Chemical-to-Mechanical Energy Conversion in Biomacromolecular Machines: A Plasmon and Optimum Control Theory for Directional Work. 1. General Considerations

Abstract

To rationalize coherence and mechanochemical aspects of proteins acting as molecular machines, a plasmon concept for dealing with protein nonequilibrium dynamics is introduced and tested with respect to thermodynamic consistency. A stochastic optimum-control theory for protein conformational diffusion is developed and the corresponding stochastic Newton's second law derived for optimum-controlled conformational diffusion in proteins. The plasmon concept is shown to be consistent with this theory, in that optical plasmons can pump entropy out of (or into) the protein, decreasing (or increasing) its conformational diffusion and, at the same time, help decrease intra- and intermolecular friction, as well as (potentially) break the symmetry of the latter. Instead, acoustic plasmons may break the spatial symmetry of a protein's "potential of mean force", thus converting it into an effective Brownian ratchet potential by applying quasistatic deformational corrections to the former. These concepts seem to be of rather general applicability and might also be useful when studying, for example, intercalation of cationic dyes into DNA duplexes, positively charged oligopeptide transduction through cell membranes, or even DNA translocation through nanopores.

On the Energetics of ATP Hydrolysis in Solution

“…Our work suggested that the energetics of the ATP hydrolysis is associated with electrostatic work, and the origin of the free energy change involves a significant contribution from the charge separation in solution outside the ATPase active sites . A related idea has been recently considered by Ross and co-workers and a similar concept also by Panas and Nordén …”

“…13 A related idea has been recently considered by Ross and co-workers 14 and a similar concept also by Panas and Norde ´n. 15 In addition to the uncertainty about the microscopic nature of the energy conversion process, it is not clear what the entropic contribution to the overall free energy change is, what fraction of the energy relapsed is transferred into heat, and what the time scale of the energy dissipation process is. Furthermore, although the requirements for the efficiency of ATPases have been studied in some detail, 4,13,16,17 their relationship to the microscopic features of the system has not yet been elucidated.…”

Enthalpy–Entropy Compensation (EEC) Effect: A Revisit

“…The proposition has novelty, but the existence of the proposed “refrigerator” and “heat pump” requires support from concept and reasoning from rational internal conditions. Starikov et al have discussed this in a series of publications. − Constant Δ G for processes similar or nonsimilar may manifest equivalence between the experimental and the compensation temperature; variable free-energy changes of different similar or related processes mostly at a constant temperature produce the so-called EEC, which has led researchers to search for an explanation. From the thermodynamic point of view we believe that eq has a say in this.…”

A possible overestimation of the effect of acetylation on lysine residues in KQ mutant analysis

“…To calculate binding energies more precisely, a theoretical notion that enables to describe the physical-chemical dynamics of a protein, e.g., protein plasmons theory, [46] should be applied because the entropy contribution to the binding energy cannot be ignored. If entropic effects are considered, the differences in the binding energy among various mutants may be more clearly represented.…”