BIOL 200 Lecture Notes - Lecture 11: Structural Alignment, Supersecondary Structure, Protein Tertiary Structure
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The concept of the domain was first proposed in 1973 by Wetlaufer after X-ray crystallographic
studies of hen lysozyme and papain and by limited proteolysis studies
of immunoglobulins. Wetlaufer defined domains as stable units of protein structure that could
fold autonomously. In the past domains have been described as units of compact
structure,function and evolution,folding. Each definition is valid and will often overlap. Nature
often brings several domains together to form multidomain and multifunctional proteins with a
vast number of possibilities. In a multidomain protein, each domain may fulfill its own function
independently, or in a concerted manner with its neighbours. Domains can either serve as
modules for building up large assemblies such as virus particles or muscle fibres, or can provide
specific catalytic or binding sites as found in enzymes or regulatory proteins.
An appropriate example is pyruvate kinase, a glycolytic enzyme that plays an important role in
regulating the flux from fructose-1,6-biphosphate to pyruvate. It contains an all-β regulatory
domain, an α/β-substrate binding domain and an α/β-nucleotide binding domain, connected by
several polypeptide linkers (see figure, right). Each domain in this protein occurs in diverse sets
of protein families.
The central α/β-barrel substrate binding domain is one of the most common enzyme folds. It is
seen in many different enzyme families catalysing completely unrelated reactions. The α/β-barrel
is commonly called the TIM barrel named after triose phosphate isomerase, which was the first
such structure to be solved. It is currently classified into 26 homologous families in the CATH
domain database. The TIM barrel is formed from a sequence of β-α-β motifs closed by the first
and last strand hydrogen bonding together, forming an eight stranded barrel. There is debate
about the evolutionary origin of this domain. One study has suggested that a single ancestral
enzyme could have diverged into several families, while another suggests that a stable TIM-
barrel structure has evolved through convergent evolution.
The TIM-barrel in pyruvate kinase is 'discontinuous', meaning that more than one segment of the
polypeptide is required to form the domain. This is likely to be the result of the insertion of one
domain into another during the protein's evolution. It has been shown from known structures that
about a quarter of structural domains are discontinuous. The inserted β-barrel regulatory domain
is 'continuous', made up of a single stretch of polypeptide.
Covalent association of two domains represents a functional and structural advantage since there
is an increase in stability when compared with the same structures non-covalently
associated. Other, advantages are the protection of intermediates within inter-domain enzymatic
clefts that may otherwise be unstable in aqueous environments, and a fixed stoichiometric ratio
of the enzymatic activity necessary for a sequential set of reactions.
The primary structure (string of amino acids) of a protein ultimately encodes its uniquely folded
3D conformation. The most important factor governing the folding of a protein into 3D structure
is the distribution of polar and non-polar side chains. Folding is driven by the burial of
hydrophobic side chains into the interior of the molecule so to avoid contact with the aqueous
environment. Generally proteins have a core of hydrophobic residues surrounded by a shell of
hydrophilic residues. Since the peptide bonds themselves are polar they are neutralised by
hydrogen bonding with each other when in the hydrophobic environment. This gives rise to
regions of the polypeptide that form regular 3D structural patterns called secondary structure.
There are two main types of secondary structure: α-helices and β-sheets.
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