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Title: Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Abstract

Self-assembling peptides containing aromatic groups are an attractive target for bioelectronic materials design because of their ease of manufacture, biocompatibility, aqueous solubility, and chemical tunability. Microscopic understanding of the properties that control assembly is a prerequisite for rational design. In this work, we study the assembly of a family of DXXX-Π–XXXD oligopeptides possessing a π-conjugated core flanked by Asp-terminated tetrapeptide wings that display pH-triggered assembly into supramolecular aggregates. We develop a coarse-grained patchy particle model to conduct molecular dynamics simulations of the assembly of ten thousand oligopeptides over hundreds of nanometers and hundreds of microseconds. We study the effects of core and side chain interaction strength and side chain steric volume upon the morphology and kinetics of assembly. By characterizing the rate and fractal dimension of hierarchical nanoaggregate growth, we identify parameter regimes that favor rapid assembly of linear aggregates and map these regimes to sequence-defined candidate peptides for experimental synthesis and testing. Here, this work establishes new understanding of assembly on previously unexplored time and length scales and presents an efficient and extensible protocol for computational screening and prediction of promising peptide chemistries to assemble nanostructures with desirable optoelectronic properties.

Authors:
 [1]; ORCiD logo [2]
+ Show Author Affiliations
  1. Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Physics
  2. Univ. of Illinois, Urbana-Champaign, IL (United States). Dept. of Physics, Dept. of Materials Science and Engineering, and Dept. of Chemical and Biomolecular Engineering
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
National Science Foundation (NSF); USDOE Office of Science (SC)
OSTI Identifier:
1492675
Report Number(s):
LA-UR-18-28703
Journal ID: ISSN 1520-6106
Grant/Contract Number:  
89233218CNA000001; DMR-1841807; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 122; Journal Issue: 44; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Mansbach, Rachael A., and Ferguson, Andrew L. Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides. United States: N. p., 2018. Web. doi:10.1021/acs.jpcb.8b05781.
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Mansbach, Rachael A., & Ferguson, Andrew L. Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides. United States. https://doi.org/10.1021/acs.jpcb.8b05781
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Mansbach, Rachael A., and Ferguson, Andrew L. Mon . "Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides". United States. https://doi.org/10.1021/acs.jpcb.8b05781. https://www.osti.gov/servlets/purl/1492675.
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@article{osti_1492675,
title = {Patchy Particle Model of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides},
author = {Mansbach, Rachael A. and Ferguson, Andrew L.},
abstractNote = {Self-assembling peptides containing aromatic groups are an attractive target for bioelectronic materials design because of their ease of manufacture, biocompatibility, aqueous solubility, and chemical tunability. Microscopic understanding of the properties that control assembly is a prerequisite for rational design. In this work, we study the assembly of a family of DXXX-Π–XXXD oligopeptides possessing a π-conjugated core flanked by Asp-terminated tetrapeptide wings that display pH-triggered assembly into supramolecular aggregates. We develop a coarse-grained patchy particle model to conduct molecular dynamics simulations of the assembly of ten thousand oligopeptides over hundreds of nanometers and hundreds of microseconds. We study the effects of core and side chain interaction strength and side chain steric volume upon the morphology and kinetics of assembly. By characterizing the rate and fractal dimension of hierarchical nanoaggregate growth, we identify parameter regimes that favor rapid assembly of linear aggregates and map these regimes to sequence-defined candidate peptides for experimental synthesis and testing. Here, this work establishes new understanding of assembly on previously unexplored time and length scales and presents an efficient and extensible protocol for computational screening and prediction of promising peptide chemistries to assemble nanostructures with desirable optoelectronic properties.},
doi = {10.1021/acs.jpcb.8b05781},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 44,
volume = 122,
place = {United States},
year = {Mon Oct 15 00:00:00 EDT 2018},
month = {Mon Oct 15 00:00:00 EDT 2018}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/acs.jpcb.8b05781
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Cited by: 13 works
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Figures / Tables:

