Protein structure determination & predictionSlide 2Slide 3Slide 4X-ray crystallographySlide 6Slide 7Nuclear magnetic resonance spectroscopySlide 9Slide 10Slide 11Slide 12Ab initio protein predictionSlide 14Slide 15Slide 16Fold recognition (structural profiles)ThreadingProtein structure determination & predictionTertiary protein structure: protein foldingThree 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 crystallizationSteps in obtaining a protein structure Target selection Obtain, characterize protein Determine, refine, model the structure Deposit in databaseX-ray crystallographyhttp://en.wikipedia.org/wiki/X-ray_diffractionSperm Whale MyoglobinNuclear magnetic resonance spectroscopyhttp://en.wikipedia.org/wiki/Nuclear_magnetic_resonanceArticleAb initio protein predictionStarts with an attempt to derive secondary structure from the amino acid sequencePredicting the likelihood that a subsequence will fold into an alpha-helix, beta-sheet, or coil, using physicochemical parameters or HMMs and ANNsAble to accurately predict 3/4 of all local structuresSecondary structure predictionChou 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 algorithmModern algorithms: use multiple sequence alignmentsand achieve higher success rate (about 70-75%) Page 279-280Fold recognition (structural profiles)Attempts to find the best fit of a raw polypeptide sequence onto a library of known protein foldsA prediction of the secondary structure of the unknown is made and compared with the secondary structure of each member of the library of foldsThreadingTakes 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
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