Download presentation
Presentation is loading. Please wait.
Published byErnest Phillips Modified over 9 years ago
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
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
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
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.