DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Resolving the Morphology of Peptoid Vesicles at the 1 nm Length Scale Using Cryogenic Electron Microscopy

Abstract

Vesicle formation in a series of amphiphilic sequence-defined polypeptoid block co-polymers comprising a phosphonated hydrophilic block and an amorphous hydrophobic block, poly-N-(2-ethyl)hexylglycine-block-poly-N-phosphonomethylglycine (pNeh-b-pNpm), is studied. The hydrophobic/hydrophilic block ratio was varied keeping the total chain length of the co-polymers constant. A new approach for characterizing the vesicle membrane morphology based on low-dose cryogenic electron microscopy (cryo-EM) is described. The individual low-dose micrographs cannot be interpreted directly due to low signal-to-noise ratio. Sorting and averaging techniques, developed in the context of protein structure determination, were thus applied to vesicle micrographs. Molecular dynamic simulations of the vesicles were used to establish the relationship between membrane morphology and averaged cryo-EM images. This approach enables resolution of the local thickness of the hydrophobic membrane core at the 1 nm length scale. The thickness of the hydrophobic core of the pNeh-b-pNpm membranes increases linearly with the length of the hydrophobic block.

Authors:
ORCiD logo; ; ORCiD logo [1]; ; ORCiD logo; ORCiD logo; ORCiD logo [2]
  1. Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department, School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
  2. Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
Publication Date:
Research Org.:
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1492105
Alternate Identifier(s):
OSTI ID: 1508807; OSTI ID: 1594906
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Name: Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry Journal Volume: 123 Journal Issue: 5; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE

Citation Formats

Jiang, Xi, Spencer, Ryan K., Sun, Jing, Ophus, Colin, Zuckermann, Ronald N., Downing, Kenneth H., and Balsara, Nitash P. Resolving the Morphology of Peptoid Vesicles at the 1 nm Length Scale Using Cryogenic Electron Microscopy. United States: N. p., 2019. Web. doi:10.1021/acs.jpcb.8b11752.
Jiang, Xi, Spencer, Ryan K., Sun, Jing, Ophus, Colin, Zuckermann, Ronald N., Downing, Kenneth H., & Balsara, Nitash P. Resolving the Morphology of Peptoid Vesicles at the 1 nm Length Scale Using Cryogenic Electron Microscopy. United States. https://doi.org/10.1021/acs.jpcb.8b11752
Jiang, Xi, Spencer, Ryan K., Sun, Jing, Ophus, Colin, Zuckermann, Ronald N., Downing, Kenneth H., and Balsara, Nitash P. Thu . "Resolving the Morphology of Peptoid Vesicles at the 1 nm Length Scale Using Cryogenic Electron Microscopy". United States. https://doi.org/10.1021/acs.jpcb.8b11752.
@article{osti_1492105,
title = {Resolving the Morphology of Peptoid Vesicles at the 1 nm Length Scale Using Cryogenic Electron Microscopy},
author = {Jiang, Xi and Spencer, Ryan K. and Sun, Jing and Ophus, Colin and Zuckermann, Ronald N. and Downing, Kenneth H. and Balsara, Nitash P.},
abstractNote = {Vesicle formation in a series of amphiphilic sequence-defined polypeptoid block co-polymers comprising a phosphonated hydrophilic block and an amorphous hydrophobic block, poly-N-(2-ethyl)hexylglycine-block-poly-N-phosphonomethylglycine (pNeh-b-pNpm), is studied. The hydrophobic/hydrophilic block ratio was varied keeping the total chain length of the co-polymers constant. A new approach for characterizing the vesicle membrane morphology based on low-dose cryogenic electron microscopy (cryo-EM) is described. The individual low-dose micrographs cannot be interpreted directly due to low signal-to-noise ratio. Sorting and averaging techniques, developed in the context of protein structure determination, were thus applied to vesicle micrographs. Molecular dynamic simulations of the vesicles were used to establish the relationship between membrane morphology and averaged cryo-EM images. This approach enables resolution of the local thickness of the hydrophobic membrane core at the 1 nm length scale. The thickness of the hydrophobic core of the pNeh-b-pNpm membranes increases linearly with the length of the hydrophobic block.},
doi = {10.1021/acs.jpcb.8b11752},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 5,
volume = 123,
place = {United States},
year = {2019},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/acs.jpcb.8b11752

