Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Mansbach, Rachael A.; Ferguson, Andrew L.

doi:10.1021/acs.jpcb.6b10165

Title: Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Abstract

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately a branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.

Authors:

Mansbach, Rachael A.;

Publication Date:: Fri Feb 10 00:00:00 EST 2017

Research Org.:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1342529

Grant/Contract Number:: SC0011847

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry

Additional Journal Information:: Journal Volume: 121; Journal Issue: 7; Journal ID: ISSN 1520-6106

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

Subject:: 36 MATERIALS SCIENCE; self-assembly; pi-conjugated oligopeptides; molecular simulation; Smoluchowski coagulation process

Citation Formats


                    Mansbach, Rachael A., and Ferguson, Andrew L. Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides.  United States: N. p., 2017. 
Web.  doi:10.1021/acs.jpcb.6b10165.

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                    Mansbach, Rachael A., & Ferguson, Andrew L. Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides.  United States.  https://doi.org/10.1021/acs.jpcb.6b10165

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                    Mansbach, Rachael A., and Ferguson, Andrew L. Fri .  
"Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides".  United States.  https://doi.org/10.1021/acs.jpcb.6b10165.  https://www.osti.gov/servlets/purl/1342529.

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@article{osti_1342529,

  title        = {Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides},

  author       = {Mansbach, Rachael A. and Ferguson, Andrew L.},

  abstractNote = {Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately a branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.},

  doi          = {10.1021/acs.jpcb.6b10165},

  journal      = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},

  number       = 7,

  volume       = 121,

  place        = {United States},

  year         = {Fri Feb 10 00:00:00 EST 2017},

  month        = {Fri Feb 10 00:00:00 EST 2017}

}

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Works referenced in this record:

Computational Approaches to Understanding the Self-assembly of Peptide-based Nanostructures
journal, March 2015

Tuttle, Tell
Israel Journal of Chemistry, Vol. 55, Issue 6-7
DOI: 10.1002/ijch.201400188

Design of Polymer Scaffolds for Tissue Engineering Applications
journal, February 2015

Mehdizadeh, Hamidreza; Somo, Sami I.; Bayrak, Elif S.
Industrial & Engineering Chemistry Research, Vol. 54, Issue 8
DOI: 10.1021/ie503133e

Self-Assembled Proteins and Peptides for Regenerative Medicine
journal, March 2013

Hosseinkhani, Hossein; Hong, Po-Da; Yu, Dah-Shyong
Chemical Reviews, Vol. 113, Issue 7
DOI: 10.1021/cr300131h

Biomimetic Systems for Hydroxyapatite Mineralization Inspired By Bone and Enamel
journal, November 2008

Palmer, Liam C.; Newcomb, Christina J.; Kaltz, Stuart R.
Chemical Reviews, Vol. 108, Issue 11
DOI: 10.1021/cr8004422

Self-Assembly and Mineralization of Peptide-Amphiphile Nanofibers
journal, November 2001

Hartgerink, Jeffrey D.; Beniash, Elia; Stupp, Samuel I.
Science, Vol. 294, Issue 5547, p. 1684-1688
DOI: 10.1126/science.1063187

Stimulus responsive peptide based materials
journal, January 2010

Löwik, Dennis W. P. M.; Leunissen, E. H. P.; van den Heuvel, M.
Chemical Society Reviews, Vol. 39, Issue 9
DOI: 10.1039/b914342b

Designing peptide based nanomaterials
journal, January 2008

Ulijn, Rein V.; Smith, Andrew M.
Chemical Society Reviews, Vol. 37, Issue 4
DOI: 10.1039/b609047h

Self-Assembled Peptide Amphiphile Nanofibers Conjugated to MRI Contrast Agents
journal, January 2005

Bull, Steve R.; Guler, Mustafa O.; Bras, Rafael E.
Nano Letters, Vol. 5, Issue 1
DOI: 10.1021/nl0484898

Next-generation peptide nanomaterials: molecular networks, interfaces and supramolecular functionality
journal, January 2010

Zelzer, Mischa; Ulijn, Rein V.
Chemical Society Reviews, Vol. 39, Issue 9
DOI: 10.1039/c0cs00035c

Designing π-conjugated polymers for organic electronics
journal, December 2013

Guo, Xin; Baumgarten, Martin; Müllen, Klaus
Progress in Polymer Science, Vol. 38, Issue 12
DOI: 10.1016/j.progpolymsci.2013.09.005

