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Alejandro Giorgetti
3rd Permanent School in Bioinformatics
Madrid 2005
Protein Structure Modeling Alejandro Giorgetti
Alejandro Giorgetti
The number of different protein folds is limited:
[ last update: Oct 2001 ]New Folds
Known Folds
100
1'000
10'000
100'000
1'000'000
1986 1988 1990 1992 1994 1996 1998 2000 2002 2004
TrEMBL
SwissProt
PDB
Public Database Holdings:
Alejandro Giorgetti
Fold recognition
Principle: Find a compatible fold
>Target Sequence XYMSTLYEKLGGTTAVDLAVAAVAGAPAHKRDVLNQ
Build model of target protein based on each
template structure
Rank models according to
SCORE or ENERGY
Profile methods
Threading
M
A
TE
A
F
TS
G
Q
AlaAlaP
AlaAlaPkTAlaAlaE
unfolded
folded
(
)(ln)(
Fold =f(environment)Local Secondary StructureSolvent AccessibilityDegree of burial of polar / apolar
Fragment based methods: New fold prediction
Alejandro Giorgetti
Some remarks concerning fold recognition:
Capable of detecting quite remote sequence-structure matches.
Sensitivity depends on the size of the protein and its secondary structure content.
The two most versatile enzymatic functions (hydrolases and o-glycosyl- glucosidases) are associated with seven folds each.
Better for detecting: all-α > αβ > all-β
Alejandro Giorgetti
Homology modeling
Comparative protein modeling
Idea: Proteins evolving from a common ancestor maintained similar core 3D structures.
Known structure/s is/are used as a template to model an unknown structure with known sequence.
Both of them should be related by evolution.
First applied in late 1970’s by Tom Blundell
Alejandro Giorgetti
10 %
30 %
50 %
70 %
90 %
Drug design?
Biochemistry?
Molecular Biology?
[ Chothia & Lesk (1986) ]
Evolution of protein structure families
X-r
ay c
rist
allo
grap
hy:
MR
Alejandro Giorgetti
Template(s) selection
Sequence Alignment
Structure Modeling
Structure E
valuation
Final Structural Models
Comparative Modeling
Known Structures (templates)
Target sequence
>hTEIIMSSPQAPEDGQGCGDRGDPPGDLRSVLVTTVLNLEPLDEDLFRGRHYWVPAKRLFGGQIVGQALVAAAKSVSEDVHVHSLHCYFVRAGDPKLP
Alejandro Giorgetti
Template(s) selection
Sequence Alignment
Structure Modeling
Structure E
valuation
Final Structural Models
Target sequence
Protein Data Bank PDB http://www.pdb.org
Database of templates
Separate into single chainsRemove bad structures (models)
Create BLAST database
Comparative Modeling
Known Structures (templates)
Alejandro Giorgetti
Known Structures (templates)
Sequence Alignment
Structure Modeling
Structure E
valuation
Final Structural Models
Target sequence
Sequence Similarity / Fold recognition
Structure quality (resolution, experimental method)
Experimental conditions (ligands and cofactors)
Comparative Modeling
Template(s) selection
Alejandro Giorgetti
Known Structures (templates)
Template(s) selection
Structure Modeling
Structure E
valuation
Final Structural Models
Target sequence
Key step in homology modelingGlobal alignment is requiredSmall error in alignment can lead to big error in modelMultiple alignments are better than pairwise alignmentsDo we know something else? Experiments?
