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P9 Extra Discussion Slides

Sequence-Structure-Function Relationships

• Proteins of similar sequences fold into similar

structures and perform similar biological

functions.

• The protein sequence has the intrinsic

information to encode the protein structure.

From Nobel Lecture, December 11, 1972, by Christian Anfinsen

The protein sequence is sufficient to specify its 3D structure

Structure Prediction from sequence

1.Homology (or comparative) modelling

2.Threading

3.Ab initio calculations

Homology modelling is most accurate and powerful

What is Homology Modeling?

• Homology modeling also known as comparative

modeling uses homologous sequences with known 3D

structures for the modelling and prediction of the

structure of a target sequence

• Homology modeling is one of the most best

performing prediction methods that gives “accurate”

predicted models.

How does it work• A homology modeling routine needs three items of input:

– The sequence of the protein with unknown 3D structure, the "target sequence".

– A 3D template is chosen by virtue of having the highest sequence identity with the target sequence. The 3D structure of the template must be determined by reliable empirical methods such as crystallography or NMR, and is typically a published atomic coordinate "PDB" file from the Protein Data Bank.

– An alignment between the target sequence and the template sequence. • First, the homology modeling routine arranges the backbone identically to

that of the template. This means that not only the positions of alpha carbons, but also the phi and psi angles and secondary structure, are made identical to the template. Next, the more sophisticated homology modeling packages adjust side chain positions to minimize collisions, and may offer further energy minimization or molecular dynamics in an attempt to improve the model.

6Taken from: http://www.umass.edu/molvis/workshop/homolmod.htm

Homology modelling practical steps,in brief

• Retrieving the sequence to be modeled (target sequence)

• Identifying suitable templates from PDB using BLAST

– Go for the best hit (> 30 - 40% identity)

– No need to do modeling if hit is 100% identical to target

• Aligning target sequence with template sequences

– Remove gapped positions

– Remove residues in target that are missing in template

– Final alignment should be in PIR format

• Performing homology modeling using MODELLER

– Change the aligned PIR file to add additional information required by MODELLER

– Mind the syntax (most errors occur because of not following the syntax)

• Model quality check – WHATIF, PROCHECK, VERIFY3D, ERRAT

• Quantitative comparison of model with experimental structure

– Assess RMSD using SUPERPOSE

Quantitative comparison between model and experimental 3D structure using RMSD

• 0.0-0.5 Å

• <1.5 Å

• < 5.0 Å

• 5.0-7.0 Å

• > 7.0 Å

• > 12.0 Å

• Essentially Identical

• Very good fit

• Moderately good fit

• Structurally related

• Dubious relationship

• Completely unrelated

Taken from: http://redpoll.pharmacy.ualberta.ca/bioinfo301/Bioinf301-3Dvisualize.ppt