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Quaternary Structure

What is Quaternary Structure ?

• Form in which units of tertiary structure units (proteins or nucleic acids) aggregate to form multimers eg Hemoglobin (tetramer formed of two alpha and two beta subunits).

• Important in understanding the biological function of the macromolecule inside the body.

• Quaternary structure not always evident from the contents of the coordinates deposited in the PDB.

Aggregation State

•Ultracentrifugation/sedimentation

•Chromatography

•Mass spectrometry

These methods provide clues to what the quaternary aggregation state is possible but no details on how the complex is formed and/or which regions are involved in forming the aggregate.

Assumptions

• A folded protein generally has patches on its surface that allows it to interact with other proteins. There are also surface features which allow them to dock with other proteins.

• A crystal is a well-ordered arrangement of molecules interacting with one another.

• Crystal structures can often provide clues to the overall quaternary structure in biological function.

CRYSTAL

UNIT CELL

Asymmetric UnitThis is what is in the PDB !!

Mannose-Binding Protein (PDB entry 1BUU)

In the PDB File Actual Quaternary Structure

PDB entry 1e94

In the PDB File(6 Chains)

Actual Quaternary Structure(hexameric)

Virus Capsids (PDB 2BU1)

In the PDB FileViral Capsid

Multiple Assemblies (PDB 1H2I)

In the PDB File

Two Quaternary Structures

Divining Quaternary Structure

Deriving probably quaternary structures from the deposited coordinates requires extensive computation and consideration of protein contacts, interfaces, surface complementarity and energetics. The PDBe has two services for the derivation of Quaternary Structure. At best all methods are accurate to within about 80-90% of experimentally determined aggregation states.

•PQS – Protein Quaternary Structure (http://pqs.ebi.ac.uk/). Partially manually annotated for all entries in the PDB.

•PISA – Proteins Interfaces, Surfaces and Assemblies (interactive and automatic procedure, include database searches).