Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Saturday Abstracts
Closing the Loop: Comparing the Results of Experiment and Computer Simulations in the
Study of DNA Minicircles
Sarah Harris
.
University of Leeds, Leeds, United Kingdom.
Small DNA circles offer a controllable model system for the systematic exploration of the
dependence of DNA structure on supercoiling. We use computer simulation to explore the
supercoiling-dependent conformation of small DNA circles and how this is affected by
supercoiling, salt concentration, DNA sequence and the size of the circles [1]. The calculations
use atomistic molecular dynamics simulation, and employ both implicit and explicit solvent
models.
However, even given the most powerful supercomputers currently available, and the current
interest in using state of the art experimental biophysical and biochemical techniques to study
very small DNA loops, it can be challenging to identify situations in which the results of
simulation and experiment can be directly compared. I will present a critical comparison of our
computer models with results from cryoEM [2], AFM, gel electrophoresis [3] and biochemical
measurements [4] on DNA minicircles, and will then invite discussion of the successes and
caveats associated with both the theory and the experimental data.
[1] Mitchell J. S., Laughton C. A. & Harris S. A., Atomistic simulations reveal bubbles, kinks
and wrinkles in supercoiled DNA. Nucleic Acids Res. 2011. 39: p. 3928-3938.
[2] Lionberger T. A. et al, Co-operative kinking at distant sites in mechanically stressed DNA
Nucleic Acids Res., 2011, 39, 9820-9832.
[3] Fogg et al, Exploring writhe in minicircle DNA J. Phys Condensed. Matter, 2006, 18, S145-
S159.
[4] Du, Q., A. Kotlyar, and A. Vologodskii, Kinking the double helix by bending deformation.
Nucleic Acids Res., 2008. 36: p. 1120-1128.
Knotting a Protein in the Computer - From Simple Models to Explicit Solvent Simulations
Jose N. Onuchic
.
Rice University, Houston, USA.
Recently, experiments have confirmed that trefoil knotted proteins can fold spontaneously,
consistent with predictions from simulations of simplified protein models. These simulations
suggest folding the knot involves threading the protein terminal across a twisted loop via a
slipknot configuration. To further support these conclusions, we have performed unbiased all-
atom explicit-solvent simulations of the knotting dynamics of a protein. In simulations totaling
40 μs, we find that 5 out of 15 simulations reach the knotted native state when initiated from
unknotted, slipknotted intermediates. The completed threading events had durations of 0.1–2 μs.
Comparison of explicit-solvent to structure-based simulations shows that similar native contacts
are responsible for threading the slipknot through the loop; however, competition between native
and non-native salt bridges during threading results in increased energetic roughness. Overall,
these simulations support a slipknotting mechanism for proteins with complex topology, and
help verify that simplified models are useful tools for studying knotted proteins.
* Supported by the NSF
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