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Biology Articles » Cell biology » Protein Forces & Structure - Bonds Stabilizing the Folded 3D Conformation

Protein Forces & Structure - Bonds Stabilizing the Folded 3D Conformation

Virtually every biochemical process in the living cell is catalysed, sustained and regulated by protein. While fundamentally dependant on the linear amino acid sequence, it is the precise folding of the polypeptide chain into a discrete three-dimensional structure (or conformation) that ultimately confers its biological function. Deviation from this 'native state' - i.e. through misfolding, damage, mutation or denaturation - can lead to abnormal, depleted or even absent proteins, all of which can be devastating to the cell.

Since protein folding is thought to occur spontaneously following mRNA translation, the question of how a protein achieves such structural precision from billions of possibilities is not yet fully understood. What is known, however, is that prions caused by protein manifolding are now being implicated in neurodegenerative diseases and cancer, therefore identifying and understanding the underlying mechanisms of the folding process is a significant area of biomedical research. Given that the integrity of protein structure is so vital to effective cell function, this essay will explore the various molecular forces which are known to contribute to its stability.

A protein folds into a three-dimensional structure according to the chemical properties of its constituent amino acids. Therefore, prior to the folding process the linear amino acid sequence must first be consolidated to serve as the basis for its spatial organization. This is achieved by peptide bonding which generates a resonance force to give stabilizing double-bond characteristics which are shorter, more rigid and have a planar orientation preventing free rotation. This bond can resist de-naturation by normal methods (such as heat and urea) and can only be broken by hydrolysis with a strong acid or base at very high temperatures in the absence of enzyme activity. This establishes a strong covalent backbone which is also polar, allowing for hydrogen bonding.

Such hydrogen bonding between the established backbone NH-CO groups constitute a proteins secondary structure. Hydrogen atoms of the amine groups are attracted to the more electronegative carboxyl groups, resulting in electrons being shared. While a hydrogen bond in itself is non-covalent, the multiple repeated nature of such bonding offers much stability. Many proteins display repeated patterns of hydrogen bonding to form α helices and β-pleated sheets, the latter being composed of short β strands (usually no more than 8 residues) laid out parallel or anti-parallel to each other with hydrogen bonds perpendicular to the polypeptide backbone. These structures can interact to form motifs often referred to as super-secondary structure and are common in structural proteins like collagen and keratin. Branched amino acids (e.g. val or ile) can interfere with these arrangements if in large numbers, causing coils, loops and turns in the secondary structure - as too does proline because it has a secondary rather than a primary amine group. However, rather than disrupt stability, these features allow close packing and proximity of variable side chains which can take part in further bonding.

Bonding between side-chainsgives rise to tertiary structure and this is what ultimately divides the protein into functional domains. Side chain interactions depend on their chemical properties. One example of tertiary bonding is the formation of ionic bonds (or salt bridges) between charged amino acid side chains. For instance, the negatively charged oxygen on an aspartic acid residue can bond to the positively charged nitrogen atom in lysine as an electrostatic force of attraction. Two cysteine residues can cross-link to form covalent disulphide bonds, which are important in stabilising smaller or extracellular proteins such as albumin. Serine and other polar uncharged amino acids contain hydroxyl groups that can hydrogen bond with water or hydrophilic residues such as glutamate acid, both of which are usually found on the surface of water soluble proteins. Phenylalanine and tyrosine, both aromatic and hydrophobic, can also form hydrogen bonds with other residues and the peptide backbone, as well as forming special hydrophobic interactions called pie stacks. The complexity of these tertiary interactions transforms the protein into a functional unit.

Despite the fact that most functional residues are usually found on the protein surface, the major driving force for protein stability is thought to be the formation of a hydrophobic core. Hydrophobic amino acids such as alanine and methionine will tend to cluster together in order to exclude water. This occurs because the hydrophobic amino acids have no, or small, electrical charges which would disrupt the normal hydrogen bonding between water molecules. By excluding these molecules, most of which have hydrocarbon side-chains, the protein structure is more thermodynamically stable and is entropy driven at room temperature. Recent experiments using mutagenesis show that substituting amino acids on the surface does little to affect protein stability but substitutions at the protein core can be severely destabilizing.

 

Note: Article contributed by the author, Kellieanne McMilla, for publication in Biology-Online.org Articles. Contact us for any authorship issues associated with the article.


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