Recent progress in the design of narrow bandgap conjugated polymers for high-efficiency organic solar cells
journal, September 2012

Bian, Linyi; Zhu, Enwei; Tang, Jian
Progress in Polymer Science, Vol. 37, Issue 9
DOI: 10.1016/j.progpolymsci.2012.03.001

A model for the controlled assembly of semiconductor peptides
journal, January 2012

Kim, Se Hye; Parquette, Jon R.
Nanoscale, Vol. 4, Issue 22
DOI: 10.1039/c2nr32140h

About Supramolecular Assemblies of π-Conjugated Systems
journal, April 2005

Hoeben, Freek J. M.; Jonkheijm, Pascal; Meijer, E. W.
Chemical Reviews, Vol. 105, Issue 4
DOI: 10.1021/cr030070z

On-resin dimerization incorporates a diverse array of π-conjugated functionality within aqueous self-assembling peptide backbones
journal, January 2010

Vadehra, Geeta S.; Wall, Brian D.; Diegelmann, Stephen R.
Chemical Communications, Vol. 46, Issue 22
DOI: 10.1039/c0cc00301h

Supramolecular Polymorphism: Tunable Electronic Interactions within π-Conjugated Peptide Nanostructures Dictated by Primary Amino Acid Sequence
journal, May 2014

Wall, Brian D.; Zacca, Ashley E.; Sanders, Allix M.
Langmuir, Vol. 30, Issue 20
DOI: 10.1021/la500222y

Synthesis and characterization of π-conjugated peptide-based supramolecular materials
journal, March 2012

Wall, Brian D.; Tovar, John D.
Pure and Applied Chemistry, Vol. 84, Issue 4
DOI: 10.1351/PAC-CON-11-10-24

Variation of Formal Hydrogen-Bonding Networks within Electronically Delocalized π-Conjugated Oligopeptide Nanostructures
journal, September 2014

Wall, Brian D.; Zhou, Yuecheng; Mei, Shao
Langmuir, Vol. 30, Issue 38
DOI: 10.1021/la501999g

Fluidic-Directed Assembly of Aligned Oligopeptides with π-Conjugated Cores
journal, August 2013

Marciel, Amanda B.; Tanyeri, Melikhan; Wall, Brian D.
Advanced Materials, Vol. 25, Issue 44
DOI: 10.1002/adma.201302496

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides
journal, March 2016

Thurston, Bryce A.; Tovar, John D.; Ferguson, Andrew L.
Molecular Simulation, Vol. 42, Issue 12
DOI: 10.1080/08927022.2015.1125997

Atomic structure and hierarchical assembly of a cross- amyloid fibril
journal, March 2013

Fitzpatrick, A. W. P.; Debelouchina, G. T.; Bayro, M. J.
Proceedings of the National Academy of Sciences, Vol. 110, Issue 14
DOI: 10.1073/pnas.1219476110

The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008

Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier
Journal of Chemical Theory and Computation, Vol. 4, Issue 5
DOI: 10.1021/ct700324x

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

Coarse-grained molecular dynamics simulations of membrane proteins and peptides
journal, March 2007

Bond, Peter J.; Holyoake, John; Ivetac, Anthony
Journal of Structural Biology, Vol. 157, Issue 3
DOI: 10.1016/j.jsb.2006.10.004

Perspective: Coarse-grained models for biomolecular systems
journal, September 2013

Noid, W. G.
The Journal of Chemical Physics, Vol. 139, Issue 9
DOI: 10.1063/1.4818908

Coarse-grained protein molecular dynamics simulations
journal, January 2007

Derreumaux, Philippe; Mousseau, Normand
The Journal of Chemical Physics, Vol. 126, Issue 2
DOI: 10.1063/1.2408414

Coarse-grained models for proteins
journal, April 2005

Tozzini, Valentina
Current Opinion in Structural Biology, Vol. 15, Issue 2
DOI: 10.1016/j.sbi.2005.02.005

Global ribosome motions revealed with elastic network model
journal, September 2004

Wang, Yongmei; Rader, A. J.; Bahar, Ivet
Journal of Structural Biology, Vol. 147, Issue 3
DOI: 10.1016/j.jsb.2004.01.005

Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum
journal, December 2006

Arkhipov, Anton; Freddolino, Peter L.; Imada, Katsumi
Biophysical Journal, Vol. 91, Issue 12
DOI: 10.1529/biophysj.106.093443

Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field
journal, March 2010

Gautieri, Alfonso; Russo, Antonio; Vesentini, Simone
Journal of Chemical Theory and Computation, Vol. 6, Issue 4
DOI: 10.1021/ct100015v

Simulation of polyethylene glycol and calcium-mediated membrane fusion
journal, March 2014

Pannuzzo, Martina; De Jong, Djurre H.; Raudino, Antonio
The Journal of Chemical Physics, Vol. 140, Issue 12
DOI: 10.1063/1.4869176

Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes
journal, June 2013

López, Cesar A.; de Vries, Alex H.; Marrink, Siewert J.
Scientific Reports, Vol. 3, Issue 1
DOI: 10.1038/srep02071

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes
journal, April 2012

Guo, Cong; Luo, Yin; Zhou, Ruhong
ACS Nano, Vol. 6, Issue 5
DOI: 10.1021/nn300015g

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides
journal, April 2012

Seo, Mikyung; Rauscher, Sarah; Pomès, Régis
Journal of Chemical Theory and Computation, Vol. 8, Issue 5
DOI: 10.1021/ct200876v

Perspective on the Martini model
journal, January 2013

Marrink, Siewert J.; Tieleman, D. Peter
Chemical Society Reviews, Vol. 42, Issue 16
DOI: 10.1039/c3cs60093a

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008

Hess, Berk; Kutzner, Carsten; van der Spoel, David
Journal of Chemical Theory and Computation, Vol. 4, Issue 3
DOI: 10.1021/ct700301q

PRODRG : a tool for high-throughput crystallography of protein–ligand complexes
journal, July 2004

Schüttelkopf, Alexander W.; van Aalten, Daan M. F.
Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 8
DOI: 10.1107/S0907444904011679

Comparison of simple potential functions for simulating liquid water
journal, July 1983

Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
The Journal of Chemical Physics, Vol. 79, Issue 2
DOI: 10.1063/1.445869

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^†
journal, April 1998

MacKerell, A. D.; Bashford, D.; Bellott, M.
The Journal of Physical Chemistry B, Vol. 102, Issue 18
DOI: 10.1021/jp973084f

A unified formulation of the constant temperature molecular dynamics methods
journal, July 1984

Nosé, Shuichi
The Journal of Chemical Physics, Vol. 81, Issue 1
DOI: 10.1063/1.447334

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

Parrinello, M.; Rahman, A.
Journal of Applied Physics, Vol. 52, Issue 12
DOI: 10.1063/1.328693

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

Hess, Berk; Bekker, Henk; Berendsen, Herman J. C.
Journal of Computational Chemistry, Vol. 18, Issue 12
DOI: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H

A smooth particle mesh Ewald method
journal, November 1995

Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
The Journal of Chemical Physics, Vol. 103, Issue 19
DOI: 10.1063/1.470117

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
journal, February 1977

Torrie, G. M.; Valleau, J. P.
Journal of Computational Physics, Vol. 23, Issue 2
DOI: 10.1016/0021-9991(77)90121-8

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 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

Calculation of conformational ensembles from potentials of mena force
journal, June 1990

Sippl, Manfred J.
Journal of Molecular Biology, Vol. 213, Issue 4
DOI: 10.1016/S0022-2836(05)80269-4

Versatile Object-Oriented Toolkit for Coarse-Graining Applications
journal, November 2009

Rühle, Victor; Junghans, Christoph; Lukyanov, Alexander
Journal of Chemical Theory and Computation, Vol. 5, Issue 12
DOI: 10.1021/ct900369w

Polarizable Water Model for the Coarse-Grained MARTINI Force Field
journal, June 2010

Yesylevskyy, Semen O.; Schäfer, Lars V.; Sengupta, Durba
PLoS Computational Biology, Vol. 6, Issue 6
DOI: 10.1371/journal.pcbi.1000810

Canonical sampling through velocity rescaling
journal, January 2007

Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
The Journal of Chemical Physics, Vol. 126, Issue 1
DOI: 10.1063/1.2408420

