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Title: Evidence for cis Amide Bonds in Peptoid Nanosheets

Abstract

Peptoid nanosheets are supramolecular protein-mimetic materials that form from amphiphilic polypeptoids with aromatic and ionic side chains. Nanosheets have been studied at the nanometer scale, but the molecular structure has been difficult to probe. We introduce the use of 13C-13C dipolar recoupling solid-state NMR measurements to reveal the configuration of backbone amide bonds selected by 13C isotopic labeling of adjacent α-carbons. Measurements on the same molecules in the amorphous state and in nanosheets revealed that amide bonds in the center of the amino block of peptoid (NaeNpe)7-(NceNpe)7(B28) favor the trans configuration in the amorphous state and the cis configuration in the nanosheet. This unexpected conclusion contrasts with previous NMR and theoretical studies of short solvated peptoids. Moreover, examination of the amide bond at the junction of the two charged blocks within B28 revealed a mixture of both cis and trans configurational states, consistent with the previously predicted brickwork-like intermolecular organization.

Authors:
 [1];  [2];  [2];  [2]; ORCiD logo [2];  [2]; ORCiD logo [2]; ORCiD logo [1]
  1. Georgia Inst. of Technology, Atlanta, GA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); Defense Threat Reduction Agency (DTRA); Georgia Inst. of Technology
OSTI Identifier:
1515161
Grant/Contract Number:  
AC02-05CH11231; DTRA10027-15875
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry Letters
Additional Journal Information:
Journal Volume: 9; Journal Issue: 10; Journal ID: ISSN 1948-7185
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Hudson, Benjamin C., Battigelli, Alessia, Connolly, Michael D., Edison, John, Spencer, Ryan K., Whitelam, Stephen, Zuckermann, Ronald N., and Paravastu, Anant K. Evidence for cis Amide Bonds in Peptoid Nanosheets. United States: N. p., 2018. Web. doi:10.1021/acs.jpclett.8b01040.
Hudson, Benjamin C., Battigelli, Alessia, Connolly, Michael D., Edison, John, Spencer, Ryan K., Whitelam, Stephen, Zuckermann, Ronald N., & Paravastu, Anant K. Evidence for cis Amide Bonds in Peptoid Nanosheets. United States. https://doi.org/10.1021/acs.jpclett.8b01040
Hudson, Benjamin C., Battigelli, Alessia, Connolly, Michael D., Edison, John, Spencer, Ryan K., Whitelam, Stephen, Zuckermann, Ronald N., and Paravastu, Anant K. Mon . "Evidence for cis Amide Bonds in Peptoid Nanosheets". United States. https://doi.org/10.1021/acs.jpclett.8b01040. https://www.osti.gov/servlets/purl/1515161.
@article{osti_1515161,
title = {Evidence for cis Amide Bonds in Peptoid Nanosheets},
author = {Hudson, Benjamin C. and Battigelli, Alessia and Connolly, Michael D. and Edison, John and Spencer, Ryan K. and Whitelam, Stephen and Zuckermann, Ronald N. and Paravastu, Anant K.},
abstractNote = {Peptoid nanosheets are supramolecular protein-mimetic materials that form from amphiphilic polypeptoids with aromatic and ionic side chains. Nanosheets have been studied at the nanometer scale, but the molecular structure has been difficult to probe. We introduce the use of 13C-13C dipolar recoupling solid-state NMR measurements to reveal the configuration of backbone amide bonds selected by 13C isotopic labeling of adjacent α-carbons. Measurements on the same molecules in the amorphous state and in nanosheets revealed that amide bonds in the center of the amino block of peptoid (NaeNpe)7-(NceNpe)7(B28) favor the trans configuration in the amorphous state and the cis configuration in the nanosheet. This unexpected conclusion contrasts with previous NMR and theoretical studies of short solvated peptoids. Moreover, examination of the amide bond at the junction of the two charged blocks within B28 revealed a mixture of both cis and trans configurational states, consistent with the previously predicted brickwork-like intermolecular organization.},
doi = {10.1021/acs.jpclett.8b01040},
journal = {Journal of Physical Chemistry Letters},
number = 10,
volume = 9,
place = {United States},
year = {2018},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 11 works
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Figures / Tables:

Figure 1 Figure 1: A) and B) Planar representations of a backbone peptoid amide bond in the cis and trans configurations, respectively. C) Primary structure of peptoid B28 with the positively charged amino block colored in blue and the negatively charged carboxylic acid block colored in red.

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Works referenced in this record:

Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers
journal, April 2010

  • Nam, Ki Tae; Shelby, Sarah A.; Choi, Philip H.
  • Nature Materials, Vol. 9, Issue 5
  • DOI: 10.1038/nmat2742

Simple, Helical Peptoid Analogs of Lung Surfactant Protein B
journal, January 2005


Helical Peptoid Mimics of Lung Surfactant Protein C
journal, November 2003


Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets
journal, January 2016

  • Robertson, Ellen J.; Battigelli, Alessia; Proulx, Caroline
  • Accounts of Chemical Research, Vol. 49, Issue 3
  • DOI: 10.1021/acs.accounts.5b00439

Sequence Programmable Peptoid Polymers for Diverse Materials Applications
journal, April 2015

  • Knight, Abigail S.; Zhou, Effie Y.; Francis, Matthew B.
  • Advanced Materials, Vol. 27, Issue 38
  • DOI: 10.1002/adma.201500275

Development and use of an atomistic CHARMM-based forcefield for peptoid simulation
journal, November 2013

