Lecture 18 -Protein Design and Engineering

Database statistical nearest neighbors output

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database (statistical) • Nearest neighbors output: probability for each residue to be in α, β, or Loop • Artificial intelligence/neural networks – Train a computer to recognize patterns – the more information and the “more practice” the higher the accuracy (in progress)
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Design • Minibody • Chymohelizyme • Calcium sensor
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Minibody • 61 residue synthetic peptide •A l l • Template: Heavy chain variable domain of the immunoglobulin • Hypervariable loops • Binding site: Histidines in each hypervariable loop • The protein folds and binds Zn 2+ • Nature 362: March 25, 1993
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Chymohelizyme • Design: Computer-assisted protein design • Four helix bundle – parallel, amphipathic • Serine protease catalytic triad –Ser, His, Asp at the N-end of the four-helix bundle in the same spatial arrangement as chymotrypsin • Oxyanion hole and substrate binding pocket for acetyltyrosineethylester, a classical substrate of CT were included in the design • Synthetic enzyme folds, is catalytically active and sensitive to a specific inhibitor Science 248:1544, 1990)
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database statistical Nearest neighbors output probability...

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