Protein structure determination & prediction

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

X-ray crystallographyhttp://en.wikipedia.org/wiki/X-ray_diffraction

Sperm Whale Myoglobin

Nuclear magnetic resonance spectroscopy

http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance

Article

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

Threading

Takes the fold recognition process a step further:Empirical-energy functions for residue pair

interactions are used to mount the unknown onto the putative backbone in the best possible manner