Thermodynamics and the structure of biological macromolecules

Abstract

In this review, I will discuss the role of thermodynamics in both the determination and evaluation of the structure of biological macromolecules. The presentation relates to the historical context, state-of-the-art and projection into the future. Fundamental features relate to the effect of charge, exemplified in the study of synthetic and natural polyelectrolytes. Hydrogen bonding and water structure constitute basic aspects of the medium in which biological reactions occur. Viscosity is a classical tool to determine the shape and size of biological macromolecules. The thermodynamic analysis of multicomponent systems is essential fo the correct understanding of the behavior of biological macromolecules in solution and for the evaluation of results from powerful experimental techniques such as ultracentrifugation, light, X-ray and neutron scattering. The hydration, shape and flexibility of DNA have been studied, as well as structural transitions in nucleosomes and chromatin. A particularly rewarding field of activity is the study of unusual structural features of enzymes isolated from the extreme halophilic bacteria of the Dead Sea, which have adapted to saturated concentrations of salt. Future studies in various laboratories will concentrate on nucleic-acid--protein interactions and on the so-called 'crowding effect', distinguishing the behavior in bacteria, or other cells, from simple test-tube experiments.

Effect of Salt on the Activity and Stability of Aspartate Aminotransferase from the Halophilic Archaebacterium Haloferax mediterranei

“…The hydrophobic interactions m ust play a main role in the stability of hAspAT as seems to occur in other halophilic proteins [26]. The effect o f cations observed in our case is in opposition with the H of meister series, which gives of following order for the hydrophobic interactions (M g2+ > Li+ > N a+ > K + > N H 4+).…”

“…Thus, the free-energy changes associated with the dissociation process may be treated according to the "salting-out" theories [28,32], where the free-energy change is linearly dependent on the salt concentration [33]. The halophilic m alate dehydrogenase shows a similar behavior, its denaturation by low salt con centration involves enzyme-dimer dissociation [26,34],…”

“…The effects of salt on the activity and structure of halophilic enzymes has been discussed taking into account the electrostatic and hydrophobic in teractions, although the competition in the form a tion o f hydrate bonds between protein-solvent and protein-protein as the most im portant contribut ing factor to polypeptide folding of these proteins has been proposed recently [25,26].…”

Purification and Characterization of Nitrate Reductase from the Halophile Archaebacterium Haloferax mediterranei

“…In general, the salts have a strong effect on the activity and stability of the halophilic enzymes, as it has been observed in all the cases analyzed (see reviews [27,28]). The stability of the halophilic ni trate reductase at 21 °C is increased with the pres ence of salt in the medium.…”

Physical and chemical characterization of the oligomerization state of the Aeromonas hydrophila lipase/acyltransferase

“…The apparent partial specific volumes of both the lipase and T-lipase are different from those determined from their amino acid sequences (see Table I) and in addition, there is an important change accompanying oligomerization. In a three-component system, 4: can 298 be related to the preferential hydration parameter 5, of a protein by the following equation [9] It may be seen that the change in @ upon dimerization of T-lipase must reflect either changes in hydration and/ or salt binding as a result of the association of monomers. Since the values of @: clearly must be more representative of the properties of the proteins than the theoretical VZ values estimated from the amino acid composition, they were used in the conformational calculations shown in Table I.…”