Entropic approach to Brownian movement
journal, May 1980

Neumann, Richard M.
American Journal of Physics, Vol. 48, Issue 5
DOI: 10.1119/1.12095

Energy transfer within responsive pi-conjugated coassembled peptide-based nanostructures in aqueous environments
journal, January 2015

Ardoña, Herdeline Ann M.; Tovar, John D.
Chemical Science, Vol. 6, Issue 2
DOI: 10.1039/C4SC03122A

Multiscale modeling of soft matter: scaling of dynamics
journal, January 2011

Fritz, Dominik; Koschke, Konstantin; Harmandaris, Vagelis A.
Physical Chemistry Chemical Physics, Vol. 13, Issue 22
DOI: 10.1039/c1cp20247b

Electrostatic interactions in dissipative particle dynamics—simulation of polyelectrolytes and anionic surfactants
journal, June 2003

Groot, R. D.
The Journal of Chemical Physics, Vol. 118, Issue 24
DOI: 10.1063/1.1574800

Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E.
The Journal of Physical Chemistry B, Vol. 108, Issue 2
DOI: 10.1021/jp036508g

Mesoscale Simulation of Asphaltene Aggregation
journal, August 2016

Wang, Jiang; Ferguson, Andrew L.
The Journal of Physical Chemistry B, Vol. 120, Issue 32
DOI: 10.1021/acs.jpcb.6b05925

Graph Theory
report, November 1969

Harary, Frank
DOI: 10.21236/AD0705364

VMD: Visual molecular dynamics
journal, February 1996

Humphrey, William; Dalke, Andrew; Schulten, Klaus
Journal of Molecular Graphics, Vol. 14, Issue 1
DOI: 10.1016/0263-7855(96)00018-5

Measuring the strangeness of strange attractors
journal, October 1983

Grassberger, Peter; Procaccia, Itamar
Physica D: Nonlinear Phenomena, Vol. 9, Issue 1-2
DOI: 10.1016/0167-2789(83)90298-1

Shape of unperturbed linear polymers: polypropylene
journal, November 1985

Theodorou, Doros N.; Suter, Ulrich W.
Macromolecules, Vol. 18, Issue 6
DOI: 10.1021/ma00148a028

Scaling theory and exactly solved models in the kinetics of irreversible aggregation
journal, August 2003

Leyvraz, F.
Physics Reports, Vol. 383, Issue 2-3
DOI: 10.1016/S0370-1573(03)00241-2

An introduction to mathematical models of coagulation–fragmentation processes: A discrete deterministic mean-field approach
journal, October 2006

Wattis, Jonathan A. D.
Physica D: Nonlinear Phenomena, Vol. 222, Issue 1-2
DOI: 10.1016/j.physd.2006.07.024

A survey of numerical solutions to the coagulation equation
journal, November 2001

Lee, Man Hoi
Journal of Physics A: Mathematical and General, Vol. 34, Issue 47
DOI: 10.1088/0305-4470/34/47/323

On the Validity of the Coagulation Equation and the Nature of Runaway Growth
journal, January 2000

Lee, M.
Icarus, Vol. 143, Issue 1
DOI: 10.1006/icar.1999.6239

Assembly of Amyloid Protofibrils via Critical Oligomers—A Novel Pathway of Amyloid Formation
journal, January 2003

Modler, A. J.; Gast, K.; Lutsch, G.
Journal of Molecular Biology, Vol. 325, Issue 1
DOI: 10.1016/S0022-2836(02)01175-0

Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth
journal, August 2013

Gillam, J. E.; MacPhee, C. E.
Journal of Physics: Condensed Matter, Vol. 25, Issue 37
DOI: 10.1088/0953-8984/25/37/373101

An exact solution of the discrete Smoluchowski equation and its correspondence to the solution of the continuous equation
journal, July 1990

Treat, R. P.
Journal of Physics A: Mathematical and General, Vol. 23, Issue 13
DOI: 10.1088/0305-4470/23/13/035

Singularities in the kinetics of coagulation processes
journal, December 1981

Leyvraz, F.; Tschudi, H. R.
Journal of Physics A: Mathematical and General, Vol. 14, Issue 12
DOI: 10.1088/0305-4470/14/12/030

