Guy Brown wrote:
> Why is it that if a reaction has a second order rate constant of
> anything from 10^7 to 10^12 (s^-1) it is described as
> "diffusion controlled"? Surely if collisions can occur at 10^12
> then a rate constant of 10^7 can not be diffusion controlled.
> Presumably steric factors are invoked: the molecules collide
> without reacting.
The matter is even more complicated by 'nonspecific' binding, as
exemplified by linear diffusion of DNA polymerase along the
polynucleotide strand. The polymerase hits the nucleic acid only
-once-, but then it slides along until it finds a promoter site.
Something similar happens with 'processive' exo-nucleases: once the
enzyme grabs the end of the polynucleotide chain, it won't let go until
10-100 bases are chomped off, so here we have up to 100 reactions per
collision. (The molecules now "react without colliding".)
Situations like these had lead to several papers by Kuo-Chen Chou in the
1970's, in which he uses the term "surface sink" to describe the
attraction of substrate molecules by the entire protein surface, far
away from the active site. (If I may indulge in a little diversion: I
have rare reprints of Chou's English-language papers published in China
between 1972-1974, which in the preamble contain a mandatory salute to
The Chairman.)
The full citations to Chou's work are contained in several of papers of
ours:
=====
@article {Kuzm9175,
author = "P. Kuzmi\v{c} and C.-Q. Sun and Z.-C. Zhao and D. H. Rich",
title = "Nonspecific electrostatic binding of substrates and inhibitors
to porcine pepsin",
journal = "Adv. Experim. Med. Biol.",
volume = "306",
pages = "75--86",
year = "1991"}
=====
@article {Kuzm9119,
author = "P. Kuzmi\v{c} and C.-Q. Sun and Z.-C. Zhao and D. H. Rich",
title = "Long range electrostatic effects in pepsin catalysis",
journal = "Tetrahedron",
volume = "47",
pages = "2519-2534",
year = "1991"}
Petr
_____________________________________________________________
Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA
pkuzmic at biokin.com * http://www.biokin.com * 608.256.1269 fax
