Universal folding pathways of polyhedron nets.

Paul M Dodd, Pablo F Damasceno, Sharon C Glotzer
Author Information
  1. Paul M Dodd: Chemical Engineering Department, University of Michigan, Ann Arbor, MI 48109.
  2. Pablo F Damasceno: Applied Physics Program, University of Michigan, Ann Arbor, MI 48109.
  3. Sharon C Glotzer: Chemical Engineering Department, University of Michigan, Ann Arbor, MI 48109; sglotzer@umich.edu.

Abstract

Low-dimensional objects such as molecular strands, ladders, and sheets have intrinsic features that affect their propensity to fold into 3D objects. Understanding this relationship remains a challenge for de novo design of functional structures. Using molecular dynamics simulations, we investigate the refolding of the 24 possible 2D unfoldings ("nets") of the three simplest Platonic shapes and demonstrate that attributes of a net's topology-net compactness and leaves on the cutting graph-correlate with thermodynamic folding propensity. To explain these correlations we exhaustively enumerate the pathways followed by nets during folding and identify a crossover temperature [Formula: see text] below which nets fold via nonnative contacts (bonds must break before the net can fold completely) and above which nets fold via native contacts (newly formed bonds are also present in the folded structure). Folding above [Formula: see text] shows a universal balance between reduction of entropy via the elimination of internal degrees of freedom when bonds are formed and gain in potential energy via local, cooperative edge binding. Exploiting this universality, we devised a numerical method to efficiently compute all high-temperature folding pathways for any net, allowing us to predict, among the combined 86,760 nets for the remaining Platonic solids, those with highest folding propensity. Our results provide a general heuristic for the design of 2D objects to stochastically fold into target 3D geometries and suggest a mechanism by which geometry and folding propensity are related above [Formula: see text], where native bonds dominate folding.

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References

Science. 2014 Aug 8;345(6197):644-6 [PMID: 25104380]
Nat Mater. 2015 Aug;14(8):785-9 [PMID: 26099109]
Proteins. 1998 Aug 1;32(2):136-58 [PMID: 9714155]
PLoS One. 2009;4(2):e4451 [PMID: 19212438]
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19885-90 [PMID: 22139373]
Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17874-9 [PMID: 24128758]
Nat Mater. 2011 Mar;10(3):230-5 [PMID: 21317901]
Nature. 2015 Aug 13;524(7564):204-7 [PMID: 26222025]
J Phys Chem B. 2014 Apr 17;118(15):4228-44 [PMID: 24660984]
J Phys Condens Matter. 2009 Nov 18;21(46):463102 [PMID: 21715864]
PLoS One. 2012;7(12):e51085 [PMID: 23251426]
Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10890-5 [PMID: 20534497]
Angew Chem Int Ed Engl. 2012 Feb 6;51(6):1420-3 [PMID: 22105942]
Science. 2010 Jan 29;327(5965):560-3 [PMID: 20110500]
Nat Nanotechnol. 2015 Sep;10(9):779-84 [PMID: 26192207]
Artif Life. 2014 Fall;20(4):409-39 [PMID: 25148546]
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19011-6 [PMID: 19887634]
Annu Rev Phys Chem. 2010;61:391-420 [PMID: 18999998]
Philos Trans A Math Phys Eng Sci. 2013 Dec 30;372(2008):20120041 [PMID: 24379431]
Curr Opin Struct Biol. 2007 Jun;17(3):342-6 [PMID: 17572080]
Science. 2012 Jul 27;337(6093):453-7 [PMID: 22837525]
Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1942-6 [PMID: 7680482]
Nat Mater. 2007 Aug;6(8):557-62 [PMID: 17667968]
Adv Drug Deliv Rev. 2012 Nov;64(14):1579-89 [PMID: 22425612]
Proc Natl Acad Sci U S A. 2015 Jun 16;112(24):7449-53 [PMID: 26015582]
J Chem Phys. 2006 Aug 28;125(8):084110 [PMID: 16965004]
Phys Rev Lett. 2018 May 4;120(18):188001 [PMID: 29775357]
Science. 2012 Jul 27;337(6093):417-8 [PMID: 22837512]
J Chem Phys. 2014 Jun 7;140(21):214101 [PMID: 24907984]