BioPHYSICAL chemistry

Taraphder & Hummer 2003; Friedman et al. 2005; see Chapter 7). The
traditional pathways are viewed as requiring proton donors and acceptors
to be within 2 Å for the proton to be transferred. However, hydrogen has
been proposed to be capable of tunneling (see Chapter 10), which would
enable the protons to transverse longer distances (Cha et al. 1989; Liang
& Klinman 2004). Electrons have long been known to travel over long
distances in proteins (Chapter 10) but protons and hydrogen had been
thought to be not capable of such travel due to their much larger size.
Efforts are underway to delineate the combined efforts of theoreticians
and experimentalists to elucidate the factors that would control proton
tunneling and to probe the coupling of tunneling with dynamics (Francisco
et al. 2002; Tanner et al. 2003; Garcia-Viloca et al. 2004).

CHAPTER 5 EQUILIBRIA AND REACTIONS INVOLVING PROTONS 111

O

O

O

H

Ser-L223

H(1)

H

H(2)

Asp-L210

Glu-L212

His-L190

Asp-L213

Arg-L217

O

O

C

O

O

O

CH 3 CH 3

QB CH 3



NH 2

NH 2

CO

O

H

H Fe

C

O

H 2 O

NN

Figure 5.13Proton-transfer pathways to the quinone in bacterial reaction centers. Modified from
Paddock et al. (2003).

References

Benkovic, S.J. and Hammes-Schiffer, S. (2003) A
perspective on enzyme catalysis. Science 301 ,
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Benkovic, S.J. and Hammes-Schiffer, S. (2006)
Enzyme motions inside and out. Science 312 ,
208 –9.
Cha, Y., Murray, C.J., and Klinman, J.P. (1989)
Hydrogen tunneling in enzyme reactions. Science
243 , 1325 –30.

Francisco, W.A., Knapp, M.J., Blackburn, N.J., and

Klinman, J.P. (2002) Hydrogen tunneling in pep-

tidlyglycine alpha-hydroxylating monooxygenase.

Journal of the American Chemical Society 124 ,

8194 –5.

Friedman, R., Nachliel, E., and Gutman, M. (2005)

Application of classical molecular dynamics for

evaluation of proton transfer mechanism on a

protein. Biochimica Biophysica Acta 1710 , 67–77.