Protein is found in every living cell. All these proteins are made with amino acids. Generally, there are 20 types of amino acids present which are further divided into groups: 5 charged polar amino acids, 7 neutral polar amino acids and 8 hydrophobic or non-polar amino acids. These charged residues are divided into subgroups; acidic (asp, glu) and basic (arg, his, lys). These amino acids interact with each other by covalent and non-covalent bonds. Charged residues within 4 Å do not create any covalent bond; they form a salt bridge interaction. Acidic residues and basic residues interact with each other and make this salt bridge. Hence, they form 5 types of pair of salt bridges; asp-arg, asp-his, asp-lys, glu-arg, glu-lys.
There are two types of salt bridges that are generally found in proteins namely, isolated salt bridges and network salt bridges. Isolated salt bridges are formed where only one pair of salt bridge is present like Asp215-His226. Network salt bridges are formed when multiple pairs of salt bridges are linked with each other like Asp215-His226-Arg175-Lys89. Due to the long-chain in network salt bridges, their strength is also higher than isolated salt bridges. However, recently a new type of salt bridge was also discovered which is a modified network salt bridge, called the cyclic salt bridge. These cyclic salt bridges have the highest effect on protein stability than any other salt bridges.
With the enormous efforts of scientists, we have finally discovered the role of salt bridges. Although, it is still a research item for many scientists all over the world, it plays a very crucial role in extremophiles. Extremophiles are those organisms that live in very extreme conditions and operate their physiological activity. There are many types of extremophiles present on earth. Just like thermophiles (those who live in very high temperature, 41 and 122 °C), halophiles (those who live in saline water), psychrophiles (those who live in very cold temperature) and acidophiles (those who lives in an acidic environment). These salt bridges are responsible for the adaptation in extreme conditions and help in protein folding.
In my personal opinion, if these residues will be muted by any uncharged residues, protein stability will decrease. These salt bridge forming residues are a very important clue for protein engineering. By the addition of charged residues in a protein, we can create stable protein structures from unstable ones.
Aromatic-aromatic interactions are also non-covalent electrostatic interactions. Research on the aromatic interactions denoted a new intuition on the nature of these biologically predominant non-covalent interactions in terms of their performance and stability. Investigation of the binding patterns of the aromatic residues to nucleic acid layouts give some insight into the origin and nature of interactions that can take place between the amino acids and nucleic acid bases. Formally, aromatic-aromatic interactions are explained as pairs of interacting aromatic residues which fulfill the following criteria: (i) the centers of the rings of the two interacting residues have aa distance between 4 Å to 7 Å, (ii) the dihedral angle will be 30° to 90° and (iii) free energies of formation should be between -0.6 and -1.3 kcal/mole.
Another type of non-covalent interaction is Van der Waals interactions. Van der Waals (dispersion) forces help in interactions of proteins with other molecules, but because of the structural complications of protein amino acids residues, the immensity of these effects is usually based on the molecular geometry, e.g., spheres or spheroids. Because of the structural dissimilarity between peptide and water, Van der Waals interactions favor peptide intra-molecular interactions and are a crucial contributing component to the structural folding and stability. These dense structures are amino acid sequence-dependent and closely look like secondary structures, as a result of Van der Waal interaction and covalent bonding constraints.
The cation-pi interaction, a non-covalent interaction, is a stabilizing electrostatic interaction of a cation with a polarizable pi-electron cloud of an aromatic ring. Six-carbon aromatic rings occur in the side chains of 3 (phenylalanine, tryptophan, and tyrosine) of the 20 standard amino acids. Cation–π interactions play an important role in protein nature, particularly in protein structure, folding, molecular recognition and enzyme catalysis. The outcome has also been noticed and put to use in synthetic systems in industrial applications.
All these non-covalent interactions are playing a very crucial role in protein stability and folding. Increasing these interactions will increase protein stability in an extreme environment. Generally mesophilic proteins have less non-covalent interactions than those of extremophiles.