Quaternary Level of Protein Structural Organization

Quaternary structure or Quaternary level of protein structural organization, is the structure that results of  the assembly of several polypeptide to make an unique functional protein, stabilized through several noncovalent interactions between the R side chain of amino acids from different peptide chains.

 

The non covalent interactions that maintain this structure are the same non covalent interactions that maintain the tertiary structure: Hydrogen bonds, Ionic interactions, Hydrophobic attractions and Van der Waals Forces.

 

Based on the definition we gave above, not all proteins show a quaternary level of organization. For having a quaternary structure:

a)     The protein should be formed by more than one peptide chain.

b)     These chains can not be attached by covalent bonds among them.

 

Some examples for clarifying the concept:

 

Myoglobin is formed by a single peptide chain and a hem group. Since Myoglobin is formed by just one peptide chain, it does not show quaternary structure.

 

Insulin, for example, is formed by two peptide chains, but since these two chains are linked by disulfide linkage, insulin does not qualify as a protein with quaternary structure.

 

Hemoglobin is formed by four peptide chains (and four Hem groups) that are forming a unique functional protein. These peptide chains are associated through non covalent bonds between their lateral chains: Hemoglobin is the typical example of a protein with quaternary structure.

 

Hemoglobin

 

 

The quaternary structure of a protein is intimately related to the feature of Allostery or Allosterism

 

It’s the property of some proteins to change its conformation and activity (it changes from a native conformation to  a different native conformation), when interact specifically with some ligands.

 

In the case of enzymes, the ligand binds at a site different to the active site, that is called allosteric site. This change in conformation results in a change in the activity of the enzyme.

 

Characteristics of the Allosteric proteins

 

•         All reach the quaternary level

•         They have two different but native structures

•         Each structure has a different functionality

•         The two native structures are in equilibrium

•         The equilibrium between the two structures is displaced when the protein interact with specific ligands

•         The interaction with the ligand takes place in specific sites of the protein known as allosteric sites

 

Hemoglobin, mentioned above,  is a typical example of a protein with quaternary structure that shows allosterism.  

 

Hemoglobin has two different native structures:

- Oxyhemoglobin (Relaxed structure).

- Deoxyhemoglobin (Tense or Taught structure).

 

These different native structures have different functionality;

- The Relaxed (R ) structure has high O2 affinity.

- The taught or tense (T) structure has low O2 affinity.

 

These two forms are in equilibrium:

 

R ß——à T

 

Presence or absence of oxygen changes the conformation: when Hemoglobin binds to Oxygen, the equilibrium between these two kinds of structures is displaced to the R form; when Oxygen is released, the equilibrium is displaced to the T form.

 

These two animations reflect the change of Hemoglobin structure as a result of Oxygen binding:

 

http://upload.wikimedia.org/wikipedia/commons/0/07/Hb-animation2.gif

 

http://wps.prenhall.com/esm_horton_biochemistry_4/37/9593/2455870.cw/index.html

 

 

Allosterism is also an important physiological mechanism of regulation of enzyme activity.

 

 

For more information about these topics, visit the following sites:

 

Berg, J.M.; Tymoczko, J.L. Stryer, L.: Biochemistry, 5t. Edition:

 

Quaternary Structure: Polypeptide chains can assemble into multisubunits structure.

 

Oxygen binding markedly changes the quaternary Structure of Hemoglobin

 

Wikipedia

 

http://en.wikipedia.org/wiki/Quaternary_structure

 

http://en.wikipedia.org/wiki/Allostery

 

The Medical Biochemistry page

 

Quaternary structure

 

 

Hemoglobin

 

Allosteric enzymes

 

  

Supersecondary Structures (Motifs) and Domains.

 

We can define Supersecondary structures as combinations of alpha-helices and beta-structures connected through loops, that form patterns that are present in many different protein structures. These folding patterns are stabilized through the same kind of linkages than the tertiary level. Sometimes the term “motif” is used to describe these supersecondary structures.

 

These structures can be relatively simples, as alpha-alpha (two alpha helixes linked by a loop), Beta-Beta (two beta-strands linked by a loop), Beta-alpha-Beta (Beta-strand linked to an alpha helix that is also linked to other beta strand, by loops) or more complexes structures, like the Greek key motiv or the beta-barrel.

Greek Key motif

  

 

 

Beta-barrel motif

 

It is very interesting in these motifs that these repetitive structures can be very different in their primary structure and they can be present in very different proteins.  Some proteins have no supersecondary structures.

 

Domains

 

They are stable, independently folding, compact structural units  within a protein, formed by segments of the polypeptide chain, with relative independent structure and function distinguishable from other regions and stabilized through the same kind of linkages than the tertiary level.

 

Following this definition, in this representation of Pyruvate kinase, it is possible to distinguish three domains:

 

Protein domains may be considered as elementary units of protein structure and evolution, capable, to some extent, of folding and functioning autonomously. A domain sometimes contain motifs, sometimes don’t.

