Page 164 - Academic Press Encyclopedia of Physical Science and Technology 3rd BioChemistry

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Encyclopedia of Physical Science and Technology EN013D-616 July 27, 2001 12:5

204 Protein Structure

inadequate to fully explain the behavior of hydrophobic electrons. In biological systems the electronegative atoms
molecules in solution since both the standard changes in in both cases are usually nitrogen or oxygen. The dis-
the entropy and enthalpy for the transfer of a hydropho- tance between the donor and acceptor atoms is usually
˚
bic molecule to water are strongly temperature dependent. in the range 2.8–3.1 A where the D H bond tends to be
Surprisingly the value for the free energy change for the collinear with the lone pair of electrons. There is some
transfer of a hydrocarbon to water is rather temperature variability in the geometry of the hydrogen bond, which
insensitive as a consequence of compensatory changes in is consistent with the predominantly electrostatic nature
the entropy and enthalpy. These temperature dependencies of this interaction. For example, in the α-helix and an-
areaconsequenceofthelargetemperature-insensitiveheat tiparallel β-sheet the N H is approximately colinear with
capacity of hydrophobic molecules in solution. The water- the C O bond rather than be aligned with the lone pairs
ordering effect appears to be the source of the anomalously of the carbonyl oxygen. Many of the hydrogen bonds in
high heat capacity of hydrophobic compounds in water. proteins occur in networks where each donor participates
Although there is no general agreement on the molecu- in multiple interactions with acceptors and each acceptor
lar basis of the hydrophobic effect, there is a good correla- interacts with multiple donors. This is consistent with the
tionbetweenfreeenergyoftransferofanorganicmolecule ionic nature of hydrogen bonds in proteins.
to water and its hydrophobic surface area, whereas there Originally it was believed that hydrogen bonds made
are no general correlations between the molecular fea- an important contribution to protein stability on account
tures of the solute and entropic and enthalpic changes. of the extensive hydrogen bonding observed in α-helices
˚ 2
Many studies have shown that the transfer of 1 A of and β-sheets. Indeed, virtually every hydrogen donor and
hydrophobic area to water is accompanied by an unfa- acceptor in a protein are observed to form an interac-
vorable increase in the free energy of 80–100 J/mol. The tion within the folded structure or to the external sol-
fact that this correlation is found to be fairly independent vent. However, protein stability is the difference in free
of the nature of the hydrophobic solute clearly indicates energy between the unfolded state and the folded state.
that the hydrophobic effect is a fundamental property of In the unfolded state the polar components are able to
water. form perfectly satisfactory hydrogen bonds to water that
Studies on the heat capacities changes observed at the are equivalent to those found in the tertiary structure of
protein folding transition show that protein denaturation is the protein. Thus hydrogen bonding is energetically neu-
analogous to the transfer of hydrophobic molecules to wa- tral with respect to protein stability, with the caveat that
ter. Furthermore it is well established that the stability of a any absences of hydrogen bonding in a folded protein are
protein is directly proportional to the difference between thermodynamically highly unfavorable.
the exposed hydrophobic surface area in the unfolded and Although hydrogen bonds do not contribute to stability
folded state. In recent years, site-directed mutagenesis has they are a major determinant of protein conformation.
demonstrated the same thermodynamic relationship be- The necessity to form hydrogen bonds accounts for the
tween the hydrophobic buried surface area and stability α-helices and β-strands that abound in protein structures.
as observed for the transfer of organic hydrocarbons into
˚ 2
water. That is, each buried 1 A of hydrophobic surface
C. Disulfide Bonds
area contributes ∼80 J/mol to the stability of the protein
when the only difference is the change in surface area. Many extracellular proteins contain disulfide bonds. In
Clearly the behavior of a protein in solution is more com- these proteins the presence of disulfide bonds adds con-
plex than that of a simple hydrocarbon. As noted earlier, siderable stability to the folded state where in many cases
proteins are only marginally stable. It would appear that reduction of the cystine linkages is sufficient to induce un-
the change in exposed hydrophobic surface area that ac- folding. The source of the stability appears to be entropic
companies protein folding slightly more than compensates rather than enthalpic. The introduction of a disulfide bond
for the decrease in entropy of the polypeptide chain as it reduces the entropy of the unfolded state by reducing the
adopts a well-defined conformation. This explains why it degrees of freedom available to the disordered polypep-
is so difficult to predict protein structure. tide chain. This stabilizes the folded state by decreasing
the entropy difference between the folded and unfolded
state. This suggests an obvious strategy for increasing the
B. Hydrogen Bonds
stability of a protein through the introduction of disulfide
Hydrogen bonds (D H····A) are primarily electrostatic bonds. Although this might seem a simple task, the ge-
in nature and involve an interaction between a hydrogen ometry of the disulfide bond is rather restricted. As a con-
attached to an electronegative atom (D H) and another sequence the number of locations that can accommodate
electronegativeacceptoratom(A)thatcarriesalonepairof the replacement of two residues by cysteines in a protein