Comparison based on statistical thermodynamics between globule-to-coil transition of poly(N-isopropylacrylamide) and cold denaturation of a protein

Enzyme Reactions Are Accelerated or Decelerated When the Enzymes Are Located Near the DNA Nanostructure

It is known experimentally that enzymatic reactions are often accelerated when the enzymes are assembled on the scaffold of DNA nanostructures. However, the exact mechanism by which this acceleration occurs remains unclear. Here, we study the reactions of enzymes with different catalytic mechanisms assembled on a DNA scaffold with various substrates. Analysis of the hydration properties of the substrates using our accurate statistical mechanics theory classifies the substrates into two groups that behave as hydrophilic and hydrophobic solutes, respectively. The reaction of the enzyme on the DNA scaffold is accelerated with a hydrophilic substrate but decelerated with a hydrophobic substrate. We propose a mechanism of acceleration or deceleration in which, due to the formation of a high-density layer of water near the DNA surface with high negative charge density, the concentration of a substrate with high energetic affinity for water within the layer becomes higher than that near a free enzyme, whereas that of a substrate with low energetic affinity becomes lower within the layer. This study provides chemical and physical insights into a general case of biocatalysts, where the rates of chemical reactions occurring at the interface of biomolecules in aqueous environments can differ substantially from those in the bulk solution due to variations in the local concentration of a given ligand.

Statistical-Mechanics Analyses on Thermodynamics of Protein Folding Constructed by Privalov and Co-Workers

Privalov and co-workers estimated the changes in hydration enthalpy and entropy upon ubiquitin unfolding and their temperature dependences denoted by ΔHhyd(T) and ΔShyd(T), respectively, from experimentally measured enthalpies and entropies of transfer of various model compounds from gaseous phase to water. We calculate ΔHhyd(T) and ΔShyd(T) for ubiquitin by our statistical-mechanics theory where molecular and atomistic models are employed for water and protein structure, respectively. ΔHhyd(T) and ΔShyd(T) calculated are in remarkably good agreement with those estimated by Privalov and co-workers. By examining relative magnitudes and signs of the changes in a variety of constituents of ΔHhyd(T) and ΔShyd(T), we confirm that the hydrophobic effect is an essential force driving a protein to fold. Detailed and comprehensive explanations are given for our claim that the prevailing views of the hydrophobic effect are not capable of elucidating its weakening at low temperatures, whereas our updated view is. We find out problematic points of the changes in enthalpy and entropy upon protein unfolding denoted by ΔH°(T) and ΔS°(T), respectively, which are measured using the differential scanning calorimetry at low pH, suggesting a theoretical method of calculating ΔH°(T) and ΔS°(T) at pH ∼ 7.

Physical pictures of rotation mechanisms of F1- and V1-ATPases: Leading roles of translational, configurational entropy of water

We aim to develop a theory based on a concept other than the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex. Experimental results conflicting with the chemo-mechanical coupling have recently emerged. We claim that the system comprises not only the protein complex but also the aqueous solution in which the protein complex is immersed and the system performs essentially no mechanical work. We perform statistical-mechanical analyses on V₁-ATPase (the A₃B₃DF complex) for which crystal structures in more different states are experimentally known than for F₁-ATPase (the α₃β₃γ complex). Molecular and atomistic models are employed for water and the structure of V₁-ATPase, respectively. The entropy originating from the translational displacement of water molecules in the system is treated as a pivotal factor. We find that the packing structure of the catalytic dwell state of V₁-ATPase is constructed by the interplay of ATP bindings to two of the A subunits and incorporation of the DF subunit. The packing structure represents the nonuniformity with respect to the closeness of packing of the atoms in constituent proteins and protein interfaces. The physical picture of rotation mechanism of F₁-ATPase recently constructed by Kinoshita is examined, and common points and differences between F₁- and V₁-ATPases are revealed. An ATP hydrolysis cycle comprises binding of ATP to the protein complex, hydrolysis of ATP into ADP and Pi in it, and dissociation of ADP and Pi from it. During each cycle, the chemical compounds bound to the three A or β subunits and the packing structure of the A₃B₃ or α₃β₃ complex are sequentially changed, which induces the unidirectional rotation of the central shaft for retaining the packing structure of the A₃B₃DF or α₃β₃γ complex stabilized for almost maximizing the water entropy. The torque driving the rotation is generated by water with no input of chemical free energy. The presence of ATP is indispensable as a trigger of the torque generation. The ATP hydrolysis or synthesis reaction is tightly coupled to the rotation of the central shaft in the normal or inverse direction through the water-entropy effect.