Unraveling protein folding mechanism by analyzing the hierarchy of models with increasing level of detail

Abstract

Taking protein G with 56 residues for a case study, we investigate the mechanism of protein folding. In addition to its native structure possessing α-helix and β-sheet contents of 27% and 39%, respectively, we construct a number of misfolded decoys with a wide variety of α-helix and β-sheet contents. We then consider a hierarchy of 8 different models with increasing level of detail in terms of the number of entropic and energetic physical factors incorporated. The polyatomic structure is always taken into account, but the side chains are removed in half of the models. The solvent is formed by either neutral hard spheres or water molecules. Protein intramolecular hydrogen bonds (H-bonds) and protein-solvent H-bonds (the latter is present only in water) are accounted for or not, depending on the model considered. We then apply a physics-based free-energy function (FEF) corresponding to each model and investigate which structures are most stabilized. This special approach taken on a step-by-step basis enables us to clarify the role of each physical factor in contributing to the structural stability and separately elucidate its effect. Depending on the model employed, significantly different structures such as very compact configurations with no secondary structures and configurations of associated α-helices are optimally stabilized. The native structure can be identified as that with lowest FEF only when the most detailed model is employed. This result is significant for at least the two reasons: The most detailed model considered here is able to capture the fundamental aspects of protein folding notwithstanding its simplicity; and it is shown that the native structure is stabilized by a complex interplay of minimal multiple factors that must be all included in the description. In the absence of even a single of these factors, the protein is likely to be driven towards a different, more stable state.

Can the roles of polar and non-polar moieties be reversed in non-polar solvents?

“…The denaturing action of ethanol is not as simple to rationalize because polypeptide chains, in aqueous solution with high concentrations of ethanol, populate conformations having a high content of α helices 7 . A similar scenario emerged from two recent numerical studies 8,9 using an approximate, albeit accurate, method to compute the solvation free energy. It was observed that, although the native state of globular proteins is the most stable in water compared with any other competing folds having the same sequence, this is no longer the case in ethanol and in cyclohexane, where the most stable folds are those having a high content of α helices, in agreement with experimental studies.…”

Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors

“…However, it is canceled out by an increase in the sum of protein-water and water-water interaction energies. Our analyses showed that the increase is larger than the decrease (we note that many of protein-water HBs are lost upon protein folding) (Hayashi et al 2017;Hayashi et al 2018;Yasuda et al 2012;Yoshidome et al 2008).…”

“…Our theoretical method for membrane proteins has been developed on the basis of the progress made by Kinoshita and coworkers for water-soluble proteins (Harano and Kinoshita 2005;Hayashi et al 2017;Hayashi et al 2018;Kinoshita 2009a;Kinoshita 2009b;Kinoshita 2013;Murakami and Kinoshita 2016;Oshima and Kinoshita 2013;Oshima and Kinoshita 2015;Yasuda et al 2012;Yasuda et al 2010;Yoshidome et al 2008). A water-soluble protein is immersed in water molecules which energetically move around.…”

“…It is not straightforward to calculate S N or S D using a statistical-mechanical theory because the solvent must be treated not as a continuum but as an ensemble of particles with finite sizes and the solute possesses a complex polyatomic structure. We have overcome this problem by combining the integral equation theory (Hansen and McDonald 2006) for solvation with the morphometric approach (MA) (Hayashi et al 2017;Hayashi et al 2018;Roth et al 2006). The MA enables us to account for the polyatomic structure with quantitative accuracy and high speed.…”

Can Polarity-Inverted Surfactants Self-Assemble in Nonpolar Solvents?

“…4 Hayashi et al found that while proteins have well-defined unique structures in water, this is generally not the case in other non-polar solvents. 5,6 The stability of single polar and hydrophobic amino acids in water and non-polar solvents have also been studied (unpublished results). To close the triangle of life, the stability of B-DNA under non-aqueous conditions has also been recently assessed.…”