Mobility of Coenzyme Q in Membranes
book, August 2000

Lenaz, Giorgio
Coenzyme Q
DOI: 10.1201/9781420036701.pt1

Dynamic Scaling in the Kinetics of Clustering
journal, April 1985

van Dongen, P. G. J.; Ernst, M. H.
Physical Review Letters, Vol. 54, Issue 13
DOI: 10.1103/PhysRevLett.54.1396

One-Dimensional Optoelectronic Nanostructures Derived from the Aqueous Self-Assembly of π-Conjugated Oligopeptides
journal, October 2008

Diegelmann, Stephen R.; Gorham, Justin M.; Tovar, John D.
Journal of the American Chemical Society, Vol. 130, Issue 42
DOI: 10.1021/ja805491d

The computer study of transport processes under extreme conditions
journal, August 1972

Lees, A. W.; Edwards, S. F.
Journal of Physics C: Solid State Physics, Vol. 5, Issue 15
DOI: 10.1088/0022-3719/5/15/006

Extensional motions of spatially periodic lattices
journal, November 1992

Kraynik, A. M.; Reinelt, D. A.
International Journal of Multiphase Flow, Vol. 18, Issue 6
DOI: 10.1016/0301-9322(92)90074-Q

Nonlinear-response theory for steady planar Couette flow
journal, September 1984

Evans, Denis J.; Morriss, G. P.
Physical Review A, Vol. 30, Issue 3
DOI: 10.1103/PhysRevA.30.1528

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors
journal, August 2011

Rühle, Victor; Lukyanov, Alexander; May, Falk
Journal of Chemical Theory and Computation, Vol. 7, Issue 10
DOI: 10.1021/ct200388s

Interchain Interactions in Organic π-Conjugated Materials: Impact on Electronic Structure, Optical Response, and Charge Transport
journal, July 2001

Cornil, J.; Beljonne, D.; Calbert, J. -P.
Advanced Materials, Vol. 13, Issue 14
DOI: 10.1002/1521-4095(200107)13:14<1053::AID-ADMA1053>3.0.CO;2-7

Synthesis of Functionalizable Boron-Containing π-Electron Materials that Incorporate Formally Aromatic Fused Borepin Rings
journal, May 2010

Caruso, Anthony; Siegler, Maxime A.; Tovar, John D.
Angewandte Chemie, Vol. 122, Issue 25
DOI: 10.1002/ange.201000411

Conjugated “ B -Entacenes”: Polycyclic Aromatics Containing Two Borepin Rings
journal, June 2011

Caruso, Anthony; Tovar, John D.
Organic Letters, Vol. 13, Issue 12
DOI: 10.1021/ol2010159

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journal, January 2019

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DOI: 10.1039/c8me00064f

Machine learning and molecular design of self-assembling -conjugated oligopeptides
journal, April 2018

Thurston, Bryce A.; Ferguson, Andrew L.
Molecular Simulation, Vol. 44, Issue 11
DOI: 10.1080/08927022.2018.1469754

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition
journal, January 2018

Mushnoori, Srinivas; Schmidt, Kassandra; Nanda, Vikas
Organic & Biomolecular Chemistry, Vol. 16, Issue 14
DOI: 10.1039/c8ob00130h

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Journal Article Mansbach, Rachael A. ; Ferguson, Andrew L. - Organic and Biomolecular Chemistry

Self-assembled nanoaggregates of p-conjugated peptides possess optoelectronic properties due to electron delocalization over the conjugated peptide groups that make them attractive candidates for the fabrication of bioelectronic materials. We present a computational and theoretical study to resolve the microscopic effects of pH and flow on the non-equilibrium morphology and kinetics of early-stage assembly of an experimentally-realizable optoelectronic peptide that displays pH triggerable assembly. Employing coarse-grained molecular dynamics simulations, we probe the effects of pH on growth kinetics and aggregate morphology to show that control of the peptide protonation state by pH can be used to modulate the assembly rates, degreemore »« less
Cited by 16
https://doi.org/10.1039/C7OB00923B

Full Text Available
High-resolution NMR studies of fibrinogen-like peptides in solution: Structure of a thrombin-bound peptide corresponding to residues 7-16 of the A. alpha. chain of human fibrinogen

Journal Article Ni, F ; Meinwald, Y C ; Vasquez, M ; ... - Biochemistry; (USA)