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

Table 1 Table 1: Characteristics of the Diblock Polypeptoids pNehm-b-pNpmn

Save / Share:

Works referenced in this record:

Optical changes in unilamellar vesicles experiencing osmotic stress
journal, November 1996


Polymersome Shape Transformation at the Nanoscale
journal, September 2013

  • Salva, Romain; Le Meins, Jean-François; Sandre, Olivier
  • ACS Nano, Vol. 7, Issue 10
  • DOI: 10.1021/nn4039589

Morphology and Proton Transport in Humidified Phosphonated Peptoid Block Copolymers
journal, April 2016


Using cryo-EM to measure the dipole potential of a lipid membrane
journal, November 2006

  • Wang, L.; Bose, P. S.; Sigworth, F. J.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 49
  • DOI: 10.1073/pnas.0608714103

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

Bilayers and Interdigitation in Block Copolymer Vesicles
journal, June 2005

  • Battaglia, Giuseppe; Ryan, Anthony J.
  • Journal of the American Chemical Society, Vol. 127, Issue 24
  • DOI: 10.1021/ja050742y

Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles
journal, March 2016

  • Sun, Jing; Jiang, Xi; Lund, Reidar
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 15
  • DOI: 10.1073/pnas.1517169113

Effect of Block Length, Polydispersity, and Salt Concentration on PEO−PDEAMA Block Copolymer Structures in Dilute Solution
journal, May 2006

  • Adams, Dave J.; Butler, Michael F.; Weaver, Anthony C.
  • Langmuir, Vol. 22, Issue 10
  • DOI: 10.1021/la060192x

Bilayer thickness and lipid interface area in unilamellar extruded 1,2-diacylphosphatidylcholine liposomes: a small-angle neutron scattering study
journal, May 2001

  • Balgavý, Pavol; Dubničková, Martina; Kučerka, Norbert
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1512, Issue 1
  • DOI: 10.1016/S0005-2736(01)00298-X

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289

Crystallization in Sequence-Defined Peptoid Diblock Copolymers Induced by Microphase Separation
journal, January 2014

  • Sun, Jing; Teran, Alexander A.; Liao, Xunxun
  • Journal of the American Chemical Society, Vol. 136, Issue 5
  • DOI: 10.1021/ja412123y

Universal Relationship between Molecular Structure and Crystal Structure in Peptoid Polymers and Prevalence of the cis Backbone Conformation
journal, January 2018

  • Greer, Douglas R.; Stolberg, Michael A.; Kundu, Joyjit
  • Journal of the American Chemical Society, Vol. 140, Issue 2
  • DOI: 10.1021/jacs.7b11891

Polymersomes: Tough Vesicles Made from Diblock Copolymers
journal, May 1999


Effect of Polydispersity on the Self-Assembly Structure of Diblock Copolymers under Various Confined States: A Monte Carlo Study
journal, July 2008

  • Han, Yuanyuan; Cui, Jie; Jiang, Wei
  • Macromolecules, Vol. 41, Issue 16
  • DOI: 10.1021/ma800702f

Emerging applications of polymersomes in delivery: From molecular dynamics to shrinkage of tumors
journal, August 2007


Polymer Vesicles
journal, August 2002


Polymersomes for drug delivery: Design, formation and characterization
journal, July 2012


Effect of Bilayer Thickness on Membrane Bending Rigidity
journal, February 2004

  • Bermúdez, H.; Hammer, D. A.; Discher, D. E.
  • Langmuir, Vol. 20, Issue 3
  • DOI: 10.1021/la035497f

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

Direct Observation of Shear-Induced Structures in Wormlike Micellar Solutions by Freeze-Fracture Electron Microscopy
journal, March 1998


MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
journal, February 2017

  • Zheng, Shawn Q.; Palovcak, Eugene; Armache, Jean-Paul
  • Nature Methods, Vol. 14, Issue 4
  • DOI: 10.1038/nmeth.4193

Modulation of the bilayer thickness of exocytic pathway membranes by membrane proteins rather than cholesterol
journal, March 2004

  • Mitra, K.; Ubarretxena-Belandia, I.; Taguchi, T.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 12
  • DOI: 10.1073/pnas.0307332101

Electron microscopy of the stacked disk aggregate of tobacco mosaic virus protein
journal, August 1974


