pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study

Abstract

The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.

pH and the Breast Cancer Recurrent Mutation D538G Affect the Process of Activation of Estrogen Receptor α

“…This model is based on the concept of the energy landscape theory and is often used to explore protein folding and biomolecular rearrangements. [26][27][28][29][30]43,45 Despite the limitations of using a coarse-grained implicit solvent model, the computational results applying SBM have successfully provided an understanding of the physical principles that govern molecular dynamics in several systems. 26,28,30,43,45,46 Such previous success motivated us to use it to investigate the process of activation of the ER.…”

“…We performed constant-pH molecular dynamics simulations using the db-SBM to obtain trajectories with several transitions between the ER active and inactive state; these states are presented in Figure A. This model is based on the concept of the energy landscape theory and is often used to explore protein folding and biomolecular rearrangements. − ,, Despite the limitations of using a coarse-grained implicit solvent model, the computational results applying SBM have successfully provided an understanding of the physical principles that govern molecular dynamics in several systems. ,,,,, Such previous success motivated us to use it to investigate the process of activation of the ER.…”

“…42 To change the protonation state of ionizable residues, we used the same protonation/deprotonation Monte Carlo criterion from our previous works. 28,30,43 However, in this paper, only histidines are allowed to change their charge. This simplification was made to allow a larger sampling of the protonation states of the residues most affected by pH variations between 6.0 and 8.0.…”

“…The electrostatic interactions were introduced by a Coulomb screening potential (last term of eq ). − The potential energy for a conformation Γ is calculated relative to the ERα-LBD active conformation Γ α and the inactive conformation Γ β given by where G is an attractive Gaussian well: G ( r ij , r o ij ) = −exp­[−( r ij – r o ij ) 2 /(2σ 2 )]. r , θ, and ϕ are the distance between two subsequent residues, angles formed by three subsequent residues, and dihedral angles formed by four subsequent residues, respectively.…”

Adsorption of Lysozyme Into a Charged Confining Pore

“…The distribution of the residues results in an isoelectric point of about 11 22 . We model this protein according to the structure-based model (SBM), in which its residues are represented by single spheres centered at the Cα position [49][50][51][52][53][54] , and the non-ES energy is given by…”