Thermodynamic fluctuations in protein molecules.

Abstract

Apparently conflicting views of the physical nature of globular proteins, and other macromolecules, may be reconciled by consideration of the inevitable thermodynamic fluctuations inherent in microscopic systems. Discrete protein molecules, considered singly, undergo sizeable fluctuations in thermodynamic properties which are manifest in their stochastic properties. This is not incompatible with time-averaged studies of ensembles of proteins from which a more compact, rigid, and static view of these molecules may be obtained.There are still major conceptual problems involved in the visualization of the nature of globular proteins, and other macromolecules, in solution, and different types of experiment can lead to quite different views of the same molecule. Experimental techniques such as fluorescence quenching (1, 2) and relaxation (3), phosphorescence (4), nuclear magnetic resonance (5-7) point to a rather fluid, dynamic structure for globular proteins involving rapid conformational fluctuations which allow relatively easy, if somewhat transient, accessibility of interior groups to solvent and molecular probes (1). Some aspects of the dynamics of protein molecules have been recently reviewed (8). There are, in addition, indications from hydrogen exchange experiments (9) and studies of molecular fragments (10) of somewhat slower structural relaxations of importance, i.e., "breathing".On the other hand, analyses of data from x-ray crystallography (11-13) indicate that the packing densities of groups within globular proteins are as high as those found for solid, crystalline amino acids (12, 13) and small organic compounds (11), suggesting a rather compact, rigid, and static view of these molecules. The gross thermodynamic properties of proteins seem to confirm this. Thermal denaturation transitions of many globular proteins are highly cooperative (14) and reminiscent of the melting of pure, microcrystalline solids. In addition, the heat capacities (Cp) of a range of proteins in aqueous solutions lie in the range 0.30-0.35 cal g-ldeg-' (1.26-1.47 kJ.g-' K-') (14,15), which is somewhat higher than found for simple organic liquids but compares well to the heat capacities of solid, crystalline amino acids (0.316 ± 0.026 cal g-1deg-' at 250) (16)(17)(18)(19).Thus, experiment presents us with two, apparently conflicting views: one, a compact structure in which the polypeptide chain is precisely folded to give a tightly interlocking, rigid molecule; the other, a "kicking and screaming stochastic molecule' (20) in which fluctuations are frequent and dramatic. These fluctuations produce a seemingly fluid and flexible system. The intention of this note is to point out that no real paradox is involved and that, though it is difficult to conceive macroscopic systems having both fluid and solid-like behavior at one and the same time, these properties are perfectly compatible with the microscopic nature of individual protein molecules.The distribution functions for thermodynamic parameters in macroscopic systems are us...

Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure

“…However, proteins must undergo significant energy and volume fluctuations (9). Despite the mounting evidence that changes in protein structures are necessary to produce a desired function (10), the dominant paradigm of protein structure-function relationship is still based on the concept of a rigid protein with a unique structure.…”

A large compressibility change of protein induced by a single amino acid substitution

“…This is a basic problem for understanding the folding mechanism of protein molecule and the structure-function relationship of enzyme, but only limited data have been reported on this quantity because of the technical difficulty. A novel measure of the flexibility is compressibility because it is directly linked to the volume fluctuation (Cooper, 1976). Although this type of fluctuation is a thermodynamic one involving the effects of internal cavity and surface hydration, the partial specific adiabatic compressibility, a,, has been confirmed to sensitively reflect the characteristics or compactness of protein structure (Gekko & Noguchi, 1979;Gekko&Hasegawa, 1986,1989Sarvazyan, 1991;Tamuraetal., 1993;Tamura & Gekko, 1995).…”

Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution

“…High-pressure effects are of interest because they also help us to understand how macromolecules behave under normal conditions because protein compressibility is directly related to structural and conformational fluctuations of proteins at normal atmospheric pressure (Cooper 1976). Pressure is also of practical interest because it is one of the basic variables to account for when one faces the subject of life in extreme environments, as for instance in exobiology or in biology of deep-sea organisms.…”