Thermal stability limits of proteins in solution and adsorbed on a hydrophobic surface (original) (raw)
Related papers
Conformational changes of globular proteins upon adsorption on a hydrophobic surface
Physical Chemistry Chemical Physics, 2014
This paper presents a study of protein adsorption and denaturation using coarse-grained Monte Carlo simulations with simulated annealing. Intermolecular interactions are modeled using the Miyazawa-Jernigan (MJ) knowledge-based potential for an implicit solvent. Three different hydrophobicity scales are tested for adsorption of fibronectin on a hydrophobic surface. The hydrophobic scale BULDG was chosen for further analysis due to its greater stability during heating and its partial regenerative ability upon slow cooling. Differences between helical and sheet structures are observed upon denaturation -α-helices undergo spreading of their native helical order to an elliptical perturbed shape, while β-sheets transform into random coils and other more structured conformations. Electronic calculations carried out on rebuilt all-atom coordinates of adsorbed lysozymes revealed consistent destabilization of helices, while beta sheets show a greater variety of trends.
Proteins: Structure, Function, and Bioinformatics, 2003
This article shows that the stability profiles of thermophilic proteins are significantly displaced toward higher temperatures as compared to those of mesophilic proteins. A similar trend characterizes the aqueous transfer of N-alkyl amides. In fact, as a general feature of transfer processes, liquid dissolution profiles are centered at temperatures higher than those of solid ones. This behavior is governed by packing contributions. A partition of the unfolding thermodynamics based on the analysis of phenomenological temperatures common to dissolution and unfolding phenomena provides a clue to understanding the mechanism of thermal stabilization. In fact, the position of stability profiles along the temperature axis does not appear to depend on solvation of internal residues. Instead, it is notably affected by solidlike components, whose progressive decrease appears to drive the heat denaturation temperature increase of most thermostable proteins. As a corollary, it is shown that there are actually two limiting mechanisms of thermal stabilization. Proteins 2004;54:323-332.
Heat transfer in protein–water interfaces
Physical Chemistry Chemical Physics, 2010
We investigate using transient non-equilibrum molecular dynamics simulation the temperature relaxation process of three structurally different proteins in water, namely; myoglobin, green fluorescence protein (GFP) and two conformations of the Ca 2+ -ATPase protein. By modeling the temperature relaxation process using the solution of the heat diffusion equation we compute the thermal conductivity and thermal diffusivity of the proteins, as well as the thermal conductance of the protein-water interface. Our results indicate that the temperature relaxation of the protein can be described using a macroscopic approach. The protein-water interface has a thermal conductance of the order of 100-270 MW K À1 m À2 , characteristic of water-hydrophilic interfaces. The thermal conductivity of the proteins is of the order of 0.1-0.2 W K À1 m À1 as compared with E0.6 W K À1 m À1 for water, suggesting that these proteins can develop temperature gradients within the biomolecular structures that are larger than those of aqueous solutions. We find that the thermal diffusivity of the transmembrane protein, Ca 2+ -ATPase is about three times larger than that of myoglobin or GFP. Our simulation shows that the Kapitza length of these structurally different proteins is of the order of 1 nm, showing that the protein-water interface should play a major role in defining the thermal relaxation of biomolecules.
Conformational Transitions of Adsorbed Proteins on Surfaces
Combining a wide range of protein adsorption experiments (three globular proteins on eight well-defined homogeneous surfaces) with Monte Carlo simulations of lattice proteins at different concentrations and on surfaces of varying "polarity", we explore the extent and rheological behavior of adsorbed proteins as a function of substrate polarity, "on" rate constants (k a ) and steric parameters (|A 1 |) from the random sequential adsorption model, and demonstrate a folding to unfolding transition upon adsorption. We show that model globular proteins (hen egg lysozyme, ribonuclease A, and insulin dimer) behave similarly with respect to adsorption. Experimentally, above a substrate wettability cos θ > 0.4 (where θ is the sessile contact angle of water on a substrate in air), the adsorbed mass, rigidity, and k a of the proteins are diminished, while the steric factor |A 1 | is increased, suggesting a lower packing density. To analyze these results, we have invoked computer simulations. We show that changing surface polarity has two profound effects. First, the amount adsorbed increases as the surfaces become more apolar. Further, the proteins become less stable as their adsorbed amount increased because they gain a large number of interprotein and protein-surface interactions. Finally, apolar surfaces served to reduce the unfolding free energy barriers, further facilitating the reorganizing of proteins on these surfaces. Thus, increasing the nonpolar nature of the surfaces resulted in a more rigid adsorbed layer, in good agreement with the experiments.
Adsorption vs. folding of a Hydrophobic Chain Protein Model near an Attractive Surface
arXiv: Soft Condensed Matter, 2015
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones potential is assumed as an interaction potential between the effective monomers and the attractive surface. Thermodynamic properties and some structural parameters for the minimum energy conformations are calculated for comparison of the folding and adsorption cases.
Thermal denaturation of a protein (CoVE) by a coarse-grained Monte Carlo simulation
arXiv (Cornell University), 2020
Thermal response of a protein (CoVE) conformation is studied by a coarse-grained Monte Carlo simulation. Three distinct segments, the N-terminal, Trans-membrane, and Cterminal are verified from its specific contact profile. The radius of gyration (Rg) is found to exhibit a non-monotonic sub-universal thermal response: Rg decays on heating in native phase (low-temperature regime) in contrast to a continuous increase on further raising the temperature before its saturation to a random-coil in denature phase. The globularity index (a measure of effective dimension) of the protein decreases as the protein denatures from a globular to a random-coil conformation.
Biopolymers, 1989
The present paper is a systematic first approach to the problem of solvation thermodynamics of biomolecules. Most previous approaches have been only crude estimates of solvent contributions, and have simply assessed solvation free energy as proportional to surface areas. Here we estimate the various contributions and divide them into (a) hard-core interactions dependent upon the entire volume of solute and (b) the remainder of interactions manifested through surfaces, such as van der Waals, charge-charge, or hydrogen bonds. We have estimated the work to create a cavity with scaled-partide theory (SPT), the van der Waals interactions on the surface, and hydrogen bonds between the surface and the solvent. The conclusion here is that this latter term is the largest component of the solvation free energy of proteins. From estimates on nine diverse proteins, it is clear that the larger the protein, the more dominant is the hydrogen-bond term. In the next paper, we indicate that correlations between hydrogen-bonding groups on the surfaces could increase the magnitude of the hydrogen-bond contribution.