Figure 1 Figure 1: Chemical structure and patchy particle model of the DXXX-$Π$-XXXD $π$-conjugated oligopeptides. (a) Chemical structure of a generic DXXX-$Π$-XXXD oligopeptide. The peptide wings are mirror symmetric in that the N-to-C directionality progresses away from the $π$-conjugated core and the tetrapeptide sequences are identical. The side chains {R1, R2, R3}more » may be tuned to any of the 20 naturally occurring amino acids and $Π$ is a $π$-conjugated core such as oligophenylenevinylene (OPV), perylenediimide (PDI), or quaterthiophene (OT4). The four terminal carboxyl groups belonging to the two C-termini and distal Asp residue side chains deprotonate at high pH (pH ≳ 7) and protonate at low pH (pH ≲ 1) enabling pH-triggerable assembly. Image produced using Marvin 18.10.0 (ChemAxon, 2018) (b) Patchy particle model of a generic DXXX-$Π$-XXXD oligopeptide. The small green $A$ beads located on the upper and lower face of the model model cofacial aromatic interactions, the large red $SC$ beads model interactions of the peptide wings, and the large blue $BB$ beads model non-cofacial aromatic core interactions. The diameter of the $SC$ beads is a parameter of the model. The length of the core is twice the diameter of a single $BB$ bead defined as the minimum of the Lennard-Jones $BB$ interaction potential. Image produced using VMD.« less
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  • Dehsorkhi, Ashkan; Castelletto, Valeria; Hamley, Ian W.
  • Journal of Peptide Science, Vol. 20, Issue 7
  • DOI: 10.1002/psc.2633

Spiers Memorial Lecture: Effect of interaction specificity on the phase behaviour of patchy particles
journal, January 2012

  • Dorsaz, Nicolas; Filion, Laura; Smallenburg, Frank
  • Faraday Discussions, Vol. 159
  • DOI: 10.1039/c2fd20070h

Optimal experimental design for materials discovery
journal, March 2017

Measuring the strangeness of strange attractors
journal, October 1983

Singularities in the kinetics of coagulation processes
journal, December 1981

Molecular Self-Assembly on Two-Dimensional Atomic Crystals: Insights from Molecular Dynamics Simulations
journal, October 2015

Entropically Patchy Particles: Engineering Valence through Shape Entropy
journal, December 2013

  • van Anders, Greg; Ahmed, N. Khalid; Smith, Ross
  • ACS Nano, Vol. 8, Issue 1
  • DOI: 10.1021/nn4057353

General purpose molecular dynamics simulations fully implemented on graphics processing units
journal, May 2008

  • Anderson, Joshua A.; Lorenz, Chris D.; Travesset, A.
  • Journal of Computational Physics, Vol. 227, Issue 10
  • DOI: 10.1016/j.jcp.2008.01.047

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides
journal, February 2017

  • Mansbach, Rachael A.; Ferguson, Andrew L.
  • The Journal of Physical Chemistry B, Vol. 121, Issue 7
  • DOI: 10.1021/acs.jpcb.6b10165

Scaling dynamics of aerosol coagulation
journal, April 1992

Improved Parameters for the Martini Coarse-Grained Protein Force Field
journal, November 2012

  • de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300646g

Self-Assembly and Associated Photophysics of Dendron-Appended Peptide-π-Peptide Triblock Macromolecules
journal, July 2017

Biomedical Applications of Self-Assembling Peptides
journal, December 2015

Phase behavior of patchy spheroidal fluids
journal, December 2016

  • Carpency, T. N.; Gunton, J. D.; Rickman, J. M.
  • The Journal of Chemical Physics, Vol. 145, Issue 21
  • DOI: 10.1063/1.4969074

Peptide self-assembly: thermodynamics and kinetics
journal, January 2016

  • Wang, Juan; Liu, Kai; Xing, Ruirui
  • Chemical Society Reviews, Vol. 45, Issue 20
  • DOI: 10.1039/c6cs00176a

Theoretical and numerical study of the phase diagram of patchy colloids: Ordered and disordered patch arrangements
journal, April 2008

  • Bianchi, Emanuela; Tartaglia, Piero; Zaccarelli, Emanuela
  • The Journal of Chemical Physics, Vol. 128, Issue 14
  • DOI: 10.1063/1.2888997

