Protein Tertiary

Structure

Protein Data Bank (PDB)

• Contains all known 3D structural data of large biological molecules, mostly proteins and nucleic acids: ~87,000 structures.

• The data is typically obtained by X-ray crystallography or NMR (Nuclear magnetic resonance) spectroscopy and submitted by biologists and biochemists from around the world.

• Freely accessible.

PDB file

Accession number

Java based visualization tools

2ndary structure

PDB file example:

A PDB file can be viewed by different visualization tools , such as Pymol

Protein, chain, domain

• Here is a protein compound by 4 chains.

• Which protein is that?

Protein, chain, domain

• One chain may have multiple domains.

• A protein domain is a conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain.

• Each domain has a stable 3D structure.

Protein domain classifications

• Scientists have tried to classify proteins by their structural properties into a tree-like hierarchy.

• The 2 most used domain classifications are CATH and SCOP.

CATH: Protein Domain Structure ClassificationClass, Architecture, Topology and Homology

•Class: The secondary structure composition: mainly-alpha, mainly-beta and alpha-beta.

• Architecture: The overall shape of the domain structure. Orientations of the secondary structures : e.g. barrel or 3-layer sandwich.

• Topology: Structures are grouped into fold groups at this level depending on both the overall shape and connectivity of the secondary structures.

•Homologous Superfamily: Evolutionary conserved structures

http://www.cathdb.info/

CATH: Protein Domain Structure ClassificationClass, Architecture, Topology and Homology

SCOP Structural Classification of Proteins

http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html

Based on known protein structures

•Manually created by visual inspection

•Hierarchical database structure:

–Class, Fold, Superfamily, Family, Protein and Species

Parents of node

Childrenof node

Node

Protein structure alignment

• Structural alignment attempts to establish homology between two or more protein structures based on their 3D conformation.

• Structural alignmentoften implies evolutionary relationships between proteins with low seq-id.

Sequence – structure relations

• Similar sequences Similar structures.

• Different sequences ???

• Different sequences that fold into similar structures are most interesting, since they imply a common origin.

• This is what we aim to find

Protein structure alignment

• Alignment tools try to superimpose the 2 structures, so that the distance between them is minimal.

• The distance measure is RMSD - Root Mean Square Deviation.

• Given two sets of n points v and w, the RMSD is defined as follows:

2

1

1( , )

n

i ii

RMSD v w v wn

Protein structure alignment

• The structural alignment servers do LOCAL structural alignment.

• They try to align larger stretches of protein backbone with minimal RMSD.

• Thus, another parameter to assess the quality of the alignment is the alignment length.

Protein structure alignment

• Low RMSD _________ structures

• Low alignment length _________ structures

• SAS score = 100*RMSD/(alignment length)• Low SAS _________ structures

similar

similar

dissimilar

Structure alignment servers

Dalilite:

http://www.ebi.ac.uk/Tools/structure/dalilite/

• 1XIS and 1NAR have only 7% sequence identity, but they are structurally similar.

• We will download their pdb files from the PDB, and structurally align them using Dalilite.

Insert PDB files

This file can be loaded to Pymol viewer

Food for thought

How can structure alignment help us in structure prediction?

Structure prediction

• Input: protein sequence;• Output: protein 3D structure.

• This is a VERY difficult task.

• CASP: Critical Assessment of Techniques for Protein Structure Prediction

• Worldwide experiment for protein structure prediction taking place every two years.

Structure prediction

Comparative Modeling Ab Initio Modeling

build 3D protein models "from scratch", i.e., based

on physical principles rather than on previously

solved structures.

uses previously solved structures as starting points, or templates.

Protein threading:sequence to

structure alignment, against a database of ‘templates’ – known

structures.

Homology modeling:

searches similarity in sequences with

known structures.

I-TASSER structure prediction server

• based on multiple-threading alignments

• I-TASSER (as 'Zhang-Server') was ranked as the No 1 server for protein structure prediction in recent CASP7, CASP8, CASP9, and CASP10 experiments.

I-TASSER results

I-TASSER results

I-TASSER results