Part I : I ntroduction to Protein Structure A/P Shoba Ranganathan - - PDF document

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Part I : I ntroduction to Protein Structure

A/P Shoba Ranganathan Kong Lesheng

National University of Singapore

Overview

Why protein structure? The basics of protein Levels of protein structure Structural classification of protein structure

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Why protein structure?

In the factory of living cells, proteins are the

workers, performing a variety of biological tasks.

Each protein has a particular 3-D structure

that determines its function. ”Structure implies function”.

Structure is more conserved than sequence. Protein structure is central for understanding

protein functions.

Sequence Structure Function

To understand functions, we need structures

a - conotoxin ImI and its three mutants

Rogers et al., 2000, JMB 304, 911

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Anfinsen’s thermodynamic hypothesis

“The three-dimensional structure of a native protein

in its normal physiological milieu (solvent, pH, ionic strength, presence of other components such as metal ions or prosthetic groups, temperature, etc.) is the one in which the Gibbs free energy of the whole system is lowest; that is, that the native conformation is determined by the totality of interatomic interactions and hence by the amino acid sequence, in a given environment.”

• -- Anfinsen’s Nobel lecture, 1972

What drives protein folding?

Hydrophobic effects

Hydrophobic residues tend to be buried inside Hydrophilic residues tend to be exposed to solvent

Hydrogen bonds help to stabilize the structure.

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Overview

Why protein structure? The basics of protein Levels of protein structure Structural classification of protein structure

The basics of protein

Proteins have one or more polypeptide chains Building blocks: 20 amino acids. Length range from 10 to 1000 residues. Proteins fold into 3-D shape to perform

biological functions.

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Common structure of Amino Acid

H H H H

N R C α O O C +

• Amino

Carboxylate Side chain = H,CH3,… Atoms numbered β,γ,δ,ε,ζ.. Backbone Ca is the chiral center

Atom lost during peptide bond form ation

Aliphatic residues

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Aromatic residues Charged residues

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Polar residues

S

The odd couple

Side chain = H Cα Cβ Cγ Cδ Cα

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The peptide bonds Coplanar atoms

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Backbone torsion angles Ramachandran / phi-psi plot

α-helix (right handed) β-sheet α-helix (left handed)

φ ψ

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Overview

Why protein structure? The basics of protein Levels of protein structure Structural classification of protein structure

Primary structure

The amino acid sequences of

polypeptides chains.

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Secondary structure

Local organization of protein backbone:

α-helix, β-strand (which assemble into β-sheet), turn and interconnecting loop.

Ramachandran / phi-psi plot

α-helix (right handed) β-sheet α-helix (left handed)

φ ψ

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The α-helix

First structure to be predicted

(Pauling, Corey, Branson, 1951) and experimentally solved (Kendrew et al., 1958) – myoglobin

One of the most closely packed

arrangement of residues.

3.6 residues per turn 5.4 Å per turn

The β-sheet

Backbone almost fully extended, loosely

packed arrangement of residues.

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Topologies of β-sheets Tertiary structure

Packing the secondary

structure elements into a compact spatial unit.

“Fold” or domain– this

is the level to which structure prediction is currently possible.

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Quaternary structure

Assembly of homo or

heteromeric protein chains.

Usually the functional

unit of a protein, especially for enzymes

Structure comparison facts

Proteins adopt only a limited number of folds. Homologous sequences show very similar

structures: variations are mainly in non-conserved regions.

There are striking regularities in the way in which

secondary structures are assembled (Levitt & Chothia, 1976).

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Overview

Why protein structure? The basics of protein Levels of protein structure Structural classification of protein structure There are two major databases for protein

structural classification: SCOP and CATH.

They have different classification hierarchy

and domain definitions.

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SCOP

http://scop.mrc-lmb.cam.ac.uk/scop/ Structural Classification Of Proteins database Classification is done manually All nodes are annotated

SCOP at the top of the hierarchy

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The hierarchy in SCOP

Root Class Fold Superfamily Family Protein

Clear evolutionary relationship Probable common ancestry Have the same major secondary structure & topological connections 5 classes: All-α, All-ß, α/ ß, α+ ß, multi-domain

CATH

• http:/ / www.biochem.ucl.ac.uk/ bsm/ cath
• Class-Architecture-Topology-Homologous

superfamily

• Manual classification at Architecture level but

automated at Topology level

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Class Class Architecture Architecture Topology Topology Homologous Homologous Superfamily Superfamily

Sequence Sequence

3 classes: Mainly-α, Mainly-ß, α-ß Classified based on sequence identity Share a common ancestor Both the overall shape & connectivity

• f secondary structure

Overall shape as determined by

• rientations of secondary structures

The hierarchy in CATH