Universal Convergence of the Specific Volume Changes of Globular Proteins Upon Unfolding

Pressure is a well-known environmental stressor that can either stabilize or destabilize proteins. The volumetric change upon protein unfolding determines the effect of pressure on protein stability, where negative volume changes destabilized proteins at high pressures. High temperature often accompanies high pressure, for example, in the ocean depths near hydrothermal vents or near faults, so it is important to study the effect of temperature on the volumetric change upon unfolding. We previously detailed the magnitude and sign of the molecular determinants of volumetric change, allowing us to quantitatively predict the volumetric change upon protein unfolding. Here, we present a comprehensive analysis of the temperature dependence of the volumetric components of proteins, showing that hydration volume is the primary component that defines expansivities of the native and unfolded states and void volume only contributes slightly to the folded state expansivity.

Section: ■ Results and Discussionmentioning

confidence: 99%

Section: ■ Results and Discussionmentioning

confidence: 99%

Molecular Determinants of Temperature Dependence of Protein Volume Change upon Unfolding

Chen

Makhatadze

2017

“…Computational analyses suggest that these substitutions introduce internal voids into the eglin c molecule on the order of 60 Å 3 . 11 Experimental studies using PPC show that the volume changes upon unfolding, ΔV, of V14A and V54A eglin variants are indeed more negative than the wild type eglin c. 11 Interestingly, the α N (T) and E N,sp (T) functions for these three proteins are very similar and are independent of pH ( Figure 3). These observations suggest that single-site substitutions, even though creating sizable internal voids inside the protein, appear to only minimally perturb α N (T) and E N,sp (T) functions.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Molecular Determinants of Expansivity of Native Globular Proteins: A Pressure Perturbation Calorimetry Study

Vasilchuk¹,

Pandharipande²,

Suladze³

et al. 2014

There is a growing interest in understanding how hydrostatic pressure (P) impacts the thermodynamic stability (ΔG) of globular proteins. The pressure dependence of stability is defined by the change in volume upon denaturation, ΔV = (∂ΔG/∂P)T. The temperature dependence of change in volume upon denaturation itself is defined by the changes in thermal expansivity (ΔE), ΔE = (∂ΔV/∂T)P. The pressure perturbation calorimetry (PPC) allows direct experimental measurement of the thermal expansion coefficient, α = E/V, of a protein in the native, αN(T), and unfolded, αU(T), states as a function of temperature. We have shown previously that αU(T) is a nonlinear function of temperature but can be predicted well from the amino acid sequence using α(T) values for individual amino acids (J. Phys. Chem. B 2010, 114, 16166-16170). In this work, we report PPC results on a diverse set of nine proteins and discuss molecular factors that can potentially influence the thermal expansion coefficient, αN(T), and the thermal expansivity, EN(T), of proteins in the native state. Direct experimental measurements by PPC show that αN(T) and EN(T) functions vary significantly for different proteins. Using comparative analysis and site-directed mutagenesis, we have eliminated the role of various structural or thermodynamic properties of these proteins such as the number of amino acid residues, secondary structure content, packing density, electrostriction, dynamics, or thermostability. We have also shown that αN(T) and EN,sp(T) functions for a given protein are rather insensitive to the small changes in the amino acid sequence, suggesting that αN(T) and EN(T) functions might be defined by a topology of a given protein fold. This conclusion is supported by the similarity of αN(T) and EN(T) functions for six resurrected ancestral thioredoxins that vary in sequence but have very similar tertiary structure.

“…Additionally, ∆𝛼 tends to be greater than zero, which may be due to the greater degree of hydration of unfolded proteins. 38 The P and T dependencies of ∆𝑆 is the other factor that contributes to the elliptical phase diagram. Since a folded protein has a lower entropy than that of an unfolded protein, heat shifts the population to the phase with highest entropy.…”

Section: Overview Of Pressure-denaturationmentioning

confidence: 99%

A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure

Gasic

Cheung

2020

Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure-dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse-grained molecular simulations of protein folding and unfolding under hydrostatic pressure. Although both PMF includes a desolvation barrier separating the well of a direct contact and the well of a solvent-mediated contact, how these features vary with hydrostatic pressure is still debated. There is a need of a systematic comparison of these two PMFs on a protein. We investigated the two different pressure-dependencies on the desolvation potential in a structure-based protein model using coarse-grained molecular 2 simulations. We compared them to the known behavior a real protein based on experimental evidence. We showed that the protein's folding transition curve on the pressure-temperature phase diagram depends on the relationship between the potential well minima and pressure. For protein that reduces the total volume under pressure, it is essential for the PMF to carry the feature that the direct contact well is essential less stable than the water-mediated contact well at high pressure.We also comment on the practicality and importance of structure-based minimalist models for understanding the phenomenological behavior of a protein under a wide range of phase space.