APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014;
Denver, Colorado
Session Q12: Invited Session: Irreversibilty and Entropy Production in Biological Dynamics
2:30 PM–5:30 PM,
Wednesday, March 5, 2014
Room: 205
Sponsoring
Units:
GSNP DBIO
Chair: Jeremy England, Massachusetts Institute of Technology
Abstract ID: BAPS.2014.MAR.Q12.1
Abstract: Q12.00001 : Roles of Entropic Funnels and Irreversibility in RecA Mediated Homology Recognition
2:30 PM–3:06 PM
Preview Abstract
Abstract
Author:
Mara Prentiss
(Harvard University)
The self-assembly complex systems requiring the correct pairing of more than
approximately 3 distinct binding sites faces significant entropic barriers
and can suffer from kinetic trapping in conformations containing some
correct pairings. If the pairings have energies of the order of the thermal
energy kT, then thermodynamic pairing cannot provide the stringencies
required for biological systems. It is well known that kinetic proofreading
systems can provide much better stringency by including an irreversible
step; however, simple versions of such systems fundamentally tradeoff speed
and stringency. RecA mediated homology recognition is an example of a system
that can provide excellent rapid recognition that can last for days without
irreversibility. The combination of speed and stability in the absence of
irreversibility depends on the probability that accidental matches extend
over of m contiguous binding sites. If the probability decreases
sufficiently strongly with m, rapid and efficient homology recognition can
occur via a system of checkpoints that limit the number of binding sites
that can come in contact, which provides enthalpic and entropic advantages.
Increasing the number of contacts requires passing sequence dependent energy
barriers. The simplest version of such a system is an initial weakly bound
state that is independent of site matching, which is separated from the next
conformation by a sequence dependent barrier. The sequence dependent barrier
for correct matches must be low enough for the correct match to progress to
the next conformation before unbinding from the initial state, whereas the
barrier for mismatches must be high enough that it is highly probable that
the mismatch will unbind before they pass through the barrier. RecA employs
a series of several sequence dependent barriers. The energy gap that reduces
the need for irreversibility is the result of the correct pairing having
orders of magnitude more contiguous matching sites than the nearest mismatch
present in the sample.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2014.MAR.Q12.1