Protein structure determination & prediction
Dec 30, 2015
Tertiary protein structure: protein folding
Three main approaches:
[1] experimental determination (X-ray crystallography, NMR)
[2] Comparative modeling (based on homology)
[3] Ab initio (de novo) prediction (Dr. Ingo Ruczinski at JHSPH)
Experimental approaches to protein structure
[1] X-ray crystallography-- Used to determine 80% of structures-- Requires high protein concentration-- Requires crystals-- Able to trace amino acid side chains-- Earliest structure solved was myoglobin
[2] NMR-- Magnetic field applied to proteins in solution-- Largest structures: 350 amino acids (40 kD)-- Does not require crystallization
Steps in obtaining a protein structure
Target selection
Obtain, characterize protein
Determine, refine, model the structure
Deposit in database
Ab initio protein prediction
Starts with an attempt to derive secondary structure from the amino acid sequence Predicting the likelihood that a subsequence will fold into an
alpha-helix, beta-sheet, or coil, using physicochemical parameters or HMMs and ANNs
Able to accurately predict 3/4 of all local structures
Secondary structure prediction
Chou and Fasman (1974) developed an algorithmbased on the frequencies of amino acids found in helices, -sheets, and turns.
Proline: occurs at turns, but not in helices.
GOR (Garnier, Osguthorpe, Robson): related algorithm
Modern algorithms: use multiple sequence alignmentsand achieve higher success rate (about 70-75%)
Page 279-280
Fold recognition (structural profiles)
Attempts to find the best fit of a raw polypeptide sequence onto a library of known protein folds
A prediction of the secondary structure of the unknown is made and compared with the secondary structure of each member of the library of folds