Alternate Pathways for Folding in the Flavodoxin Fold
Family Revealed by a Nucleation-growth Model
Erik D. Nelson* and Nick V. Grishin
Howard Hughes Medical
Institute, University of Texas
Southwestern Medical Center
6001 Forest Park Blvd., Room
ND10.124, Dallas, TX
A recent study of experimental results for flavodoxin-like folds suggests
that proteins from this family may exhibit a similar, signature pattern of
folding intermediates. We study the folding landscapes of three proteins
from the flavodoxin family (CheY, apoflavodoxin, and cutinase) using a
simple nucleation and growth model that accurately describes both
experimental and simulation results for the transition state structure, and
the structure of on-pathway and misfolded intermediates for CheY.
Although the landscape features of these proteins agree in basic ways
with the results of the study, the simulations exhibit a range of folding
behaviours consistent with two alternate folding routes corresponding to
nucleation and growth from either side of the central b-strand.
q 2006 Published by Elsevier Ltd.
Keywords: fold families; equilibrium intermediates; non-native interactions
From a folding perspective, the topology of a
protein is interpreted by the shape of its native
backbone which loosely determines the pattern of
atom-to-atom cross-links between its amino acid
residues. Over the past several years, simple
theoretical and computational models based essen-
tially on topology and minimal entropy loss1–3have
demonstrated that native topology is a “first order”
effect deciding the way a protein folds.4–12While
the data so far still provide a very incomplete
picture, it suggests that if we could provide any
consistent description of protein folding it would be
that evolutionary changes which, roughly speaking,
conserve topology13–15and act as perturbations
affecting mainly the depths of intermediates and the
heights offree energy barriers on a protein’s folding
landscape rather than the basic mechanism16–18that
allows it to fold.
However, among these results have now
appeared a growing number of excursions away
from axiomatic correspondence between folding
and topology that must somehow find a place
within this picture.19–24For example, the small
proteins L and G share an almost identical,
symmetric topology, but both proteins nucleate
one of their two b-sheets preferentially, breaking
the symmetry of the native fold.20,21The small,
all-helical proteins Im7 and Im9 share essentially
the same topology, but Im7 folds through an on-
pathway intermediate in which a distorted arrange-
ment of its helices is stabilised by non-native
interactions.22,23Perhaps, it is not so surprising
that the folding mechanisms of these proteins are
varied. Their native shapes are not frustrated
mechanically7so they should have greater freedom
to respond to structural and energetic pertur-
bations, and their responses (the modulation of
intermediates and pathways by these pertur-
bations) may even be somewhat continuous.
On the other hand, even small perturbations
such as amino acid substitutions can sometimes
cause discrete interconversions of protein struc-
ture within a fold family (for instance, changing
b-strands to b-helices24,25). Moreover, the struc-
tural family of a protein (its fold type or fold
classification) often allows large loop insertions,
sometimes within secondary structure units, and
the substitution of one secondary structure type
for another, all of which can affect the entropy of
its folding units, the pattern of native contacts
between them, and the capacity of these units to
evolve more favourable contacts. Accordingly,
this more flexible interpretation of topology
(fold type) should permit more substantial
variations to occur among protein folding mech-
The landscape features that define the folding
pathways of larger proteins (w200 amino acid
residues) are more discrete, and should have more
capacity to accommodate perturbations. These
0022-2836/$ - see front matter q 2006 Published by Elsevier Ltd.
E-mail address of the corresponding author:
doi:10.1016/j.jmb.2006.02.026J. Mol. Biol. (2006) xx, 1–8
ARTICLE IN PRESS
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Edited by M. Levitt
(Received 12 October 2005; received in revised form 10 February 2006; accepted 10 February 2006)
Alternate Pathways for Flavodoxin Folding
ARTICLE IN PRESS