The interaction of the following human fibrinogen-like peptides with bovine thrombin was studied by one- and two-dimensional NMR techniques in aqueous solution: acetyl-Phe(8)-Leu(9)-Ala(10)-Glu(11)-Gly(12)-Gly(13)-Gly(14)-Val(15)-Arg(16)-Gly(17)-Pro(18)-NHMe (F6), acetyl-Phe-Leu-Ala-Glu-Gly-Gly-Gly-Val-Arg(16) (tF6), acetyl-Asp(7)-Phe-Leu-Ala-Glu-Gly-Gly-Gly-Val-Arg(16)-Gly(17)-Pro-Arg(19)-Val(20)-NHMe (F8), and acetyl-Asp-Phe-Leu-Ala-Glu-Gly-Gly-Gly-Val-Arg(16) (tF8). At pH 5.3 and 25{degree}C, the Arg(16)-Gly(17) peptide bonds in both F6 and F8 were cleaved instantaneously in the presence of 0.5 mM thrombin, producing truncated peptides tF6 and tF8 and other peptide fragments. On the basis of observations of line broadening, thrombin was found to bind to the cleavage products, tF6 and tF8, of peptides F6 and F8. Transferred NOE (TRNOE) measurements were made of the complexes betweenmore »« less
https://doi.org/10.1021/bi00433a053

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Title: Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

Abstract

Citation Formats

Computational Approaches to Understanding the Self-assembly of Peptide-based Nanostructures journal, March 2015

Design of Polymer Scaffolds for Tissue Engineering Applications journal, February 2015

Self-Assembled Proteins and Peptides for Regenerative Medicine journal, March 2013

Biomimetic Systems for Hydroxyapatite Mineralization Inspired By Bone and Enamel journal, November 2008

Self-Assembly and Mineralization of Peptide-Amphiphile Nanofibers journal, November 2001

Stimulus responsive peptide based materials journal, January 2010

Designing peptide based nanomaterials journal, January 2008

Self-Assembled Peptide Amphiphile Nanofibers Conjugated to MRI Contrast Agents journal, January 2005

Next-generation peptide nanomaterials: molecular networks, interfaces and supramolecular functionality journal, January 2010

Designing π-conjugated polymers for organic electronics journal, December 2013

Recent progress in the design of narrow bandgap conjugated polymers for high-efficiency organic solar cells journal, September 2012

A model for the controlled assembly of semiconductor peptides journal, January 2012

About Supramolecular Assemblies of π-Conjugated Systems journal, April 2005

On-resin dimerization incorporates a diverse array of π-conjugated functionality within aqueous self-assembling peptide backbones journal, January 2010

Supramolecular Polymorphism: Tunable Electronic Interactions within π-Conjugated Peptide Nanostructures Dictated by Primary Amino Acid Sequence journal, May 2014

Synthesis and characterization of π-conjugated peptide-based supramolecular materials journal, March 2012

Variation of Formal Hydrogen-Bonding Networks within Electronically Delocalized π-Conjugated Oligopeptide Nanostructures journal, September 2014

Fluidic-Directed Assembly of Aligned Oligopeptides with π-Conjugated Cores journal, August 2013

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides journal, March 2016

Atomic structure and hierarchical assembly of a cross- amyloid fibril journal, March 2013

The MARTINI Coarse-Grained Force Field: Extension to Proteins journal, April 2008

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

Coarse-grained molecular dynamics simulations of membrane proteins and peptides journal, March 2007

Perspective: Coarse-grained models for biomolecular systems journal, September 2013

Coarse-grained protein molecular dynamics simulations journal, January 2007

Coarse-grained models for proteins journal, April 2005

Global ribosome motions revealed with elastic network model journal, September 2004

Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum journal, December 2006

Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field journal, March 2010

Simulation of polyethylene glycol and calcium-mediated membrane fusion journal, March 2014

Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes journal, June 2013

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes journal, April 2012

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides journal, April 2012

Perspective on the Martini model journal, January 2013

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal, February 2008

PRODRG : a tool for high-throughput crystallography of protein–ligand complexes journal, July 2004

Comparison of simple potential functions for simulating liquid water journal, July 1983

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal, April 1998

A unified formulation of the constant temperature molecular dynamics methods journal, July 1984

Polymorphic transitions in single crystals: A new molecular dynamics method journal, December 1981

LINCS: A linear constraint solver for molecular simulations journal, September 1997

