2. Using molecular simulations it is possible to compute the free energy change AG for the nonphysical reaction CH3-CH2-CH3 CH3-CH3 (Propane Ethane) in any desired solvent. Simulation data give the following results AG°(vacuum)=0.5 kcal/mol AG (octanol)=2.0 kcal/mol AG (water) 1.0 kcal/mol (a) The experimentally measured free energy of transfer AGx(propane) of propane from octanol to water is 4 kcal/mol and from vacuum (gas phase) to water is -0.2 kcal/mol. Calculate the corresponding values of AGOx(ethane) from octanol to water and from vacuum to water. b) Assume that the free energy of transfer of a methylene group from water to octanol is a measure of the strength of the hydrophobic driving force for burial of such a group during protein folding. Calculate the expected approximate decrease in stability (as a result of reduced hydrophobicity) for a Leu Ala substitution at a buried site in a monomeric globular protein. The measured decrease in stability is twice the theoretical amount. Suggest possible explanation. c) The wildtype protein has a free energy of unfolding AG of 7 kcal/mol at 300 K. Calculate the fraction unfolded protein fu for the mutant protein at 300 K.

2. Using molecular simulations it is possible to compute the free energy change AG for the nonphysical reaction CH3-CH2-CH3 CH3-CH3 (Propane Ethane) in any desired solvent. Simulation data give the following results AG°(vacuum)=0.5 kcal/mol AG (octanol)=2.0 kcal/mol AG (water) 1.0 kcal/mol (a) The experimentally measured free energy of transfer AGx(propane) of propane from octanol to water is 4 kcal/mol and from vacuum (gas phase) to water is -0.2 kcal/mol. Calculate the corresponding values of AGOx(ethane) from octanol to water and from vacuum to water. b) Assume that the free energy of transfer of a methylene group from water to octanol is a measure of the strength of the hydrophobic driving force for burial of such a group during protein folding. Calculate the expected approximate decrease in stability (as a result of reduced hydrophobicity) for a Leu Ala substitution at a buried site in a monomeric globular protein. The measured decrease in stability is twice the theoretical amount. Suggest possible explanation. c) The wildtype protein has a free energy of unfolding AG of 7 kcal/mol at 300 K. Calculate the fraction unfolded protein fu for the mutant protein at 300 K.

Chemical Principles in the Laboratory

11th Edition

ISBN:9781305264434

Author:Emil Slowinski, Wayne C. Wolsey, Robert Rossi

Publisher:Emil Slowinski, Wayne C. Wolsey, Robert Rossi

Chapter21: Rates Of Chemical Reactions, Ii. A Clock Reaction

Section: Chapter Questions

Problem 2ASA

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