Protein structure determination & prediction. Tertiary protein structure: protein folding Three main approaches: [1] experimental determination (X-ray.

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Presentation transcript:

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 crystallography Sperm Whale Myoglobin

Nuclear magnetic resonance spectroscopy

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 algorithm based 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 alignments and achieve higher success rate (about 70-75%) Page

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