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.
2Structural Bioinformatics analysisis of
protein structures and their functions by
informatic tools
3Tools and techniques for
- Analize
- Save
- Visualize
- Predict
- Compare
- Evaluate
- ESTRUCTURE OF PROTEINS
41-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
6Complexity 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)
7Tertiary 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
8X ray difraction
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10NMR
11 12Protein data Bank Tour
- Statistics
- Look for the active form (closed
- Conformation from human glucokinase)
- Take a look to the file
- Save archive
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14PDB archives
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16Molecular Visualization
FIRST GLANCE JMOL
JMOL web
JMOL molecular visualization program
Example of a tutorial on glucokinase
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18Molecular Visualization Programs
- Rasmol (1995)
- Chime
- Protein Explorer ( Chime interface, requieres
Chime, problems with Chime) - Jmol (java)
- Deep View
- Others professionals Pymol
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23Tools 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)
24Structural alignment
25Structural 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
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29Derived Data bases and classification of proteins
based on 3D structures
- PDBsum
- Clasification SCOP, CATH
30PDBSUM
31CATH 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)
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36SCOP. Structural Classification of Proteins
- Family. Clear evolutive relationship
- Superfamily. Probably common evolutive origin
- Folding. Strong structural homology
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