Cryogenic Transmission Electron Microscopy Imaging of Vesicles Formed by a Polystyrene−Polyisoprene Diblock Copolymer
journal, August 2005

  • Kesselman, Ellina; Talmon, Yeshayahu; Bang, Joona
  • Macromolecules, Vol. 38, Issue 16
  • DOI: 10.1021/ma0510587

Effects of Polydispersity on Phase Behavior of Diblock Copolymers
journal, September 2006

  • Cooke, David M.; Shi, An-Chang
  • Macromolecules, Vol. 39, Issue 19
  • DOI: 10.1021/ma060717s

Nanostructure of Complexes Between Cationic Lipids and an Oppositely Charged Polyelectrolyte
journal, January 2012


Gctf: Real-time CTF determination and correction
journal, January 2016


Self-Assembly of β-Cyclodextrin in Water. Part 1:  Cryo-TEM and Dynamic and Static Light Scattering
journal, February 2006

  • Bonini, Massimo; Rossi, Simona; Karlsson, Göran
  • Langmuir, Vol. 22, Issue 4
  • DOI: 10.1021/la052878f

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data
journal, September 2008


Small-angle neutron scattering study of the lipid bilayer thickness in unilamellar dioleoylphosphatidylcholine vesicles prepared by the cholate dilution method: n-decane effect
journal, April 2003

  • Uhrı́ková, Daniela; Kučerka, Norbert; Islamov, Akhmed
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1611, Issue 1-2
  • DOI: 10.1016/S0005-2736(02)00705-8

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

Direct Observation of a Defect-Mediated Viscoelastic Transition in a Hydrogel of Lipid Membranes and Polymer Lipids
journal, June 1997


Polymersomes from Amphiphilic Glycopolymers Containing Polymeric Liquid Crystal Grafts
journal, September 2015


Preirradiation and minimum beam microscopy of periodic biological specimens
journal, August 1978

  • Baker, Timothy S.
  • Proceedings, annual meeting, Electron Microscopy Society of America, Vol. 36, Issue 2
  • DOI: 10.1017/S0424820100080870

Cryogenic Transmission Electron Microscopy (Cryo-TEM) of Micelles and Vesicles Formed in Water by Poly(ethylene oxide)-Based Block Copolymers
journal, April 2002

  • Won, You-Yeon; Brannan, Aaron K.; Davis, H. Ted
  • The Journal of Physical Chemistry B, Vol. 106, Issue 13
  • DOI: 10.1021/jp013639d

ABCA Tetrablock Copolymer Vesicles
journal, November 2004

  • Brannan, Aaron K.; Bates, Frank S.
  • Macromolecules, Vol. 37, Issue 24
  • DOI: 10.1021/ma048858m

A Bayesian View on Cryo-EM Structure Determination
journal, January 2012


Advanced Computing in Electron Microscopy
book, January 2010


Effect of Polydispersity on the Formation of Vesicles from Amphiphilic Diblock Copolymers
journal, July 2005

  • Jiang, Ying; Chen, Tao; Ye, Fangwei
  • Macromolecules, Vol. 38, Issue 15
  • DOI: 10.1021/ma050424j

RELION: Implementation of a Bayesian approach to cryo-EM structure determination
journal, December 2012


Cryo transmission electron microscopy of liposomes and related structures
journal, November 2000

  • Almgren, Mats; Edwards, Katarina; Karlsson, Göran
  • Colloids and Surfaces A: Physicochemical and Engineering Aspects, Vol. 174, Issue 1-2
  • DOI: 10.1016/S0927-7757(00)00516-1

Selecting analytical tools for characterization of polymersomes in aqueous solution
journal, January 2015

  • Habel, Joachim; Ogbonna, Anayo; Larsen, Nanna
  • RSC Advances, Vol. 5, Issue 97
  • DOI: 10.1039/C5RA16403F

Bilayer Membrane Permeability of Ionic Liquid-Filled Block Copolymer Vesicles in Aqueous Solution
journal, July 2012

  • Bai, Zhifeng; Zhao, Bin; Lodge, Timothy P.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 28
  • DOI: 10.1021/jp3033098

Stacking in lipid vesicle-tubulin mixtures is an artifact of negative staining
journal, September 1980