A smooth particle mesh Ewald method journal, November 1995

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling journal, February 1977

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

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

Calculation of conformational ensembles from potentials of mena force journal, June 1990

Versatile Object-Oriented Toolkit for Coarse-Graining Applications journal, November 2009

Polarizable Water Model for the Coarse-Grained MARTINI Force Field journal, June 2010

Canonical sampling through velocity rescaling journal, January 2007

Entropic approach to Brownian movement journal, May 1980

Energy transfer within responsive pi-conjugated coassembled peptide-based nanostructures in aqueous environments journal, January 2015

Multiscale modeling of soft matter: scaling of dynamics journal, January 2011

Electrostatic interactions in dissipative particle dynamics—simulation of polyelectrolytes and anionic surfactants journal, June 2003

Coarse Grained Model for Semiquantitative Lipid Simulations journal, January 2004

Mesoscale Simulation of Asphaltene Aggregation journal, August 2016

Graph Theory report, November 1969

VMD: Visual molecular dynamics journal, February 1996

Measuring the strangeness of strange attractors journal, October 1983

Shape of unperturbed linear polymers: polypropylene journal, November 1985

Scaling theory and exactly solved models in the kinetics of irreversible aggregation journal, August 2003

An introduction to mathematical models of coagulation–fragmentation processes: A discrete deterministic mean-field approach journal, October 2006

A survey of numerical solutions to the coagulation equation journal, November 2001

On the Validity of the Coagulation Equation and the Nature of Runaway Growth journal, January 2000

Assembly of Amyloid Protofibrils via Critical Oligomers—A Novel Pathway of Amyloid Formation journal, January 2003

Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth journal, August 2013

An exact solution of the discrete Smoluchowski equation and its correspondence to the solution of the continuous equation journal, July 1990

Singularities in the kinetics of coagulation processes journal, December 1981

Mobility of Coenzyme Q in Membranes book, August 2000

Dynamic Scaling in the Kinetics of Clustering journal, April 1985

One-Dimensional Optoelectronic Nanostructures Derived from the Aqueous Self-Assembly of π-Conjugated Oligopeptides journal, October 2008

The computer study of transport processes under extreme conditions journal, August 1972

Extensional motions of spatially periodic lattices journal, November 1992

Nonlinear-response theory for steady planar Couette flow journal, September 1984

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors journal, August 2011

Interchain Interactions in Organic π-Conjugated Materials: Impact on Electronic Structure, Optical Response, and Charge Transport journal, July 2001

Synthesis of Functionalizable Boron-Containing π-Electron Materials that Incorporate Formally Aromatic Fused Borepin Rings journal, May 2010

Conjugated “ B -Entacenes”: Polycyclic Aromatics Containing Two Borepin Rings journal, June 2011

Computational Approaches to Understanding the Self-assembly of Peptide-based Nanostructures
journal, March 2015

Design of Polymer Scaffolds for Tissue Engineering Applications
journal, February 2015

Self-Assembled Proteins and Peptides for Regenerative Medicine
journal, March 2013

Biomimetic Systems for Hydroxyapatite Mineralization Inspired By Bone and Enamel
journal, November 2008

Self-Assembly and Mineralization of Peptide-Amphiphile Nanofibers
journal, November 2001

Stimulus responsive peptide based materials
journal, January 2010

Designing peptide based nanomaterials
journal, January 2008

Self-Assembled Peptide Amphiphile Nanofibers Conjugated to MRI Contrast Agents
journal, January 2005

Next-generation peptide nanomaterials: molecular networks, interfaces and supramolecular functionality
journal, January 2010

Designing π-conjugated polymers for organic electronics
journal, December 2013

Recent progress in the design of narrow bandgap conjugated polymers for high-efficiency organic solar cells
journal, September 2012

A model for the controlled assembly of semiconductor peptides
journal, January 2012

About Supramolecular Assemblies of π-Conjugated Systems
journal, April 2005

On-resin dimerization incorporates a diverse array of π-conjugated functionality within aqueous self-assembling peptide backbones
journal, January 2010

Supramolecular Polymorphism: Tunable Electronic Interactions within π-Conjugated Peptide Nanostructures Dictated by Primary Amino Acid Sequence
journal, May 2014

Synthesis and characterization of π-conjugated peptide-based supramolecular materials
journal, March 2012

