Abstract
Guang Song, Nancy M. Amato, "Using Motion Planning to Study Protein Folding Pathways," Journal of Computational Biology, 9(2):149-168, Nov 2002.
Journal(ps, pdf, abstract)
We present a framework for studying protein folding
pathways and potential landscapes which is based
on techniques recently developed in the robotics motion
planning community. Our focus in this work is
to study the protein folding mechanism assuming we
know the native fold. That is, instead of performing
fold prediction, we aim to study issues related
to the folding process, such as the formation of secondary
and tertiary structure, and the dependence of
the folding pathway on the initial denatured conformation.
Our work uses Probabilistic Roadmap (prm)
motion planning techniques which have proven successful
for problems involving high-dimensional con-figuration spaces. A strength of these methods is their efficiency n rapidly covering the planning space
without becoming trapped in local minima. We have
applied our prm technique to several small proteins
( 60 residues) and validated the pathways computed
by comparing the secondary structure formation order
on our paths to known hydrogen exchange experimental
results.
An advantage of the prm framework over other
simulation methods is that it enables one to easily
and efficiently compute folding pathways from any
denatured starting state to the (known) native fold.
This aspect makes our approach ideal for studying
global properties of the protein's potential landscape,
most of which are dicult to simulate and study
with other methods. For example, in the proteins we
study, the folding pathways starting from different
denatured states sometimes share common portions
when they are close to the native fold, and moreover,
the formation order of the secondary structure appears
largely independent of the starting denatured
conformation. Another feature of our technique is
that the distribution of the sampled conformations is
correlated with the formation of secondary structure,
and in particular appears to dierentiate situations
in which secondary structure clearly forms first and
those in which the tertiary structure is obtained more
directly. Overall our results applying prm techniques
are very encouraging, and indicate the promise of our
approach for studying proteins for which experimental
results are not available.