Comparative Modeling
Sequence Alignment
Alejandro Giorgetti
Known Structures (templates)
Template(s) selection
Structure E
valuation
Final Structural Models
Target sequence
Template based fragment Assembly (SwissMod). Satisfaction of Spatial Restraints: MODELLER
Comparative Modeling
Sequence Alignment
Structure Modeling
Alejandro Giorgetti
Known Structures (templates)
Template(s) selection
Sequence Alignment
Structure Modeling
Final Structural Models
Target sequence
Errors in template selection or alignment result in bad models
Iterative cycles of alignment, modeling and evaluation
Comparative Modeling
Structure E
valuation
Alejandro Giorgetti
[ http://www.expasy.org/spdbv/ ]
I. Template based fragment assembly (SwissModel)
Alejandro Giorgetti
• SwissPdb downloading: a) Read and Accept licenceb) Download: SwissPdb viewer v3.7sp5(linux)• Installation:a) gunzip spdbv37sp5-Linux.tar.gzb) tar –xvf spdbv37sp5-Linux.tarc) cd SPDBV_Distribution and do: ./install.shd) Local installation : ..../guestxx/e) Run: /guestxx/SPDBV/bin/spdbv
• SwissModel submission:a) Search template: http://www.expasy.org/swissmod/SWISS-
MODEL.html Interactive tools: Search the template...(paste sequence) b) Model request submission: Save project (SwissPdb Viewer); c) Swiss- Model web page: Modelling Requests – Optimise mode.d) Fill the form and Upload your project asking for Short mode output.
Day activities. Morning
Alejandro Giorgetti
Corresponds to the most stable regions. Highest sequence conservation and fewer gaps. In general: secondary structures elements.
a) Build conserved core framework (Structurally conserved regions -SCRs)
I. Template based fragment assembly
[ http://www.expasy.org/spdbv/ ]
Alejandro Giorgetti
Least stable or more flexible regions.
Highest level of gapping
Lowest sequence conservation
Loops and turns
Loop-Database
“ab-initio” rebuilding of loops (Monte Carlo,
molecular dynamics, genetic algorithms, etc.)
b) Loop modeling (Structural variable regions - SVRs) and backbone completion
I. Template based fragment assembly
[ http://www.expasy.org/spdbv/ ]
Alejandro Giorgetti
c) Side Chain placement
Find the most probable side chain
conformation, using
homologues structures
back-bone dependent rotamer libraries
energetic and packing criteria
I. Template based fragment assembly
[ http://www.expasy.org/spdbv/ ]
Alejandro Giorgetti
modeling will produce unfavorable contacts and bonds
idealization of local bond and angle geometry
extensive energy minimization will move coordinates away
keep it to a minimum
SwissModel is using GROMOS 96 force field
d) Energy minimization
I. Template based fragment assembly
ji ijijij
ji
ji
bonds angles dihedralsb
rrr
nVkxxkV
612
0
20
20
4
1
)cos(1()()(
Alejandro Giorgetti
Find the most probable structure given its alignment Satisfy spatial restraints derived from the alignment. Uses probability density functions. Minimizes violations on restraints.
Comparative protein modeling by satisfaction of spatial restraints. A. Šali and T.L. Blundell. J. Mol. Biol. 234, 779-815
II. Modeling by Satisfaction of Spatial restraints
Alejandro Giorgetti
Model Evaluation ?Topics:
correct fold
model coverage (%)
C - deviation (rmsd)
alignment accuracy (%)
side chain placement
Structure Analysis and Verification Server:
http://nihserver.mbi.ucla.edu/SAVS/
Alejandro Giorgetti
EVA
Evaluation of Automatic protein structure prediction
[ Burkhard Rost, Andrej Sali, http://maple.bioc.columbia.edu/eva ]
CASPCommunity Wide Experiment on the Critical Assessment of Techniques for Protein Structure Predictionhttp://PredictionCenter.llnl.gov/casp6
3D - Crunch
Very Large Scale Protein Modelling Project
http://www.expasy.org/swissmod/SM_LikelyPrecision.html
Model Accuracy Evaluation
Alejandro Giorgetti
Protein Structure Resources
PDB http://www.pdb.org PDB – Protein Data Bank of experimentally solved structures (RCSB)
CATH http://www.biochem.ucl.ac.uk/bsm/cath Hierarchical classification of protein domain structures
SCOP http://scop.mrc-lmb.cam.ac.uk/scop Alexey Murzin’s Structural Classification of proteins
DALI http://www2.ebi.ac.uk/dali Lisa Holm and Chris Sander’s protein structure comparison server
SS-Prediction and Fold Recognition
PHD http://cubic.bioc.columbia.edu/predictprotein Burkhard Rost’s Secondary Structure and Solvent Accessibility Prediction Server
PSIPRED http://bioinf.cs.ucl.ac.uk/psipred/L.J McGuffin, K Bryson & David T. Jones Secndary struture prediction Server
3DPSSM http://www.sbg.bio.ic.ac.uk/~3dpss Fold Recognition Server using 1D and 3D Sequence Profiles coupled.
