Proteins: “Boil ’Em, Mash ’Em, Stick ’Em in a Stew”

Abstract

Cells of the vast majority of organisms are subject to temperature, pressure, pH, ionic strength, and other stresses. We discuss these effects in the light of protein folding and protein interactions in vitro, in complex environments, in cells, and in vivo. Protein phase diagrams provide a way of organizing different structural ensembles that occur under stress and how one can move among ensembles. Experiments that perturb biomolecules in vitro or in cells by stressing them have revealed much about the underlying forces that are competing to control protein stability, folding, and function. Two phenomena that emerge and serve to broadly classify effects of the cellular environment are crowding (mainly due to repulsive forces) and sticking (mainly due to attractive forces). The interior of cells is closely balanced between these emergent effects, and stress can tip the balance one way or the other. The free energy scale involved is small but significant on the scale of the “on/off switches” that control signaling in cells or of protein–protein association with a favorable function such as increased enzyme processivity. Quantitative tools from biophysical chemistry will play an important role in elucidating the world of crowding and sticking under stress.

Gas Phase Protein Folding Triggered by Proton Stripping Generates Inside-Out Structures: A Molecular Dynamics Simulation Study

“…Anfinsen also recognized that folding is spontaneous because the native conformation represents the state with the lowest free energy . These basic tenets are undisputed, despite possible complications such as chaperones, aggregation, and crowding . Much has been learned in recent years about protein folding in solution. − For example, the rapid (subsecond) time scale of folding has been attributed to funneled energy landscapes that guide the protein toward the native state. , …”

Protein folding and surface interaction phase diagrams in vitro and in cells

“…Thus, destabilization of the protein by ‘sticking’ to the cytoplasmic matrix is mitigated by high pressure (better crowding), but enhanced by high temperature (stronger hydrophobic effect [34]). It thus is plausible that thermophiles would use electrostatic interactions more than hydrophobic interactions to stabilize proteins, whereas in piezophiles, hydrophobic interactions are more likely to assist stability [35].…”

TMAO: Protecting Proteins from Feeling the Heat

“…While there is developing consensus on how TMAO resists chemical and pressure denaturation, the interaction of TMAO and water at higher temperature has not been studied in detail. The unfolding of proteins due to temperature is distinct from chemical and pressure denaturation (22). Proteins undergo both cold and heat denaturation (23): due to loss of hydrophobic interactions at low temperature (24) and increased configurational entropy of the chain at high temperature (25).…”