGRAM
TUESDAY, June 28th
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Welcome to the students and introduction to the course (Prof. I. Castellano)
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Gene and Protein evolution (Prof. M. Gerdol)
Morning (09.30-12.00)
Theoretic Lecture:
Constrains that structure exerts on function and evolution of proteins, evolutionary divergence and convergence of proteins, evolution of protein complexity (protein families); enzyme promiscuity, examples from the sea.
Afternoon (15.00-18.00)
Practical Lecture:
Databases of proteins (InterPro). Exercises on protein alignments and building of phylogenetic tree.
WEDNESDAY, June 29th
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Evolution of metabolic pathways (Prof. A. Peracchi)
Morning (10.00-12.00)
Theoretic Lecture:
The limits of enzyme specificity: liabilities and opportunities in the evolution of metabolism. Examining our current understanding on how new activities and metabolic pathways emerge in the course of evolution.
Afternoon (14.30-17.30)
Practical session:
Practical Lesson: Databases of metabolic pathways (MetaCyc, KEGG) and of enzyme activities (BRENDA). Exercises on filling gaps in predicted metabolic pathways and on identifying candidates for orphan activities.
Social Dinner (starting at 20:00/20:30)
THURSDAY, June 30th
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Engineering of metabolic pathways by enzyme design (Dr. Jae-Seong Yang)
Morning (10.00-12.00)
Theoretic Lecture:
The relationship between sequence conservation and protein functional sites, such as catalytic and allosteric sites. How to use sequence conservation for protein engineering and adaptive laboratory evolution.
Afternoon (15.00-18.00)
Practical session:
Database of experimentally obtained protein structures (RCSB PDB) and predicted ones (AIphaFold). Explaining about PDB structure format, protein structure visualization and parameter mapping on the structure (such as sequence conservation scores).