Variation of Formal Hydrogen-Bonding Networks within Electronically Delocalized π-Conjugated Oligopeptide Nanostructures
journal, September 2014

Fluidic-Directed Assembly of Aligned Oligopeptides with π-Conjugated Cores
journal, August 2013

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides
journal, March 2016

Atomic structure and hierarchical assembly of a cross- amyloid fibril
journal, March 2013

The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008

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

Coarse-grained molecular dynamics simulations of membrane proteins and peptides
journal, March 2007

Perspective: Coarse-grained models for biomolecular systems
journal, September 2013

Coarse-grained protein molecular dynamics simulations
journal, January 2007

Coarse-grained models for proteins
journal, April 2005

Global ribosome motions revealed with elastic network model
journal, September 2004

Coarse-Grained Molecular Dynamics Simulations of a Rotating Bacterial Flagellum
journal, December 2006

Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field
journal, March 2010

Simulation of polyethylene glycol and calcium-mediated membrane fusion
journal, March 2014

Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes
journal, June 2013

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes
journal, April 2012

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides
journal, April 2012

Perspective on the Martini model
journal, January 2013

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008

PRODRG : a tool for high-throughput crystallography of protein–ligand complexes
journal, July 2004

Comparison of simple potential functions for simulating liquid water
journal, July 1983

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^†
journal, April 1998

A unified formulation of the constant temperature molecular dynamics methods
journal, July 1984

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

A smooth particle mesh Ewald method
journal, November 1995

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
journal, February 1977

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

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

Calculation of conformational ensembles from potentials of mena force
journal, June 1990

Versatile Object-Oriented Toolkit for Coarse-Graining Applications
journal, November 2009

Polarizable Water Model for the Coarse-Grained MARTINI Force Field
journal, June 2010

Canonical sampling through velocity rescaling
journal, January 2007

Entropic approach to Brownian movement
journal, May 1980

Energy transfer within responsive pi-conjugated coassembled peptide-based nanostructures in aqueous environments
journal, January 2015

Multiscale modeling of soft matter: scaling of dynamics
journal, January 2011

Electrostatic interactions in dissipative particle dynamics—simulation of polyelectrolytes and anionic surfactants
journal, June 2003

Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

Mesoscale Simulation of Asphaltene Aggregation
journal, August 2016

Graph Theory
report, November 1969

VMD: Visual molecular dynamics
journal, February 1996

Measuring the strangeness of strange attractors
journal, October 1983

Shape of unperturbed linear polymers: polypropylene
journal, November 1985

Scaling theory and exactly solved models in the kinetics of irreversible aggregation
journal, August 2003

An introduction to mathematical models of coagulation–fragmentation processes: A discrete deterministic mean-field approach
journal, October 2006

A survey of numerical solutions to the coagulation equation
journal, November 2001

On the Validity of the Coagulation Equation and the Nature of Runaway Growth
journal, January 2000

Assembly of Amyloid Protofibrils via Critical Oligomers—A Novel Pathway of Amyloid Formation
journal, January 2003

Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth
journal, August 2013

An exact solution of the discrete Smoluchowski equation and its correspondence to the solution of the continuous equation
journal, July 1990

Singularities in the kinetics of coagulation processes
journal, December 1981

Mobility of Coenzyme Q in Membranes
book, August 2000

Dynamic Scaling in the Kinetics of Clustering
journal, April 1985

One-Dimensional Optoelectronic Nanostructures Derived from the Aqueous Self-Assembly of π-Conjugated Oligopeptides
journal, October 2008

The computer study of transport processes under extreme conditions
journal, August 1972

Extensional motions of spatially periodic lattices
journal, November 1992

Nonlinear-response theory for steady planar Couette flow
journal, September 1984

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors
journal, August 2011

Interchain Interactions in Organic π-Conjugated Materials: Impact on Electronic Structure, Optical Response, and Charge Transport
journal, July 2001

Synthesis of Functionalizable Boron-Containing π-Electron Materials that Incorporate Formally Aromatic Fused Borepin Rings
journal, May 2010

Conjugated “ B -Entacenes”: Polycyclic Aromatics Containing Two Borepin Rings
journal, June 2011

Transferable coarse-grained MARTINI model for methacrylate-based copolymers
journal, January 2019

Machine learning and molecular design of self-assembling -conjugated oligopeptides
journal, April 2018

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition
journal, January 2018