  • Mirijanian, Dina T.; Mannige, Ranjan V.; Zuckermann, Ronald N.
  • Journal of Computational Chemistry, Vol. 35, Issue 5
  • DOI: 10.1002/jcc.23478

Kinetics and Equilibria of Cis/Trans Isomerization of Backbone Amide Bonds in Peptoids
journal, October 2007

  • Sui, Qiang; Borchardt, Dan; Rabenstein, Dallas L.
  • Journal of the American Chemical Society, Vol. 129, Issue 39
  • DOI: 10.1021/ja0740925

Symmetry-based constant-time homonuclear dipolar recoupling in solid state NMR
journal, February 2007

  • Tycko, Robert
  • The Journal of Chemical Physics, Vol. 126, Issue 6
  • DOI: 10.1063/1.2437194

Peptoid nanosheets exhibit a new secondary-structure motif
journal, October 2015

  • Mannige, Ranjan V.; Haxton, Thomas K.; Proulx, Caroline
  • Nature, Vol. 526, Issue 7573
  • DOI: 10.1038/nature15363

Molecular Structure of RADA16-I Designer Self-Assembling Peptide Nanofibers
journal, August 2013

  • Cormier, Ashley R.; Pang, Xiaodong; Zimmerman, Maxwell I.
  • ACS Nano, Vol. 7, Issue 9
  • DOI: 10.1021/nn401562f

Polymorphism in Alzheimer Aβ Amyloid Organization Reflects Conformational Selection in a Rugged Energy Landscape
journal, August 2010

  • Miller, Yifat; Ma, Buyong; Nussinov, Ruth
  • Chemical Reviews, Vol. 110, Issue 8
  • DOI: 10.1021/cr900377t

Molecular Structures of Amyloid and Prion Fibrils: Consensus versus Controversy
journal, January 2013

  • Tycko, Robert; Wickner, Reed B.
  • Accounts of Chemical Research, Vol. 46, Issue 7
  • DOI: 10.1021/ar300282r

Self-Assembled Oligoanilinic Nanosheets: Molecular Structure Revealed by Solid-State NMR Spectroscopy
journal, November 2015


Structure elucidation of a complex CO 2 -based organic framework material by NMR crystallography
journal, January 2016

  • Leclaire, Julien; Poisson, Guillaume; Ziarelli, Fabio
  • Chemical Science, Vol. 7, Issue 7
  • DOI: 10.1039/C5SC03810C

High Field Solid-State NMR Spectroscopy Investigation of 15 N-Labeled Rosette Nanotubes: Hydrogen Bond Network and Channel-Bound Water
journal, May 2016

  • Fenniri, Hicham; Tikhomirov, Grigory A.; Brouwer, Darren H.
  • Journal of the American Chemical Society, Vol. 138, Issue 19
  • DOI: 10.1021/jacs.6b02420

Folding of xylan onto cellulose fibrils in plant cell walls revealed by solid-state NMR
journal, December 2016

  • Simmons, Thomas J.; Mortimer, Jenny C.; Bernardinelli, Oigres D.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13902

Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State
journal, December 2016

  • Reddy, G. N. Manjunatha; Huqi, Aida; Iuga, Dinu
  • Chemistry - A European Journal, Vol. 23, Issue 10
  • DOI: 10.1002/chem.201604832

Recoupling of Heteronuclear Dipolar Interactions with Rotational-Echo Double-Resonance at High Magic-Angle Spinning Frequencies
journal, September 2000

  • Jaroniec, Christopher P.; Tounge, Brett A.; Rienstra, Chad M.
  • Journal of Magnetic Resonance, Vol. 146, Issue 1
  • DOI: 10.1006/jmre.2000.2128

SPINEVOLUTION: A powerful tool for the simulation of solid and liquid state NMR experiments
journal, February 2006


Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions
journal, May 2018

  • Edison, John R.; Spencer, Ryan K.; Butterfoss, Glenn L.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 22
  • DOI: 10.1073/pnas.1800397115

Works referencing / citing this record:

Recent advances in crystallization and self‐assembly of polypeptoid polymers
journal, June 2019

  • Zeng, Guangjian; Qiu, Lu; Wen, Tao
  • POLYMER CRYSTALLIZATION, Vol. 2, Issue 3
  • DOI: 10.1002/pcr2.10065

A bio-inspired approach to ligand design: folding single-chain peptoids to chelate a multimetallic cluster
journal, January 2018

  • Nguyen, Andy I.; Spencer, Ryan K.; Anderson, Christopher L.
  • Chemical Science, Vol. 9, Issue 47
  • DOI: 10.1039/c8sc04240c

Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions
journal, May 2018

  • Edison, John R.; Spencer, Ryan K.; Butterfoss, Glenn L.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 22
  • DOI: 10.1073/pnas.1800397115

Crystallization and lamellar nanosheet formation of an aromatic dipeptoid
journal, January 2019

  • Castelletto, Valeria; Chippindale, Ann M.; Hamley, Ian W.
  • Chemical Communications, Vol. 55, Issue 42
  • DOI: 10.1039/c9cc02335f

Design and preparation of organic nanomaterials using self‐assembled peptoids
journal, February 2019


Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution
journal, March 2019

  • Roe, Leah T.; Pelton, Jeffrey G.; Edison, John R.
  • Biopolymers, Vol. 110, Issue 6
  • DOI: 10.1002/bip.23267

Stereochemistry of polypeptoid chain configurations
journal, March 2019

  • Spencer, Ryan K.; Butterfoss, Glenn L.; Edison, John R.
  • Biopolymers, Vol. 110, Issue 6
  • DOI: 10.1002/bip.23266

Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.