The Effect ofa Mechanical Force on theThermodynamics and Kinetics ofthe Protein Unfolding Reaction

Relax Your Mind

Relaxation Techniques

Get Instant Access

Considerations from ^ermodynamics and Statistical Mechanics: Equilibrium vs. Nonequilibrium Unfolding

Classical thermodynamics (equilibrium thermodynamics or "thermodynamics" for short) deals with quasistatic processes, which are idealized, "infinitely slow" processes that can be approximated in practice by performing them "very slowly." ttus, thermodynamics is not concerned with the rate at which a process takes place (i.e., kinetics). Time-dependent thermodynamic processes are studied by nonequilibrium thermodynamics. In quasistatic processes the system often goes through a sequence of states that are infinitesimally close to equilibrium, in which case the process is typically reversible, ttus, technically, "quasistatic" and "reversible" are different terms, not synonyms as they are sometimes treated in the literature. Whereas reversible processes are almost always quasistatic (only two exceptions are known at present: superfluidity and superconductivity), the converse is not always true. Similarly, nonequilibrium processes are usually irreversible. In single-molecule mechanics, the overlapping of the force-extension curves for pulling and relaxation is normally taken, in a first approximation, as a hallmark of thermodynamic reversibility for the conditions of the experiment (although, strictly speaking, curve overlapping is only a necessary but not a sufficient condition). On the other hand, the existence of different curves, i.e., hysteresis, is a sensitive indicator of the irreversibility for the process. In contrast to thermodynamics, which deals with systems composed of large molecular populations from a macroscopic point of view (i.e., "large scale"), statistical mechanics approaches these systems from a microscopic perspective (meaning atomic scale in the physicist's jargon), which in our case typically means single molecules.

Studies on the mechanical unfolding of RNA have shown that the breaking of the secondary structure elements of RNA occurs close to thermodynamic equilibrium (this also being a reversible process), within the millisecond to second times-cales of the experiment (i.e., the molecule follows the same force-extension curve upon stretching as relaxation). In contrast, breaking of the more complex tertiary structure is often a nonequilibrium process (and is also irreversible on the timescale of the experiment), in which interactions equilibrate over a slower timescale and, therefore, the pulling-relaxation cycle presents hysteresis. Because the distance to the transition state is often shorter in tertiary interactions than in secondary structures, they tend to be brittle, breaking at high forces and after small deformations. In contrast, secondary interactions are compliant, breaking at low forces and after large deformations (Bustamante et al. 2004).

Manometry Thermodynamics

Fig.8.6. Thermodynamics and kinetics of forced protein unfolding, a Equilibrium and non-equilibrium in protein unfolding-refolding (blue unfolding process, green retraction, pale blue hysteresis). 1 Force-extension curve of a "Hookean" spring such as a cantilever (a macroscopic system). 2 Force-extension curve of an elastomeric protein: elastin. This protein behaves as an entropic spring in equilibrium, showing no hysteresis (adapted from Urry et al. 2002, with per-

Fig.8.6. Thermodynamics and kinetics of forced protein unfolding, a Equilibrium and non-equilibrium in protein unfolding-refolding (blue unfolding process, green retraction, pale blue hysteresis). 1 Force-extension curve of a "Hookean" spring such as a cantilever (a macroscopic system). 2 Force-extension curve of an elastomeric protein: elastin. This protein behaves as an entropic spring in equilibrium, showing no hysteresis (adapted from Urry et al. 2002, with per-

Unlike RNA, in which secondary and tertiary interactions are independent and additive, the unfolding of most proteins seems to be highly cooperative, with the stability of secondary structures depending on their tertiary context. At the typical pulling speeds used in SMFS experiments (approximately 0.5 nm ms_1) there are only a few protein structures that show coincident stretching and relaxation curves (i.e., at thermodynamic equilibrium), ttese proteins are true elastic elements acting as reversible springs that store/restore elastic energy with 100% efficiency and no heat dissipation, ttey include elastomeric proteins (reviewed by Tatham and Shewry 2000) like elastin (Fig. 8.6a, panel 2; Urry et al. 2002), the PEVK and N2B domains of cardiac titin (Li et al. 2001, 2002), and the EH domain of myomesin (Schoenauer et al. 2005). tte myosin II tail is also an elastic protein structure though under experimental pulling conditions the pulling/relaxation curves show some hysteresis because some energy is dissipated as heat, i.e., the pulling process is close to equilibrium (pale blue area in Fig. 8.6a, panel 3, see also Fig. 8.8, Table 8.1; Schwaiger et al. 2002).

Was this article helpful?

0 0
Relaxation Audio Sounds Autumn In The Forest

Relaxation Audio Sounds Autumn In The Forest

This is an audio all about guiding you to relaxation. This is a Relaxation Audio Sounds with sounds from Autumn In The Forest.

Get My Free MP3 Audio


Post a comment