Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions

Abstract

The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mö ssbauer and neutron P roteins are the molecules that perform most biological functions, from storage of dioxygen (O 2 ) to enzyme catalysis. A central goal of protein science is to relate structure, dynamics, and function. Although investigations of protein structures and functions are well organized industries, protein dynamics is still in its infancy. Dynamics studies are best performed on proteins whose structures and functions are well known, e.g., myoglobin (Mb), the protein that gives muscles their red color. A hybrid picture of Mb is shown in Fig. 1. The lower part displays a piece of the protein backbone, namely, three ␣-helices. The upper part presents a space-filling view of the protein atoms. The active center, a heme group with a central iron atom, is red. Two cavities are also shown, Xe1 and the heme cavity. The protein is surrounded by the hydration shell, one to two layers of water, and is embedded in the bulk solvent. In Mb's role as an oxygenstorage protein, O 2 enters the protein, stays some time in Xe1, then binds at the heme iron (1). CO follows a similar path through the protein. The structure of Mb shows no permanent channel that leads from the outside to either Xe1 or the heme pocket or from Xe1 to the heme pocket. Thus, structural fluctuations are necessary for function (2).Fluctuations imply that Mb possesses numerous different conformations, called conformational substates (CS) (3). The different CS can be described by an energy landscape (EL) (4), the central concept in the folding (5), dynamics, and function of proteins. The EL is a construct in Ϸ3N dimensions, where N is the number of atoms forming the protein and the hydration shell. A substate is a point in this hyperspace, and structural fluctuations are represented by jumps between points. Initially, we assumed that protein conformations could be organized into a simple, rough EL (1). Experiments showed, however, that there are wells within wells within wells, and an organization of the EL with several tiers of decreasing free-energy barriers ensued (6). The top tier, denoted by CS0, contains a small number of CS with different structures that can have different functions: in A 0 Mb is involved in NO enzymatics; in A 1 it acts as an oxygen-storage system (7). Each of the CS0 substates can assume a very large number of CS1, called statistical substates. They perform the same function but with different rates. Here, we will show that the statistical substates comprise two tiers, CS1␣ and CS1␤. Fluctuations between CS1␣ substates are slaved to the solvent motions and involve sizeable structural changes (8). ...

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

“…Because the PEG molecules are somewhat immobilized by cross-linkers as compared to the solvent, the water molecules that are close to PEG are expected to have much slower translational and rotational dynamics than water far away from PEG, similar to the behavior observed in confining environments [79,80] and around biomacromolecules such as proteins [81,82,83] and DNA [84,85,86]. From an inspection of the radial distribution function between polymer ether oxygen and water oxygen, as shown in Figure 4.1, the perturbation of the water distribution around PEG ether groups, relative to the average water density, extended to a radius of about 1.04 nm from the polymer ether oxygen.…”

From shell to cell: neutron scattering studies of biological water dynamics and coupling to activity

“…Devoid of hydration water, proteins are inactive 10 and lack essential motions, thus implicitly suggesting a close relationship between protein and hydration water dynamics. The term 'slaving' has been used to express that water can impose its dynamical fingerprint on a protein 11,12 . Cryo-temperature dependent neutron scattering experiments revealed the solvent dependence of dynamical transitions in soluble proteins [13][14][15][16][17][18][19][20][21] and in RNA 22 and provided insights into the coupling between them.…”

The protein glass transition as measured by dielectric spectroscopy and differential scanning calorimetry

“…Thus, in this case, such large scale protein fluctuations will disappear at the dynamic crossover temperature of the solvent, giving rise to a glass-like transition of the protein-solvent system. Below the crossover temperature the remaining secondary solvent process will only be able to promote more local protein motions [13]. In addition to this crossover also another dynamic crossover for hydration water, measured by quasielastic neutron scattering techniques, is observed around 220 K [16], but its physical nature will not be further discussed in this paper.…”

“…Protein dynamics involve many different types of motions, both local and more global movements, including transitions between several conformational substates [13]. When lowering the temperature these transitions become increasingly slower with decreasing temperature, and at a certain temperature the protein becomes frozen in a specific substate [17,24].…”

“…Anyhow, irrespective of the exact physical origin of the dynamic crossover most results suggest that the process below the crossover temperature should be considered as a secondary process, distinguished from the cooperative and viscosity related α-relaxation, which is unobservable with both dielectric spectroscopy and NMR techniques [10], at least below the crossover temperature [6,7]. If the α-relaxation of the hydration water disappears, due to confinement effects, at the crossover temperature, it should have an impact on protein dynamics, and consequently also on protein function, since it has been shown that protein conformational changes [13,14], and escape of carbon monoxide (CO) out of the heme cavity in myoglobin [15], cannot occur without the viscosity related (α) relaxation in the surrounding solvent. Thus, in this case, such large scale protein fluctuations will disappear at the dynamic crossover temperature of the solvent, giving rise to a glass-like transition of the protein-solvent system.…”