Invited Review Article: Methods for imaging weak-phase objects in electron microscopy
journal, November 2013

  • Glaeser, Robert M.
  • Review of Scientific Instruments, Vol. 84, Issue 11
  • DOI: 10.1063/1.4830355

Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics
journal, August 2004

  • Srinivas, Goundla; Discher, Dennis E.; Klein, Michael L.
  • Nature Materials, Vol. 3, Issue 9
  • DOI: 10.1038/nmat1185

Negative staining and cryo-negative staining of macromolecules and viruses for TEM
journal, February 2011


Cross-linking of Phospholipid Membranes is a Conserved Property of Calcium-sensitive Synaptotagmins
journal, June 2008

  • Connell, Emma; Giniatullina, Asiya; Lai-Kee-Him, Joséphine
  • Journal of Molecular Biology, Vol. 380, Issue 1
  • DOI: 10.1016/j.jmb.2008.01.084

Cryo-electron tomography of nanoparticle transmigration into liposome
journal, December 2009

  • Le Bihan, Olivier; Bonnafous, Pierre; Marak, Laszlo
  • Journal of Structural Biology, Vol. 168, Issue 3
  • DOI: 10.1016/j.jsb.2009.07.006

Theory of Polydisperse Inhomogeneous Polymers
journal, July 2003

  • Fredrickson, Glenn H.; Sides, Scott W.
  • Macromolecules, Vol. 36, Issue 14
  • DOI: 10.1021/ma034082y

Simulation of transmission electron microscope images of biological specimens: SIMULATION OF TEM IMAGES OF BIOLOGICAL SPECIMENS
journal, June 2011


Cross-linked Polymersome Membranes:  Vesicles with Broadly Adjustable Properties
journal, March 2002

  • Discher, Bohdana M.; Bermudez, Harry; Hammer, Daniel A.
  • The Journal of Physical Chemistry B, Vol. 106, Issue 11
  • DOI: 10.1021/jp011958z

Electron cryotomography of vitrified cells with a Volta phase plate
journal, May 2015

  • Fukuda, Yoshiyuki; Laugks, Ulrike; Lučić, Vladan
  • Journal of Structural Biology, Vol. 190, Issue 2
  • DOI: 10.1016/j.jsb.2015.03.004

Polymersomes hydrophilic brush scaling relations
journal, January 2009

  • Smart, Thomas P.; Mykhaylyk, Oleksandr O.; Ryan, Anthony J.
  • Soft Matter, Vol. 5, Issue 19
  • DOI: 10.1039/b908731a

Laterally Nanostructured Vesicles, Polygonal Bilayer Sheets, and Segmented Wormlike Micelles
journal, June 2006

  • Li, Zhibo; Hillmyer, Marc A.; Lodge, Timothy P.
  • Nano Letters, Vol. 6, Issue 6
  • DOI: 10.1021/nl0608700

Molecular Weight Dependence of Polymersome Membrane Structure, Elasticity, and Stability
journal, October 2002

  • Bermudez, Harry; Brannan, Aaron K.; Hammer, Daniel A.
  • Macromolecules, Vol. 35, Issue 21
  • DOI: 10.1021/ma020669l

Liposomal drug delivery systems: From concept to clinical applications
journal, January 2013


Small Angle Scattering and Zeta Potential of Liposomes Loaded with Octa(carboranyl)porphyrazine
journal, August 2007

  • Salvati, Anna; Ristori, Sandra; Oberdisse, Julian
  • The Journal of Physical Chemistry B, Vol. 111, Issue 35
  • DOI: 10.1021/jp0731710

VMD: Visual molecular dynamics
journal, February 1996


Cryo-electron microscopy of artificial biological membranes
journal, November 1985

  • Lepault, Jean; Pattus, Franc; Martin, Nadine
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 820, Issue 2
  • DOI: 10.1016/0005-2736(85)90126-9

Vesicle Membrane Thickness in Aqueous Dispersions of Block Copolymer Blends
journal, October 2008

  • Davis, Kevin P.; Lodge, Timothy P.; Bates, Frank S.
  • Macromolecules, Vol. 41, Issue 22
  • DOI: 10.1021/ma801902z

Heterogeneous MAC Initiator and Pore Structures in a Lipid Bilayer by Phase-Plate Cryo-electron Tomography
journal, April 2016