© Wiley Publishing. 2007. All Rights Reserved.
Protein 3D
Structures
Learning Objectives
Review the basics of protein structuresKnow how to predict secondary structuresWork with the PDB databaseManipulate 3D structuresAppreciate both the potentials and limitations
of 3D analysis
Outline
Predicting secondary structuresRetrieving a PDB structure from the PDB databaseGuessing the 3D structure of your sequenceFurther applications of 3D analysis
Primary, Secondary and Tertiary Structures
Proteins are made of 20 amino acidsProteins are on average 400 amino acids longProtein structure has 3 levels:
• The primary structure is the sequence of a protein• The secondary structure is the local structure • The tertiary structure is the exact position of each
atom on a 3D model
Secondary Structures
Helix• Amino acid that twists like a spring
Beta strand or extended• Amino acid forms a line without twisting
Random coils• Amino acid with a structure neither
helical nor extended• Amino-acid loops are usually coils
Guessing the Secondary Structure
of Your Protein
Secondary structure predictions are goodIf your protein has enough homologues, expect 80%
accuracyThe most accurate secondary structure prediction
server is PSIPRED
PSIPRED Output Conf = Confidence
• 9 is the best, 0 the worst Pred = Every amino acid is assigned a letter:
• C for coils• E for extended or beta-strand• H for helix
Predicting Other Secondary Features
It is also possible to predict these accurately:• Transmembrane segments• Solvent accessibility• Globularity• Coiled/coil regions
All these predictions have an expected accuracy
higher than 70%
Predicting 3D Structures
Predicting 3D structures from sequences only is almost impossible
The only reliable way to establish the 3D structure of a protein is to make a real-world experiment in • X-ray crystallography• Nuclear magnetic resonance (NMR)
Structures established this way are conserved in the PDB database
“The PDB of my protein” is synonymous with “The structure of my protein”
Retrieving Protein Structures from PDB
All PDB entries are 4-letter words!• 1CRZ, 2BHL . . .
Sometimes the chain number is added: • 1CRZA, 1CRZB . . .
To access all PDB entries, go to www.rcsb.org • PDB contains 42,000 entries• PDB contains the structure of 16,000 unique proteins or RNAs
You can download the coordinates and display the structure
Displaying a PDB Structure
You can use any of the online viewers
to display the structure
They will let you rotate the structure,
zoom in and out, or color it
PDB files themselves are not human-
readable
Predicting the Structure of Your Protein
The bad news: • It is very hard to predict protein 3D structures
The good news:• Similar proteins have similar structures
If your favorite protein has a homologue with a known structure . . .• You can do homology modeling
How?• Start with a BLAST (more about that in the next slide)
BLASTing PDB for Structures
BLAST your protein against PDB
If you get a very good hit, it
means PDB contains a protein
similar to yours
Your protein and this hit
probably have the same
structure
Be Careful!
Sometimes only one of the domains contained in your protein has been characterized
If that’s the case, the PDB will only contain this domain Always check the alignments
• Red line = full protein in PDB• Blue line = one domain only in this entry
Structures and Sequences
Highly conserved sequences are often important in the structure Make a multiple-sequence alignment to identify these important positions Highly conserved positions are either in the core or important for
protein/protein interactions
3D Predictions
If you want to predict the structure of your protein automatically, try the Swiss Model• Swiss Model makes the BLAST for you• The program does a bit of homology modeling• The process delivers a new PDB entry• You can access it at swissmodel.expasy.org
Swiss Model gives good results for proteins having homologues in PDB
3D-BLAST
Use this technique if you have a structure and you want
to find other similar structures
Use VAST or DALI to look for proteins having the same
3D shape as yours• www.eb.ac.uk/dali• www.ncbi.nlm.nih/vast
3D Movements
Most proteins need to move to do their job
Predicting protein movement is possible using molecular dynamics• Check out this site: molmolvdb.mbb.yale.edu
Good molecular dynamics requires extremely powerful computers• Don’t expect miracles from standard online resources
Protein Interaction
Knowing “who interacts with whom” is one of the ultimate goals of predicting protein movement
These predictions are called docking analyses
Docking analyses are very difficult • Try www.biosolveit/FlexX/
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