Evaluation Of Free Energy Change Research Articles

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation.

Molecular dynamics based free energy calculations allow for a robust and accurate evaluation of free energy changes upon amino acid mutation in proteins. In this chapter we cover the basic theoretical concepts important for the use of calculations utilizing the non-equilibrium alchemical switching methodology. We further provide a detailed step-by-step protocol for estimating the effect of a single amino acid mutation on protein thermostability. In addition, the potential caveats and solutions to some frequently encountered issues concerning the non-equilibrium alchemical free energy calculations are discussed. The protocol comprises details for the hybrid structure/topology generation required for alchemical transitions, equilibrium simulation setup, and description of the fast non-equilibrium switching. Subsequently, the analysis of the obtained results is described. The steps in the protocol are complemented with an illustrative practical application: a destabilizing mutation in the Trp cage mini protein. The concepts that are described are generally applicable. The shown example makes use of the pmx software package for the free energy calculations using Gromacs as a molecular dynamics engine. Finally,we discuss how the current protocol can readily be adapted to carry out charge-changing or multiple mutations at once, as well aslarge-scale mutational scans.

Dynamic analysis of human tyrosinase intra-melanosomal domain and mutant variants to further understand oculocutaneous albinism type 1.

Human tyrosinase (Tyr) is a Type I membrane glycoprotein that is the rate-limiting enzyme for controlling the production of melanin pigment in melanosomes. Currently, ~300 Tyr mutations are known to be involved in the genetic disease oculocutaneous albinism type 1 (OCA1), which exists in two forms, OCA1A and OCA1B. OCA1A is caused by a full loss of Tyr enzymatic activity, resulting in the absence of pigment in the skin, hair, and eyes, while OCA1B has reduced Tyr activity and pigment. Here, we used molecular modeling to try to understand the role of genetic changes at the protein level in inherited disease. The significant part of Tyr intra-melanosomal domain and five OCA1 mutant variants were built by homology modeling, glycosylated in silico, and refined using molecular dynamics in water. The modeling confirmed experimental results that N347 and N371 glycosylation is vital for protein stability. The changes caused by the T373K mutation indicate a significant impact on protein structure, as expected for OCA1A. In addition, evaluation of free energy changes in OCA1B mutants showed a strong association with the changes observed in our unfolding/refolding experiments in vitro. In conclusion, our results could be useful for understanding the role of OCA1 mutant variants in melanin pigment production, in silico searching for inhibitors and activators of tyrosinase activity, and genotype-to- phenotype analysis in OCA1.

Polymer extension under flow: A path integral evaluation of the free energy change using the Jarzynski relation.

The Jarzynski relation (and its variants) has provided a route to the experimental evaluation of equilibrium free energy changes based on measurements conducted under arbitrary non-equilibrium conditions. Schroeder and co-workers [Soft Matter 10, 2178 (2014) and J. Chem. Phys. 141, 174903 (2014)] have recently exploited this fact to determine the elastic properties of model DNA from simulations and experiments of chain extension under elongational flow, bypassing the need to make these measurements mechanically using sophisticated optical trapping techniques. In this paper, motivated by these observations, we investigate chain elasticity analytically, using the Jarzynski relation and a finitely extensible nonlinear elastic-type Rouse model within a path integral formalism to calculate (essentially exactly) both the flow-induced free energy change between chain conformations of definite average end-to-end distance, as well as the force-extension curve that follows from it. This curve, based on a new analytic expression, matches the trends in the corresponding curve obtained from a model of chain stretching developed by Marko and Siggia [Macromolecules 28, 8759 (1995)], which itself is in very satisfactory agreement with the numerical and experimental data from the work of Schroeder et al.

Theoretical Study of Magnesium Fluoride in Aqueous Solution

A series of magnesium fluorides (MgF(n)(2-n)), multiply charged anions, in the gas phase and in aqueous solution were theoretically studied with a hybrid approach of quantum chemistry and statistical mechanics, called RISM-SCF-SEDD theory. In the gas phase, MgF(3)(-) is the most stable species among the complexes (n = 1-6). In contrast, due to compensation between the intramolecular energy and solvation free energy, the stabilities of a number of complexes with different n are comparable in aqueous solution. Based on accurate evaluation of free energy change, the mole fraction of MgF(4)(2-) is the highest in the range from pF = 2.0 to 3.0 of aqueous solution. This is consistent with the available PDB data of the enzymes that catalyze the phosphoryl transfer reactions. The hydration structures of magnesium fluorides obtained by RISM-SCF-SEDD theory provide insight into their structural changes from the gas phase to aqueous solution.

A preliminary report on a quantum-mechanical model for the energetics of a solute at the surface separating two immiscible liquid phases

The model considered here is directed to the problem of evaluation of free energy changes in the course of the passage of a solute M from solvent A to the second solvent B. It is applied to detailed description of the energetics of the solute passage (M in contact with the A/B separating surface) for n-alkanes, n-alcohols and n-primary amines. The difference in the behaviour due to the different composition of M is evident (engulfing versus buoyancy processes). The further text regards the transfer free energy change (A = water, B = p-xylene) for amines. A discussion of possible improvements of the model is presented also.