Tema 14. Bases of protein structure and structural prediction. Structural data bank. Protein Data Ba - PowerPoint PPT Presentation

1 / 37
About This Presentation
Title:

Tema 14. Bases of protein structure and structural prediction. Structural data bank. Protein Data Ba

Description:

Clasification: SCOP, CATH. PDBSUM. CATH Hierarchy. C: Class (secondary structure content) ... SCOP. Structural Classification of Proteins. Family. Clear evolutive relationship ... – PowerPoint PPT presentation

Number of Views:360
Avg rating:3.0/5.0
Slides: 38
Provided by: gabrie71
Category:

less

Transcript and Presenter's Notes

Title: Tema 14. Bases of protein structure and structural prediction. Structural data bank. Protein Data Ba


1
  • Tema 14. Bases of protein structure and
    structural prediction. Structural data bank.
    Protein Data Bank. Molecular Visualization Tools
    for 3D. Prediction based on sequence. Folding
    prediction. 3D structural prediction by homology.
    Quality criteria.

2
Structural Bioinformatics analysisis of
protein structures and their functions by
informatic tools
3
Tools and techniques for
  • Analize
  • Save
  • Visualize
  • Predict
  • Compare
  • Evaluate
  • ESTRUCTURE OF PROTEINS

4
1-GLSDGEWQLV LNVWGKVEAD IPGHGQEVLI RLFKGHPETL
EKFDKFKHLK SEDEMKASED LKKHGATVLT ALGGILKKKG
HHEAEIKPLA QSHATKHKIP VKYLEFISEC IIQVLQSKHP
GDFGADAQGA MNKALELFRK DM ASNYKELG FQG-153
5
-Ala-Ser-Ile-Met-Arg-
Función
Aminoacid sequence determines one significative
form. 3D form of the protein determines its
function
6
Complexity levels Hierarchics Primary so
far Secundary a-helix 35 of residues ß -
sheet, 25 of residues ß turns, O turns, 3/10
helix Total 65-75 Rest inclasificable
subestructures, hazard forms (ramdom coils)
7
Tertiary Structure
  • Simple Clasification
  • All alfa (gt50 helix lt10 ß)
  • All ß (gt30 beta lt5 heix)
  • Mixture
  • Refined Clasification
  • Topologies, motifs, domains
  • Foldings . Most of the proteins will be
    classified in one or other way from about 1000
    distinct basic foldings

Quaternary structure
8
X ray difraction
9
(No Transcript)
10
NMR
11
  • 3D structural Data Bank

12
Protein data Bank Tour
  • Statistics
  • Look for the active form (closed
  • Conformation from human glucokinase)
  • Take a look to the file
  • Save archive

13
(No Transcript)
14
PDB archives
15
(No Transcript)
16
Molecular Visualization
FIRST GLANCE JMOL
JMOL web
JMOL molecular visualization program
Example of a tutorial on glucokinase
17
(No Transcript)
18
Molecular Visualization Programs
  • Rasmol (1995)
  • Chime
  • Protein Explorer ( Chime interface, requieres
    Chime, problems with Chime)
  • Jmol (java)
  • Deep View
  • Others professionals Pymol

19
(No Transcript)
20
(No Transcript)
21
(No Transcript)
22
(No Transcript)
23
Tools for 3D structures analysis and comparison
  • Check structures
  • Looking for similars in structures. VAST
  • (1 mbn, whale myoglobin)
  • Structure alignment servers and deepview
  • conserved surfaces (glucokinase)

24
Structural alignment
25
Structural alignment
  • Goal Obtain best superposition from several
    structures
  • Dinamic program scoring from geometric
    characteristics
  • Matrices of intramolecular distances
  • Clustering in 3D
  • It is possible to classify proteins based on
    structural homology

Servidor
26
(No Transcript)
27
(No Transcript)
28
(No Transcript)
29
Derived Data bases and classification of proteins
based on 3D structures
  • PDBsum
  • Clasification SCOP, CATH

30
PDBSUM
31
CATH Hierarchy
  • C Class (secondary structure content)
  • A Architecture (disposition of the secondary
    structure elements)
  • T Topology (disposition of the connexions
    between elements)
  • H Homology (Structural homology)
  • S Sequence (Sequence homology)

32
(No Transcript)
33
(No Transcript)
34
(No Transcript)
35
(No Transcript)
36
SCOP. Structural Classification of Proteins
  • Family. Clear evolutive relationship
  • Superfamily. Probably common evolutive origin
  • Folding. Strong structural homology

37
(No Transcript)
Write a Comment
User Comments (0)
About PowerShow.com