THREADER: http://bioinf.cs.ucl.ac.uk/threader/threader.html David T. Jones threading program
Alejandro Giorgetti
• UCL, Janet Thornton & Christine Orengo
• Class (C), Architecture(A), Topology(T), Homologous superfamily (H)
Protein Structure Classification
CATH - Protein Structure Classification[ http://www.biochem.ucl.ac.uk/bsm/cath_new/ ]
SCOP - Structural Classification of Proteins
• MRC Cambridge (UK), Alexey Murzin, Brenner S. E., Hubbard T., Chothia C.
• created by manual inspection
• comprehensive description of the structural and evolutionary relationships
[ http://scop.mrc-lmb.cam.ac.uk/scop/ ]
Alejandro Giorgetti
• Class(C)
derived from secondary structure
content is assigned automatically
• Architecture(A)
describes the gross orientation of
secondary structures,
independent of connectivity.
• Topology(T)
clusters structures according to
their topological connections and
numbers of secondary structures
• Homologous superfamily (H)
Alejandro Giorgetti
Protein Homology Modeling Resources
SWISS MODEL: http://www.expasy.org/swissmod/SWISS-MODEL.html
Deep View - SPDBV:homepage: http://www.expasy.ch/spdbv Tutorials http://www.expasy.org/spdbv/text/tutorial.htm
WhatIf http://www.cmbi.kun.nl:1100/Gert Vriend’s protein structure modeling analysis program WhatIf
Modeller: http://guitar.rockefeller.edu/modeller Andrej Sali's homology protein structure modelling by satisfaction of spatial restraints
ROBETTA: http://robetta.bakerlab.org/ Full-chain Protein Structure Prediction Server
Programs and www servers very useful in Comparative modeling: http://salilab.org/tools/
Alejandro Giorgetti
Day activities SwissPdb Viewer: downloading and installation. Target accession number (Swiss-Prot): O14734 1) Template Search Method: Blast - FASTA – PsiBlast – QuickBlast (from Swiss-Prot). 2) Sequence Alignment and Secondary Structure Pred. Pairwise - Multiple sequence alignment (free to choose method) Secondary structure prediction. (Predict Protein Meta server or PHD advanced submission form). Results comparison. 3) SwissPdb viewer: Load Raw sequence to model.(SwissModel menu) Find appropriate template (SwissModel menu) Load template (1C8U.pdb) (File menu) Update threading display now (item of the SwissModel menu). This function threads your sequence into the template. Manually optimize the alignment (Wind menu: Sequences Alignments):
Align the catalytic triad and secondary structure elements Alignment editing. (Back-Space or Space to delete and add gaps). It is useful to color by secondary structure in Template
Target: Asp231, Ser253 and Gln303.
Template: Asp204, Thr228 and Gln278
Make sure the current layer is PTE1, click on the little black arrow in Align Window. "smooth" with smoothing factor =1.
"Auto Color by Threading Energy" item of the SwissModel menu.
Threading evaluation: "select aa making clashes" items of the "Select" menu.
Submit a modeling request to Swiss-Model "Submit modeling request" of the SwissModel menu. (Otherwise save the project, and submit from SwissModel web page: Optimize mode.
4 ) Model Validation Structural Controls: Loops modeling? Regions :Scan Loop Data Base (Build menu). Need refinement? If yes, few steps of MD minimization: Select all residues In SwissPdb viewer Prefs menu – Energy minimization set to 200 steps of steepest descent (electrostatics interactions?) In Tools menu: Energy minimization.
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