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Research areas in the Simmerling Lab
Protein Folding and Unfolded States
Understanding
the protein folding problem is of fundamental importance. Interest arises from
the intrinsic importance of proteins to molecular biology, from the ability of
these polymers to fold to their native state from a potentially vast number of
alternate structures,
and from the role of protein misfolding or agreggation in multiple human health
conditions
including Alzheimer’s, type II diabetes and vCJD (and other prion-type
diseases). Despite recent advances in experimental and computer simulation
methods, the process by which a flexible polypeptide chain adopts the native
conformation remains poorly understood. Since much of the scientific community
is concerned with protein function, the native (functional) state has received
the most attention. Although the unfolded state was traditionally assumed to
have a randomly fluctuating structure, mounting evidence suggests that it can
contain significantly more well-defined structure, which can have either native
or non-native character, with implications for protein stability,
folding mechanism and rate. Rapid folding can result from native-like topology
in the unfolded state, while non-native contacts can delay folding. Either can
affect the extent to which the interactions observed in the native state
contribute to net stability. To test these and other hypotheses, several small,
fast-folding model systems have recently been developed. These are particularly
important because their size and speed of folding have provided unprecedented
comparison of experimental and computational approaches to study proteins.
Although
characterization of the unfolded state allows for a greater understanding of
stability, folding pathways and the temporal ordering of folding events, experimental
studies of the unfolded state face significant challenges. They are hampered by
the low solubility, dynamic nature and the diversity of the unfolded ensembles
as compared to the native state. Other obstacles
include the short lifetime of the unfolded state in refolding experiments and weak
populations at equilibrium. For example, infrared and circular dichroism
spectroscopy experiments can only suggest basic information about residual
secondary structure if the unfolded structural ensemble is well populated.
Our studies aim to provide insight into the nature of early events in protein folding,
and how folding and stability are related not only to specific interactions in
the native state but also to the composition of the unfolded ensemble. Gaining
insight into the stability of the native fold and the composition of the
unfolded state both require sampling of non-native conformations in proper
Boltzmann-weighted proportions. Success is critically dependent on both the
quality of the energy function used and the extent of conformational sampling
achieved in the simulations, issues that we consider to be substantially
coupled.
The recent convergence of all of these areas - ultrafast
experimental measurements, improved conformational sampling and
accuracy in
simulations, and optimization or design of small, stably folded
polypeptides
with non-trivial structure that are accessible to both
computation and experiment - have facilitated tremendous advances in
the
detailed investigation of the interplay between various factors
involved in
folding. Perhaps as important, however, is the potential of these small
systems
to enable rapid feedback between theory, computation and experiment.
Improvements in the time resolution of experimental techniques
have enabled the study of folding kinetics on rapid timescales. These
in
turn have enabled the study and optimization of folding rates of these
model
proteins, with ever-faster systems nearing a “speed limit”
for folding. While most of these model systems have little direct
biological
relevance, they are extremely valuable for probing the timescales and
types of
local structuring events clarify, expand that may occur prior to the
transition
state of folding in more complex proteins. Through experimental
measurement and
theoretical analysis of formation rates for individual contacts and
secondary
structure elements such as a-helices and b-turns, the nature of these
dynamic events in the
unfolded ensemble are just beginning to be unraveled.
Our recent publications on this topic:
Wickstrom, L., Bi, Y., Hornak, V., Raleigh, D.
and Simmerling, C., “Reconciling the Solution and X-ray Structures of the
Villin Headpiece Helical Subdomain: Molecular Dynamics Simulations and Double
Mutant Cycles Reveal a Stabilizing Cation-Pi Interaction”, Biochemistry, 46:3624-3634
(2007) (listed as “Hot Article” by Biochemistry) (link)
Wickstrom, L.,
Okur, A., Song, K., Hornak, V., Raleigh, D. and Simmerling, C., “The Unfolded
State of the Villin Headpiece Helical Subdomain: Computational Studies of the
Role of Locally Stabilized Structure”, J. Mol. Biol., 360:1094-1107 (2006).
(link)
Roe, D., Hornak, V.
and Simmerling, C., “Folding Cooperativity in a Three-stranded beta-sheet Model”, J. Mol. Biol., 352, 370-281
(2005)
(link)
Simmerling, C.,
Strockbine, B and Roitberg, A., ‘All-Atom Structure Prediction and Folding
Simulations of a Stable Protein’, J. Am. Chem. Soc, 124:11258, 2002.
(link)
Many
of our articles on conformational sampling and force fields also
address protein folding and unfolded states, since these are used as
model systems for development of improved parameters and algorithms.
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