All-atom numerical studies of self-assembly of zwitterionic peptide amphiphiles

Stefan Tsonchev, Alessandro Troisi, George C Schatz, Mark A Ratner

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4×4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure exhibits the tendency to curve around an axis parallel to the direction of the dipoles and the hydrogen bonds, forming a cylindrical micelle.

Original languageEnglish
Pages (from-to)15278-15284
Number of pages7
JournalJournal of Physical Chemistry B
Volume108
Issue number39
DOIs
Publication statusPublished - Sep 30 2004

Fingerprint

Amphiphiles
Self assembly
Peptides
peptides
self assembly
Hydrogen bonds
dipoles
Atoms
Periodic structures
Micelles
Macromolecules
hydrogen bonds
atoms
Molecular dynamics
Boundary conditions
macromolecules
assemblies
field theory (physics)
Molecules
Water

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

All-atom numerical studies of self-assembly of zwitterionic peptide amphiphiles. / Tsonchev, Stefan; Troisi, Alessandro; Schatz, George C; Ratner, Mark A.

In: Journal of Physical Chemistry B, Vol. 108, No. 39, 30.09.2004, p. 15278-15284.

Research output: Contribution to journalArticle

@article{c2d5195785b3471798efc0c3b420f4cb,
title = "All-atom numerical studies of self-assembly of zwitterionic peptide amphiphiles",
abstract = "We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4×4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure exhibits the tendency to curve around an axis parallel to the direction of the dipoles and the hydrogen bonds, forming a cylindrical micelle.",
author = "Stefan Tsonchev and Alessandro Troisi and Schatz, {George C} and Ratner, {Mark A}",
year = "2004",
month = "9",
day = "30",
doi = "10.1021/jp047880e",
language = "English",
volume = "108",
pages = "15278--15284",
journal = "Journal of Physical Chemistry B",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "39",

}

TY - JOUR

T1 - All-atom numerical studies of self-assembly of zwitterionic peptide amphiphiles

AU - Tsonchev, Stefan

AU - Troisi, Alessandro

AU - Schatz, George C

AU - Ratner, Mark A

PY - 2004/9/30

Y1 - 2004/9/30

N2 - We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4×4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure exhibits the tendency to curve around an axis parallel to the direction of the dipoles and the hydrogen bonds, forming a cylindrical micelle.

AB - We present an approach to study the self-assembly of organic macromolecules, based on all-atom empirical force field calculations. The approach is applied to self-assemblies of zwitterionic peptide amphiphiles possessing large dipoles in their hydrophilic headgroups. The assembly is built from the bottom up by first optimizing the diad amphiphile, which is then used as a basic unit to subsequently first build quartets, and then 4×4 supercells of molecules to be studied in periodic boundary conditions. Explicit water solvent is added to the surface of the periodic structures and molecular dynamics simulations are performed on them. The calculations reveal an interesting structure of the resulting assemblies: the dipoles in the upper parts of the headgroups are aligned in an antiparallel fashion with respect to each other and along one of the periodic axes, while hydrogen bonds in the lower, rigid parts of the headgroups form a parallel beta sheet along the same direction. It is shown that the structure exhibits the tendency to curve around an axis parallel to the direction of the dipoles and the hydrogen bonds, forming a cylindrical micelle.

UR - http://www.scopus.com/inward/record.url?scp=6344258878&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=6344258878&partnerID=8YFLogxK

U2 - 10.1021/jp047880e

DO - 10.1021/jp047880e

M3 - Article

VL - 108

SP - 15278

EP - 15284

JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

SN - 1520-6106

IS - 39

ER -