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Protein Strucure Comparison

Protein Strucure Comparison. Chapter 6,7 Orengo. Describing Coarse Level Structure. Helices. α -helix 4-turn helix, min. 4 residues 3 10 -helix 3-turn helix, min. 3 residues π -helix 5-turn helix, min. 5 residues. Formed by H-Bonds between residues in the same helix.

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Protein Strucure Comparison

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  1. Protein Strucure Comparison Chapter 6,7 Orengo

  2. Describing Coarse Level Structure Helices • α-helix 4-turn helix, min. 4 residues 310-helix 3-turn helix, min. 3 residues π-helix 5-turn helix, min. 5 residues • Formed by H-Bonds between residues in the same helix

  3. Describing Coarse Level Structure Strands and Sheets • Formed by successive H-Bonds between residues can be far apart in sequence.

  4. Cartoons for Secondary Structure Elements (SSE) • Topology of Protein Structure (TOPS) • Triangular symbols represent beta strands • Circular symbols represent helices (alpha and 310)

  5. Some families show great structural diversity Gabrielle Reeves Multiple structural alignment by CORA allows identification of consensus secondary structure and embellishments 2DSEC algorithm In 117 superfamilies relatives expanded by >2 fold or more These families represent more than half the genome sequences of known fold

  6. Strategy

  7. Two Approaches

  8. Example

  9. Intra

  10. RMSD

  11. Example • Alignment • ACSL-DRTS-IRV • A-TLREKSSLIR- • Know first 5 residues • ACSL-D • A-TLRE

  12. But not so with structures Dynamic Programming cannot be used directly for structure alignment highest score alignment of entire structures highest score alignment of first five residues

  13. Finding optimal Root mean square deviation

  14. Process Degrees of freedom include Equivalenced elements Rotation Translation (usually centroid)

  15. Example • In two dimensions

  16. Translation • In two dimensions Shift Centroids to the origin

  17. Example HW 9.2 • In two dimensions • Rotation Matrix

  18. The matrix in the book is just an angular rotation

  19. The first step • Transpose centroids to the origin • Foreach angular displacement in x • Foreach angular displacement in y • Foreach angular displacement in x • Calculate RMSD • If this RMSD is less than current minimum, save it

  20. But, how did we get the equivalenced elements? • First seed the problem with an initial equivalence E0 • Then find the Transformation that results in a minimum RMSD • Use this Transformation to find a better equivalence

  21. Alternating Superposition and Alignment

  22. Example The best rotation and translation is then found and a new alignment is generated

  23. Structural Classification of Proteins (SCOP) SCOP describes protein structures using a hierarchical classification scheme: Classes Folds Superfamilies (likely evolutionary relationship) Families Domains Individual PDB entries http://scop.mrc-lmb.cam.ac.uk/scop/

  24. Class, Architecture, Topology, and Homologous Superfamily (CATH) database CATH clusters proteins at four levels: C Class (a, b, a&b folds) A Architecture (shape of domain, e.g. jelly roll) T Topology (fold families; not necessarily homologous) H Homologous superfamily http://www.biochem.ucl.ac.uk/basm/cath_new Page 293

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