Sometimes high sequence similarity yields different structures. 
Sequencesimilarity structuresimilarity Why Comparing Protein Folded Structures?
Sometimes high sequence similarity yields different structures Sequence Structure FunctionĪlignment of 1xis and 1nar (TIM-Barrels) 1xis and 1nar have only 7% sequenceidentity, but approximately 70% of the residues are structurally similar. Low sequence similarity may yield very similar structures. Sequencesimilarity Why Comparing Protein Folded Structures? Given a new structure, the probability is high that it is similar to an existing one. Three possible reasons: - evolution, - physical constraints (e.g., few ways to maximize hydrophobic interactions), - limits in techniques used for structure determination. Is expected to reflect functional similarities (interaction with other molecules). 1xis 1nar backbone format Alignment computed by DALI ahelix axes Expected to reflect functional similarities (interaction with other molecules) Proteins in the TIM barrel fold familyĪlignment of 1xis and 1nar (TIM-Barrels) ribbon format Sayle, R. Refers to how well (or poorly) 3D folded structures of proteins can be aligned. 
Protein Data Bank Only about 10% of structures have been determined for known protein sequences Protein Structure Initiative (PSI) 1990 250 new structures 1999 2500 new structures 2000 >20,000 structures total 2004 ~30,000 structures total Protein Data Bank 1990 250 new structures 1999 2500 new structures 2000 >20,000 structures total 2004 ~30,000 structures total Nuclear magnetic resonance spectroscopy.Experimental tools X-ray crystallography.NMR spectrometry Structure Prediction/Determination Secondary Structure Elements: a helices, b strands/sheets, & loops
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