protein structure prediction anttu kurttio ville pietiläinen
TRANSCRIPT
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Protein structure prediction
Anttu Kurttio
Ville Pietiläinen
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Introduction
• Proteins are one of the most important parts in any biological systems.
• Understanding the folding of the amino-acid chain to produce functional proteins is essential for studying cellular systems.
• Fast and accessible methods of solving the 3D structure of a protein are in high demand.
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Protein structure
• This topic has been covered several times. Next!
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Computational methods
• Ab initio- methods– Laws of physics + amino-acid sequence =
protein structure– Computes potential energy functions.– Minimum potential energy is the most stable
structure and as such the most likely.– Computationally demanding.
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Comparative methods
• Based on the limited amount of possible tertiary structure types.
• Approximately 2000 different types of protein folds.
• Comparing the sample to a database of known structures, for example Protein Data Bank.
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Homology modelling
• Based on the assumption that homologous (related) proteins fold in a similar fashion.
• Folding is a highly conserved factor, much more so than amino-acid sequence.
• Finding a match between two distantly related proteins can be difficult.
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Protein threading
• Based on the assumption that similar folding has already been found.
• Comparing parts of the sequence to a database of known three dimensional structures using a scoring function.
• Works at least somewhat on approximately 80% of new protein sequences.
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Programs
• A lot of free programs are available. • Server based programs do the
computational work. For example Swiss-Model, Rosetta or PSIPRED.
• Downloadable applications are used for viewing the results. For example Swiss-PdbViewer or Rasmol.
• Distributed computing promises increases in computational capacity.
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DEMO
• Swiss-Model in four easy steps.
swissmodel.expasy.org
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Step 1: Send in the sequence
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Step 2: Coffee break
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Step 3: Recieve mail
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Step 4: Open PDB-file
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Rejoice!
• Study your brand new model of a protein.