In such cases a protonatable amino acid residue is always found near the
active site to serve as the donor or acceptor of the proton. Enzymatic reac-
tions require repeated reactions so proteins must also have a means of
transporting protons from the bulk solution to the amino acids at the active
site. Proton conduction usually occurs by the transfer of the proton through
a pathway formed by a series of hydrogen-bonded amino acid residues
(Figure 5.12). By such pathways, protons are carried rapidly through pro-
teins up to distances of 20 Å. The amino acid side chains participating in
the pathway must serve as first a proton acceptor and then donor. The pKA
values must not be too high, and residues with moderate or low pKAvalues
are generally favored. The protons are generally thought to travel in only
very short distances (see Chapter 13), so the pathway must be unbroken.
Any breaks may be compensated for by rotations of the side chains or
the presence of bound water molecules, as found in bacteriorhodopsin
(Chapter 17). The precise proton pathway in a protein can be identified
by systematic mutation of possible participants in such a pathway (Paddock
et al. 2003). For example, in the bacterial reaction center, the protonation
of quinone was found to occur by the transfer of protons through pathways
involving two different sets of amino acid residues (Figure 5.13).
Whereas the traditional view of proton transfer involving a well-defined
pathway is appropriate for many enzymes, some research groups have
suggested that in some enzymes additional mechanisms must be considered.
Consideration of potential proton-conducting pathways in a static model
of a protein may not be sufficient to detect possible pathways. Dynamics
must also be considered because random fluctuations of amino acid residues
found on the surface of an enzyme can result in carboxylates either sharing
a common proton through a hydrogen bond or being connected through
water molecules, thus forming the desired proton pathway, as has been
found in cytochrome P450cam (Benkovic & Hammes-Schiffer 2003, 2006;
110 PARTI THERMODYNAMICS AND KINETICS
C
R
C
OOH
H
O
O
C
C
N
C
O
H
H
N
H C
R
R
R
HH
O
H
R
C
R
H
H
N
O
H
N
H
C
O
C
Figure 5.12Proton pathway formed by a hydrogen-bonded chain of
amino acid residues and bound water molecules.
