Interactions occurring between chemical groups in proteins are responsible for formation of their specific secondary, tertiary and quaternary structures. Either repulsive or attractive interactions can occur between different groups. Repulsive interactions consist of steric hindrance and electrostatic effects. Like-charges repel each other and bulky side chains, although they do not repel each other, cannot occupy the same space. Folding is also against the natural tendency to move toward randomness, i.e., increasing entropy. Folding leads to a fixed position of each atom and hence a decrease in entropy. For folding to occur this decrease in entropy, as well as the repulsive interac-tions, must be overcome by attractive interactions, i.e., hydrophobic interactions, hydrogen bonds, electro-static attraction, and van der Waals interactions. Hydration of proteins, discussed in the next section, also plays an important role in protein folding.
These interactions are all relatively weak and can be easily broken and formed. Hence, each folded protein structure arises from a fine balance between these repulsive and attractive interactions. The stabi-lity of the folded structure is a fundamental concern in developing protein therapeutics.
The hydrophobic interaction reflects a summation of the van der Waals attractive forces among nonpolar groups in the protein interior, which change the surrounding water structure necessary to accommo-date these groups if they become exposed. The transfer of nonpolar groups from the interior to the surface requires a large decrease in entropy so that hydrophobic interactions are essentially entropically driven. The resulting large positive free energy change prevents the transfer of nonpolar groups from the largely sheltered interior to the more solvent exposed exterior of the protein molecule. Thus, nonpolar groups preferentially reside in the protein interior while the more polar groups are exposed to the surface and surrounding environment. The parti-tioning of different amino acyl residues between the inside and outside of a protein correlates well with the hydration energy of their side chains, i.e., their relative affinity for water. significantly more favorable free energies (because of entropic considerations) than intermolecular hydro-gen bonds, so the contribution of all hydrogen bonds in the protein molecule to the stability of protein structures can be substantial. In addition, when the hydrogen bonds occur in the interior of protein molecules, the bonds become stronger due to the hydrophobic environment.
Electrostatic interactions occur between any two charged groups. According to Coulomb’s law, if the charges are of the same sign, the interaction is repulsive with an increase in energy, but if they are opposite in sign it is attractive, with a lowering of energy. Electrostatic interactions are strongly depen-dent upon distance, according to Coulomb’s law, and inversely related to the dielectric constant of the medium. Electrostatic interactions are much stronger in the interior of the protein molecule because of a lower dielectric constant. The numerous charged groups present, for example, between negatively charged carboxyl groups and positively chargedamino groups. However, the net effects of all possible pairs of charged groups must be considered. Thus, the free energy derived from electrostatic interactions is actually a property of the whole structure, not just of any single amino acid residue or cluster.
Weak van der Waals interactions exist between atoms (except the bare proton), whether they are polar or nonpolar. They arise from net attractive interactions between permanent dipoles and/or induced (tempor-ary and fluctuating) dipoles. However, when two atoms approach each other too closely, the repulsion between their electron clouds becomes strong and counterbalances the attractive forces. The repulsive force is even more sensitive to the distance between two atoms.
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