1. 1 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Several motifs (  -sheet, beta-alpha-beta, helix-loop-helix) combine to form a compact globular structure termed a domain or tertiary structure A domain is defined as a polypeptide chain or part of a chain that can independently fold into a stable tertiary structure Domains are also units of function (DNA binding domain, antigen binding domain, ATPase domain, etc.) Another example of the helix-loop-helix motif is seen within several DNA binding domains including the homeobox proteins which are the master regulators of development Modules (Figures from Branden & Tooze) HMMs, Profiles, Motifs, and Multiple Alignments used to define modules

2. COG 272, BRCT family P. Bork et al

3. Five Principal Fold Classes All  folds All  folds  +  folds  /  folds small irregular folds

4. SCOP - Protein Fold Hierarchy Class - 5 Fold - ~500 Superfamily - ~ 700 Family ~ 1000 Family - domains with common evolutionary origin

5. Sequence Similarity May Miss Functional Homologies Which Can Be Detected by 3D Structural Analysis Residues Aligned % Sequence Identity Homologous 3D Structure Non-homologous 3D Structure Adapted from Chris Sander } “Twilight zone”

6. Structural Validation of Homology Adenylate Kinase Guanylate Kinase 19% Seq ID Z = 12.2

7. CspA CspB Topoisomerase I Asp tRNA Synthetase Staphylococcal Nuclease Gene 5 ssDNA Binding Protein

8. 8 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu What is Protein Geometry? Coordinates (X, Y, Z’s) Dihedral Angles  Assumes standard bond lengths and bond angles

9. 9 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Other Aspects of Structure, Besides just Comparing Atom Positions Atom Position, XYZ triplets Lines, Axes, Angles Surfaces, Volumes

10. 10 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Depicting Protein Structure: Sperm Whale Myoglobin

11. 11 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Sperm Whale Myoglobin

12. 12 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Structural Alignment of Two Globins

13. 13 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Automatic Alignment to Build Fold Library Hb Mb Alignment of Individual Structures Fusing into a Single Fold “Template” Hb VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAV |||.. | |.|| |. |. | | | | | | |.|.| || | ||. Mb VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAIL Hb AHVD-DMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------ | |. || |....|.. | |..|.. | |. ||. Mb KK-KGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG Elements: Domain definitions; Aligned structures, collecting together Non-homologous Sequences; Core annotation Previous work: Remington, Matthews ‘80; Taylor, Orengo ‘89, ‘94; Artymiuk, Rice, Willett ‘89; Sali, Blundell, ‘90; Vriend, Sander ‘91; Russell, Barton ‘92; Holm, Sander ‘93 ; Godzik, Skolnick ‘94; Gibrat, Madej, Bryant ‘96; Falicov, F Cohen, ‘96; Feng, Sippl ‘96; G Cohen ‘97; Singh & Brutlag, ‘98

14. Explain Concept of Distance Matrix on Blackboard N x N distance matrix N dimensional space Metric matrix M ij = D ij 2 - D io 2 - D jo 2 Eigenvectors of metric matrix Principal component analysis

15. 15 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Automatically Comparing Protein Structures Given 2 Structures (A & B), 2 Basic Comparison Operations 1Given an alignment optimally SUPERIMPOSE A onto B Find Best R & T to move A onto B 2Find an Alignment between A and B based on their 3D coordinates

16. 16 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Some Similarities are Readily Apparent others are more Subtle Easy: Globins 125 res., ~1.5 Å Tricky: Ig C & V 85 res., ~3 Å Very Subtle: G3P-dehydro- genase, C-term. Domain >5 Å

17. 17 (c) Mark Gerstein, 1999, Yale, bioinfo.mbb.yale.edu Some Similarities are Readily Apparent others are more Subtle Easy: Globins 125 res., ~1.5 Å Tricky: Ig C & V 85 res., ~3 Å Very Subtle: G3P-dehydro- genase, C-term. Domain >5 Å

18. Distance Matices Provide a 2D Represenation of the 3D Structure

19. DALI: Protein Structure Comparison by Alignment of Distance Matrices L. Holm and C. Sander J. Mol. Biol. 233: 123 (1993) Generate C  -C  distance matrix for each protein A and B Decompose into elementary contact patterns; e.g. hexapeptide- hexapeptide submatrices Systematic comparisons of all elementary contact patterns in the 2 distance matrices; similar contact patterns are stored in a “pair list” Assemble pairs of contact patterns into larger consistent sets of pairs (alignments), maximizing the similarity score between these local structures A Monte-Carlo algorithm is used to deal with the combinatorial complexity of building up alignments from contact patterns Dali Z score - number of standard deviations away from mean pairwise similarity value

21. Structural Validation of Homology Adenylate Kinase Guanylate Kinase 19% Seq ID Z = 12.2

23. Dali Domain Dictionary Deitman, Park, Notredame, Heger, Lappe, and Holm Nucleic Acids Res. 29: 5557 (2001) Dali Domain Dictionary is a numerical taxonomy of all known domain structures in the PDB Evolves from Dali / FSSP Database Holm & Sander, Nucl. Acid Res. 25: 231-234 (1997) Dali Domain Dictionary Sept 2000  10,532 PDB enteries  17,101 protein chains  5 supersecondary structure motifs (attractors)  1375 fold types  2582 functional families  3724 domain sequence families

24. courtesy of C. Chothia

25. Most proteins in biology have been produced by the duplication, divergence and recombination of the members of a small number of protein families. courtesy of C. Chothia

30. Cadherins courtesy of C. Chothia

33. A Global Representation of Protein Fold Space Hou, Sims, Zhang, Kim, PNAS 100: 2386 - 2390 (2003) Database of 498 SCOP “Folds” or “Superfamilies” The overall pair-wise comparisons of 498 folds lead to a 498 x 498 matrix of similarity scores S ij s, where S ij is the alignment score between the ith and jth folds. An appropriate method for handling such data matrices as a whole is metric matrix distance geometry. We first convert the similarity score matrix [S ij ] to a distance matrix [D ij ] by using D ij = S max - S ij, where S max is the maximum similarity score among all pairs of folds. We then transform the distance matrix to a metric (or Gram) matrix [M ij ] by using M ij = D ij 2 - D io 2 - D jo 2 where D i0, the distance between the ith fold and the geometric centroid of all N = 498 folds. The eigen values of the metric matrix define an orthogonal system of axes, called factors. These axes pass through the geometric centroid of the points representing all observed folds and correspond to a decreasing order of the amount of information each factor represents.

34. A Global Representation of Protein Fold Space Hou, Sims, Zhang, Kim, PNAS 100: 2386 - 2390 (2003)