| We present results about the shape, size, structure, conformational stability and hydrodynamics of α-conotoxin (AuIB, a disulfide-rich peptide from the venom of Conus Aulicus, recognized as a nicotinic acetylcholine antagonist with great pharmaceutical potential) from very long (0.5 μs) massively-parallel Molecular Dynamics (MD) simulations in full atomistic detail. We extract coarse-grained descriptors of protein shape (ellipsoid), and of translational and rotational mobilities, i.e., the basic components at the lowest hierarchical level in a multiscale modeling strategy. Structural analysis reveals the folded conformation and an asymmetric shape to be strongly favored for AuIB. In accordance with experimental findings, conformational stability is observed and found to be linked to the presence of the α-helix along the 15 residues and to the existence of the two disulfide bonds. We find rotational (Dr) and translational (Dt) diffusivities to be suitable descriptors of coarse-grained dynamics, i.e. of the hydrodynamic behavior, and obtain Dr=3.62 (±0.17) × 10 s-1 and Dt = 1.08 (±0.4) × 10-10 m2s-1 from 10 ns and 100 ns MD trajectories, respectively. We further compare the MD-computed coarse-grained descriptors with first principles theoretical predictions which relate particle shape and dimensions to diffusion coefficients. The comparison strongly suggests that diffusivities of rigid biomolecules much larger than the α-conotoxin AuIB studied here can be obtained from the coarse-grained shape descriptor (ellipsoid) derived from relatively short MD simulations.
for LaTeX users @article{NCKarayiannis2009-113,
author = {N. C. Karayiannis and M. Laso and M. Kr\"oger},
title = {Detailed atomistic molecular-dynamics simulations of α-conotoxin AuIB in water},
journal = {J. Phys. Chem. B},
volume = {113},
pages = {5016-5024},
year = {2009}
}
\bibitem{NCKarayiannis2009-113} N.C. Karayiannis, M. Laso, M. Kr\"oger,
Detailed atomistic molecular-dynamics simulations of α-conotoxin AuIB in water,
J. Phys. Chem. B {\bf 113} (2009) 5016-5024.NCKarayiannis2009-113
N.C. Karayiannis, M. Laso, M. Kr\"oger
Detailed atomistic molecular-dynamics simulations of α-conotoxin AuIB in water
J. Phys. Chem. B,113,2009,5016-5024 |
mk@mat.ethz.ch
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