 

The tertiary structure of many proteins is built from several domains

 

Domain Functions:

 

Often each domain has a separate function to perform for the protein, such as:

 

- Bind a small ligand

 

- Spanning the plasma membrane (transmembrane proteins)

 

- Contain the catalytic site (enzymes)

 

- DNA-binding (in transcription factors)

 

- Providing a surface to bind specifically to another protein

 

In some (but not all) cases, each domain in a protein is encoded by a separate exon in the gene encoding that protein.

 

 

More information:

 

Supersecondary structures

 

 

Motifs

 

 

Protein domains

 

 

Tertiary Level of Protein Structural Organization

 

A very clear and concise definition of tertiary structure appears in Mark’s Medical Biochemistry, which defines this structural level as “the folding pattern of the secondary structure into a three-dimensional conformation”.

 

Another way of defining it is based on the linkages that maintain this structural level. The tertiary structure of proteins is usually defined as the spatial conformation of the protein stabilized through several interactions between the R side chains of distant amino acids residues. Distant means that they can be very apart in the sequence, but because of the molecule folding, their lateral chains can interact through their functional groups. These interactions stabilize the spatial conformation of the protein.

 

Hydrophobic interactions are very often the driven force that allows that lateral chain of distant amino acids becomes next each other. In an aqueous environment, non polar lateral chains of amino acids in a peptide or protein tend to cluster together, as a result of the hydrophobic forces. It allows other kinds of interaction between the “new neighbors” amino acids.

 

The main interactions that maintain the spatial conformation of the proteins are:

 

Hydrophobic interactions (already mentioned)

Hydrogen bonds between the R side chain of distant amino acids

Ionic interactions

Disulfide bridges

 

Hydrophobic interactions

 

Already described. The amino acids with non polar lateral chain that can be attracted among them by hydrophobic forces are Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tyrosine and Tryptophan

 

Hydrogen bonds between the side chains (R) of distant amino acids

 

Hydrogen bonds, as we know, are established between very electronegative atom and Hydrogen bonded to Fluoride, Oxygen or Nitrogen.

 

Hydrogen bonds

 

These bonds can be established between molecules (like in the former example) or between parts of the same molecule, like occurs in proteins.

 

The amino acids whose lateral chains can form Hydrogen bonds among them that stabilize the tertiary structure are those that have Oxygen or Nitrogen in their lateral chain: 

 

Serine (hydroxyl group)

Threonine (hydroxyl group)

Tyrosine (hydroxyl group)

Glutamate (carboxyl group)

Glutamine (carbamide group)

Aspartate (carboxyl group)

Asparagine (carbamide group)

Lysine (amine group)

Arginine (amidine group)

Histidine (imidazol group)

 

(The hydrogen bonds between the lateral chains of amino acids, that stabilize the tertiary structure, should not be confounded with the Hydrogen bonds between elements of the peptide bonds, which are characteristics of the secondary structure)

 

Ionic interactions

 

Charged lateral chains of amino acids can interact with charged lateral chains of other amino acids. Amino acids with charged lateral chain are Glutamate, Aspartate, Lysine, Arginine and Histidine. If the amino acids whose lateral chains are interacting  have the same charges, the interaction results in repulsion, so the parts of the peptide chain where the amino acids are located, will separate; if they have different charges, the portions of the peptide chain were they are located will be attracted.

 

Repulsion:

Interaction between aspartate and glutamate (both with negative lateral chain).

Interaction between two of the following: Lysine, Arginine, Histidine (all of them with positively charged lateral chain)

 

Attraction:

Interaction between glutamate or aspartate (negatively charged lateral chains) with Lysine, Arginine or Histidine (positively charged lateral chains).

 

Disulfide bridges

 

Disulfide bond

 

 

As you know, cystein has an R-SH group in it lateral chain

Cysteine

 

 

Disulfide bridges are formed when two residues of cysteine interact between them, experimenting an oxidation of the sulfhydril groups. As a result both cysteines become linked, forming a cystine residue.

 

Cystine

 

Disulfide bridges are very strong bonds, that can be formed between different parts of the same peptide chain (intrachain bonds) if the cystein residues that form the disulfide bridge are in the same chain, or they can form interchain bonds, maintaining together different peptide chains, if the cysteine residues that form this linkage are present in different peptide chains.

 

Disulfide bonds are very frequent in proteins. Insulin has intermolecular and intramolecular disulfide bridges. Immunoglobulin chains are maintained together by disulfide bridges. The following diagram represent an immunoglobulin, whose Heavy and Light chains are maintained together by disulfide bridges (represented in red)

Immunoglobulin

Last but not least: the tertiary structure of a protein is intimately related to its function. Proteins that lost the native tridimensional conformation lost their functions. The main causes of losing a native conformation are denaturalization or a mutation (recall that the primary structure –amino acid sequence -determines the higher structures of the protein).

 

More information about Tertiary structure of proteins can be found at:

 

http://en.wikipedia.org/wiki/Tertiary_structure

 

http://themedicalbiochemistrypage.org/protein-structure.html#tertiary

 

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=tertiary,structure&rid=stryer.section.339

 

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/TertiaryStructure.html