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Biophys. J. BioFAST: First Published January 13, 2006. doi:10.1529/biophysj.105.074906
© 2006 by the Biophysical Society.

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SUPRAMOLECULAR ASSEMBLIES

Atomistic simulation approach to a continuum description of self-assembled {beta}-sheet filaments

Jiyong Park 1, Byungnam Kahng 1, Roger D. Kamm 2 and Wonmuk Hwang 3*

1 Seoul National University
2 MIT
3 Texas A&M University

* To whom correspondence should be addressed. E-mail: hwm{at}tamu.edu.

Submitted on September 21, 2005
Revised on November 6, 2005
Accepted on 9 December 2005


  Abstract
We investigated the supramolecular structure and continuum mechanical properties of a {beta}-sheet nanofiber comprised of a self-assembling peptide ac-[RARADADA]2-am using computer simulations. The supramolecular structure was determined by constructing candidate filaments with dimensions compatible with those observed in atomic force microscopy (AFM)and selecting the most stable ones after running molecular dynamics simulations on each of them. Four structures with different backbone hydrogen bonding patterns were identified to be similarly stable. We then quantified the continuum mechanical properties of these identified structures by running three independent simulations, thermal motion analysis, normal mode analysis, and steered molecular dynamics. Within the range of deformations investigated, the filament showed linear elasticity in transverse directions with an estimated persistence length of 1.2-4.8 µm. While side chain interactions govern the propensity and energetics of filament self-assembly, we found that backbone hydrogen bonding interactions are the primary determinant of filament elasticity, as demonstrated by its effective thickness which is smaller than that estimated by AFM or from the molecular geometry, as well as by the similar bending stiffness of a model filament without charged side chains. The generality of our approach suggests that it should be applicable to developing continuum elastic ribbon models of other {beta}-sheet filaments and amyloid fibrils.

Key Words: MD simulation, amyloid fibril, beta-sheet filament, multi-scale modeling, peptide self-assembly, supramolecular structure




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Copyright © 2006 by the Biophysical Society.