An Entropic Perspective of Protein Stability on Surfaces

Abstract

The interaction of proteins with surfaces regulates numerous processes in nature, science, and technology. In many applications, it is desirable to place proteins on surfaces in an active state, and tethering represents one manner in which to accomplish this. However, a clear understanding of how tether placement and design affects protein activity is lacking. Available theoretical models predict that proteins will be stabilized when tethered to substrates. Such models suggest that the surface reduces the number of states accessible to the unfolded state of the protein, thereby reducing the entropic cost of folding on the surface compared to the bulk case. Recent studies, however, have shown that this stabilization is not always seen. The purpose of this article is to determine the validity of the theory with a thorough thermodynamic analysis of the folding of peptides attached to surfaces. Configuration-temperature-density-of-states Monte Carlo simulations are used to examine the behavior of four different peptides of different secondary and tertiary structure. It is found that the surface does reduce the entropic cost of folding for tethered peptides, as the theory suggests. This effect, however, does not always translate into improved stability because the surface may also have a destabilizing enthalpic effect. The theory neglects this effect and assumes that the enthalpy of folding is the same on and off the surface. Both the enthalpic and entropic contributions to the stability are found to be topology- and tether-placement-specific; we show that stability cannot be predicted a priori. A detailed analysis of the folding of protein A shows how the same protein can be both stabilized and destabilized on a surface depending upon how the tethering enhances or hinders the ability of the peptide to form correct tertiary structures.

Conformational Transitions at an S‐Layer Growing Boundary Resolved by Cryo‐TEM

“…This is equivalent to protein folding in strong confinement, where entropy plays the dominant role (over enthalpy) decreasing the ability of the protein to experience unfolded states. [12] These observations are consistent with the findings of Chung et al, [6] who observed S-layer formation using in situ AFM. First, they reported that the initial clusters of SbpA did not grow by adsorption of folded tetramers.…”

Thermodynamics of DNA hybridization on surfaces

“…Such a "neutral" approach to coarse-graining surfaces has been used multiple times to study protein/surface interactions with applications to protein arrays. 14,23,24 This type of surface also produces behavior seen with all-atom simulations of tethered DNA which have shown that the DNA extends away from the surface the majority of the time and does not collapse down to the surface to an appreciable extent. 6,7 Thus, while coarse graining cannot reproduce all possible surface phenomena, it has been shown to capture the behavior that is important in biochips and serves as a sufficiently accurate representation to make comparisons between surface and bulk hybridization.…”

Effects of tethering a multistate folding protein to a surface

“…Though this is the type most frequently encountered in protein/surface applications, different behavior is likely to be observed for highly attractive or repulsive surfaces. Despite this, the approach presented above has been extensively used before to study protein/surface interactions [34][35][36][37][38][39] and protein folding, [53][54][55][56][57] so it is reasonable to assume that the trends observed in the results represent realistic behavior.…”

“…Coarse-grain models are needed to sample the folding/unfolding transition with sufficient frequency to obtain statistically significant thermodynamic data. Several previous studies have used such models to investigate both protein/surface phenomena [34][35][36][37][38][39] and multistate folding. 57 The particular model used in this study extends 1st-generation Gō-like representations by introducing different energy scales to describe hydrogen bonding between side chains and sequence-dependent virtual dihedral potentials to maintain appropriate conformations.…”

“…To overcome such limitations, simulation studies seeking information on how the surface affects the stability of proteins or folding mechanisms have been done using various coarse grain models. [34][35][36][37][38][39] These studies have shown that stability is tether-site specific, that proteins are stabilized entropically by surfaces but destabilized enthalpically, that tethering in sites involved in intermediates along the folding pathway will destabilize proteins, and that stability can be correlated to tertiary structural elements in certain cases. However, a careful reading of the literatures reveals that all such studies involve proteins which fold through a two-state mechanism.…”