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
journal, October 1992

  • Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal
  • Journal of Computational Chemistry, Vol. 13, Issue 8
  • DOI: 10.1002/jcc.540130812

The Powerful Functions of Peptide-Based Bioactive Matrices for Regenerative Medicine
journal, November 2014

  • Rubert Pérez, Charles M.; Stephanopoulos, Nicholas; Sur, Shantanu
  • Annals of Biomedical Engineering, Vol. 43, Issue 3
  • DOI: 10.1007/s10439-014-1166-6

Effect of Asphaltene Structure on Association and Aggregation Using Molecular Dynamics
journal, April 2013

  • Sedghi, Mohammad; Goual, Lamia; Welch, William
  • The Journal of Physical Chemistry B, Vol. 117, Issue 18
  • DOI: 10.1021/jp401584u

Sequence dependent proton conduction in self-assembled peptide nanostructures
journal, January 2016

  • Lerner Yardeni, Jenny; Amit, Moran; Ashkenasy, Gonen
  • Nanoscale, Vol. 8, Issue 4
  • DOI: 10.1039/C5NR06750B

Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides
journal, August 2014

  • Vácha, Robert; Linse, Sara; Lund, Mikael
  • Journal of the American Chemical Society, Vol. 136, Issue 33
  • DOI: 10.1021/ja505502e

Effects of patch size and number within a simple model of patchy colloids
journal, May 2010

  • Giacometti, Achille; Lado, Fred; Largo, Julio
  • The Journal of Chemical Physics, Vol. 132, Issue 17
  • DOI: 10.1063/1.3415490

Growth and Characterization of Molecular Crystals of para -Sexiphenyl by All-Atom Computer Simulations
journal, July 2014

  • Palczynski, Karol; Heimel, Georg; Heyda, Jan
  • Crystal Growth & Design, Vol. 14, Issue 8
  • DOI: 10.1021/cg500234r

The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

  • Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
  • The Journal of Physical Chemistry B, Vol. 111, Issue 27
  • DOI: 10.1021/jp071097f

The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies
journal, March 1995

  • Eisenhaber, Frank; Lijnzaad, Philip; Argos, Patrick
  • Journal of Computational Chemistry, Vol. 16, Issue 3
  • DOI: 10.1002/jcc.540160303

Optimal conditions for opening of membrane pore by amphiphilic peptides
journal, December 2015

  • Kabelka, Ivo; Vácha, Robert
  • The Journal of Chemical Physics, Vol. 143, Issue 24
  • DOI: 10.1063/1.4933229

Supramolecular Construction of Optoelectronic Biomaterials
journal, March 2013

  • Tovar, John D.
  • Accounts of Chemical Research, Vol. 46, Issue 7
  • DOI: 10.1021/ar3002969

Peptide π-Electron Conjugates: Organic Electronics for Biology?
journal, October 2015

Photoinduced Electron Transfer within Supramolecular Donor–Acceptor Peptide Nanostructures under Aqueous Conditions
journal, March 2016

  • Sanders, Allix M.; Magnanelli, Timothy J.; Bragg, Arthur E.
  • Journal of the American Chemical Society, Vol. 138, Issue 10
  • DOI: 10.1021/jacs.5b12001

Photon management in supramolecular peptide nanomaterials
journal, December 2017

A simple patchy colloid model for the phase behavior of lysozyme dispersions
journal, August 2008

  • Gögelein, Christoph; Nägele, Gerhard; Tuinier, Remco
  • The Journal of Chemical Physics, Vol. 129, Issue 8
  • DOI: 10.1063/1.2951987

Nonlinear machine learning and design of reconfigurable digital colloids
journal, January 2016

  • Long, Andrew W.; Phillips, Carolyn L.; Jankowksi, Eric
  • Soft Matter, Vol. 12, Issue 34
  • DOI: 10.1039/c6sm01156j

Bayesian optimization for molecular communication channel capacity
conference, February 2016

  • Elsaid, Lubna; Mahamadi, Abdelrhman
  • 2016 Conference of Basic Sciences and Engineering Studies (SGCAC)
  • DOI: 10.1109/SGCAC.2016.7458026
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    Stimulus-responsive self-assembly of protein-based fractals by computational design
    journal, June 2019

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