How to predict the 3-D structure of a protein

1. Protein structure prediction
SABAHAT ALI
(16-arid-2569)

2. 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.

3. Protein structure
• This topic has been covered several
times. Next! 

4. 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.

5. 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.

6. 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.

7. Protein threading prtactical
• 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.

8. The End