Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online




Last Update:  3/2/16

Learning Goals/Objectives for Chapter 2F:  After class and this reading, students will be able to ...

  • Differentiate between general charge and specific ion-ion pairs and summarize their role in protein stability
  • Draw the structure of N-methylacetamide  (NMA) and explain why it is a useful small molecule model to study the role of H bonds in protein stability
  • Draw a thermodynamics cycle for the transfer of a hydrogen bonded dimer of NMA from water to a nonpolar environment.  From the DG0 for steps in the cycle, and extending this model to protein, predict if buried H bond formation drives protein folding
  • Explain if studies of low temperature protein denaturation, high temperature protein, and DGo transfer of nonpolar side chains from water to more nonpolar solvents support the hydrophobic effect in protein stability
  • summarize the relationship between the empirical Hofmeister series and preferential binding of reagents into the hydration sphere of protein to explain the effects of denaturants (urea, guanidine salts) and stabilizers (glycerol, ammonium sulfate) on proteins
  • Using benzene solubility in water as a model to study the role of hydrophobic effect in protein unfolding and by inference in protein stability, interpret graphs of DG0, DH0, DS0 and DCp for the transfer of benzene to water, as a function of temperature.

  • from the above graph, explain if trends in the thermodynamic parameters for benzene transfer into water predict the observed protein unfolding/stability behavior of proteins as a function of temperature?

  • Give a molecular interpretation of the observed DCp for the transfer of nonpolar molecules into water.

  • Describe chain conformational entropy, relate it to conformational changes in acyl side chains in single and double chain amphiphiles with temperatures, and describe it role in protein stability.

  • state which of several given explanations for the observed destabilizing effects of Asn to Ala mutations in protein account for those observation

  • summarize graphically the magnitude and direction of the major contributors (inter- and intramolecular forces and effects) to protein stability

F4.  Hydrophobic Interactions: Introduction

We have studied the role of the hydrophobic effect (involving the favorable entropic release of caged water molecules about solvent-exposed hydrophobic groups) in driving micelle and bilayer formation.  Does this also drive protein folding? To explore this questions, we will study the thermodynamics of small nonpolar molecules, especially  benzene, with water and ask whether the thermodynamic parameter associated with benzene solubility are similar to those associated with protein stability.  If this analogy holds, anything that will promote benzene solubility will lead to increased hydrophobic amino acid side chain exposure to water and hence protein denaturation. What is the evidence to support this?

a. crystal structures:  These structures show that most nonpolar side chains are buried inside a protein, which is tightly packed and which excludes water.  Studies  show that as the surface area of amino acid side chains increase, the free energy of transfer of amino acids from water to ethanol becomes more negative.

Figure:   Transfer of amino acids from water

(Review free energies of transfer of hydrophobic groups in Chapter 1E: Lipids in Water - Thermodynamics )

b. low temperature denaturation of proteins - It has been observed that proteins can denature at low temperatures (less than 0oC), suggesting that nonpolar residues become more "soluble" in water at low temperatures (i.e. they move from the more hydrophobic interior of a protein to the more polar outside). Compare the solubility of nonpolar gases like CO2 or N2, which are more soluble at low temperature. As you heat solutions of nonpolar gases in water, the gases become less soluble as evidenced by bubble formation (i.e. phase separation of dissolved gases as they become more insoluble). If protein behavior is governed by this same behavior (greater solubility of nonpolar groups at low temperatures), it would suggest that proteins might denature at low temperatures (leading to increased exposure to water of the nonpolar side chains).  This phenomena has been observed.

c. protein stability affected by different salt species - Over 100 years ago, Hofmeister determined the effectiveness of different cations and anions of salts to precipitate blood serum proteins in the 0.01 - 1 M concentration ranges.  The series is shown below:

Cations: NH4+ > K+ > Na+ > Li+ > Mg2+ > Ca2+ > guanidinium

Anions: SO42- > HPO42- > acetate > citrate > Cl- > NO3- > ClO3- > I- > ClO4- > SCN-

Figure:  Hofmeister Series

The solubility of benzene in aqueous salt solutions of this series increases from left to right, just as native protein stability decreases from left to right (i.e. the protein's nonpolar core residues become more "soluble" in water, leading to its denaturation).

d. conservation of hydrophobic core residues - These residues are highly conserved and correlated with structure.

e. Urea denatures proteins - Another additive, urea, at high concentrations is often used to denature proteins. People used to think that urea competed with the intrachain H bonds and hence unraveled the protein. The arguments above with H bonds disputes this contention since water should then denature protein. How does urea denature proteins?  It has been shown that the free energy of transfer of the nonpolar amino acids into 8M urea is increasing negative as the side chains become bigger and more nonpolar. 

Figure:  Free energy of transfer of the nonpolar amino acids into 8 M urea

This is also true for denaturation by guanidine hydrochloride.  Urea also increases the solubility of nonpolar molecules in a manner proportional to their surface area. 


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