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Protein Strucure Comparison Chapter 6,7 Orengo. Helices α-helix4-turn helix, min. 4 residues 3 10 -helix3-turn helix, min. 3 residues π-helix5-turn helix,

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Presentation on theme: "Protein Strucure Comparison Chapter 6,7 Orengo. Helices α-helix4-turn helix, min. 4 residues 3 10 -helix3-turn helix, min. 3 residues π-helix5-turn helix,"— Presentation transcript:

1 Protein Strucure Comparison Chapter 6,7 Orengo

2 Helices α-helix4-turn helix, min. 4 residues 3 10 -helix3-turn helix, min. 3 residues π-helix5-turn helix, min. 5 residues Formed by H- Bonds between residues in the same helix

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

6 Strategy

7 Two Approaches

8 Example

9 Intra

10

11 RMSD

12 Example Alignment –ACSL-DRTS-IRV –A-TLREKSSLIR- Know first 5 residues –ACSL-D –A-TLRE

13 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

14 Finding optimal Root mean square deviation

15 Process Degrees of freedom include 1)Equivalenced elements 2)Rotation 3)Translation (usually centroid)

16 Example In two dimensions

17 Translation In two dimensions Shift Centroids to the origin

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21 Example HW 9.2 In two dimensions Rotation Matrix

22 The matrix in the book is just an angular rotation

23 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

24 But, how did we get the equivalenced elements? First seed the problem with an initial equivalence E 0 Then find the Transformation that results in a minimum RMSD Use this Transformation to find a better equivalence

25 Alternating Superposition and Alignment

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

27 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/

28 Class, Architecture, Topology, and Homologous Superfamily (CATH) database Page 293 CATH clusters proteins at four levels: C Class ( , ,  &  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

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