© 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/