Part I : Introduction 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

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 α- conotoxin ImI and its three mutants Rogers et al., 2000, JMB 304, 911

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.

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.

Common structure of Amino Acid H H H H N R C  O O C + - Amino Carboxylate Side chain = H,CH 3,… Atoms numbered  Backbone Cα is the chiral center Atom lost during peptide bond formation

Aliphatic residues

Aromatic residues

Charged residues

Polar residues S

The odd couple Side chain = H CC CC CC CC CC

The peptide bonds

Coplanar atoms

Backbone torsion angles

Ramachandran / phi-psi plot  - helix (right handed)  - sheet  - helix (left handed)  

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.

Secondary structure Local organization of protein backbone:  -helix,  -strand (which assemble into  -sheet), turn and interconnecting loop.

Ramachandran / phi-psi plot  - helix (right handed)  - sheet  - helix (left handed)  

The  -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  -sheet Backbone almost fully extended, loosely packed arrangement of residues.

Topologies of  -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.

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).

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.

SCOP Structural Classification Of Proteins database Classification is done manually All nodes are annotated

SCOP at the top of the hierarchy

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- , All-β,  / β,  + β, multi-domain

CATH Class-Architecture-Topology-Homologous superfamily Manual classification at Architecture level but automated at Topology level

Class Architecture Topology HomologousSuperfamily Sequence 3 classes: Mainly- , Mainly-β,  -β Classified based on sequence identity Share a common ancestor Both the overall shape & connectivity of secondary structure Overall shape as determined by orientations of secondary structures The hierarchy in CATH