A general model is presented whereby ligand-induced changes in protein dynamics could produce allosteric communication between distinct binding sites, even in the absence of a macromolecular conformational change. Theoretical analysis, based on the statistical thermodynamics of ligand binding, shows that cooperative interaction free energies amounting to several kJ . mol-1 may be generated by this means. The effect arises out of the possible changes in frequencies and amplitudes of macromolecular thermal fluctuations in response to ligand attachment, and can involve all forms of dynamic behaviour, ranging from highly correlated, low-frequency normal mode vibrations to random local anharmonic motions of individual atoms or groups. Dynamic allostery of this form is primarily an entropy effect, and we derive approximate expressions which might allow the magnitude of the interaction in real systems to be calculated directly from experimental observations such as changes in normal mode frequencies and mean-square atomic displacements. Long-range influence of kinetic processes at different sites might also be mediated by a similar mechanism. We suggest that proteins and other biological macromolecules may have evolved to take functional advantage not only of mean conformational states but also of the inevitable thermal fluctuations about the mean.

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Perception of light by the retina starts with the absorption of a photon by 11-cis retinal, which is covalently incorporated into the membrane-bound protein, rhodopsin. The initial result of photon capture is the very rapid formation of a red-shifted species, bathorhodopsin (also known as prelumirhodopsin), which is (meta-)stable at liquid nitrogen temperature but which decomposes at higher temperatures, in the dark, through a series of intermediate stages, resulting in the release of all-trans retinal from the apoprotein, opsin. Bathorhodopsin formation is the only photochemical step in the overall reaction and, therefore, merits investigation. Several models for the process have been proposed, and have been critically reviewed, although no consensus yet exists as to the nature or mechanism of formation of the batho intermediate. I report here on the first direct measurement of photon energy uptake during bathorhodopsin formation from bovine rhodopsin, and on its possible significance.

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...

Protein‐based analogues of conventional thermoplastic elastomers can be designed with enhanced properties as a consequence of the precise control of primary structure. Protein 1 undergoes a reversible sol–gel transition, which results in the formation of a well‐defined elastomeric network above a lower critical solution temperature. The morphology of the network is consistent with selective microscopic phase separation of the endblock domains. This genetic engineering approach provides a method for specification of the critical architectural parameters, such as block length and sequence, which define macromolecular properties that are important for downstream applications.

The interactions of trimannosides 1 and 2 with Con A were studied to reveal the effects of displacement of well-ordered water molecules on the thermodynamic parameters of protein-ligand complexation. Trisaccharide 2 is a derivative of 1, in which the hydroxyl at C-2 of the central mannose unit is replaced by a hydroxyethyl moiety. Upon binding, this moiety displaces a conserved water molecule present in the Con A binding site. Structural studies by NMR spectroscopy and MD simulations showed that the two compounds have very similar solution conformational properties. MD simulations of the complexes of Con A with 1 and 2 demonstrated that the hydroxyethyl side chain of 2 can establish the same hydrogen bonds in a low energy conformation with the protein binding site as those mediated by the water molecule in the complex of 1 with Con A. Isothermal titration microcalorimetry (ITC) measurements showed that 2 has a more favorable entropy of binding compared to 1. This term, which was expected, arises from the return of the highly ordered water molecule to bulk solution. The favorable entropy term was, however, offset by a relatively large unfavorable enthalpy term. This observation was rationalized by comparing the extent of hydrogen bond and solvation changes during binding. It is proposed that an indirect interaction through a water molecule will provide a larger number of hydrogen bonds in the complex that have higher occupancies than in bulk solution, thereby stabilizing the complex.

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