Preferential binding of cytochrome c to anionic ligand-coated gold nanoparticles: A complementary computational and experimental approach

Emily J. Tollefson, Caley R. Allen, Gene Chong, Xi Zhang, Nikita D. Rozanov, Anthony Bautista, Jennifer J. Cerda, Joel A. Pedersen, Catherine J. Murphy, Erin E. Carlson, Rigoberto Hernandez

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

Membrane-bound proteins can play a role in the binding of anionic gold nanoparticles (AuNPs) to model bilayers; however, the mechanism for this binding remains unresolved. In this work, we determine the relative orientation of the peripheral membrane protein cytochrome c in binding to a mercaptopropionic acid-functionalized AuNP (MPA-AuNP). As this is nonrigid binding, traditional methods involving crystallographic or rigid molecular docking techniques are ineffective at resolving the question. Instead, we have implemented a computational assay technique using a cross-correlation of a small ensemble of 200 ns long molecular dynamics trajectories to identify a preferred nonrigid binding orientation or pose of cytochrome c on MPA-AuNPs. We have also employed a mass spectrometry-based footprinting method that enables the characterization of the stable protein corona that forms at long time-scales in solution but remains in a dynamic state. Through the combination of these computational and experimental primary results, we have established a consensus result establishing the identity of the exposed regions of cytochrome c in proximity to MPA-AuNPs and its complementary pose(s) with amino-acid specificity. Moreover, the tandem use of the two methods can be applied broadly to determine the accessibility of membrane-binding sites for peripheral membrane proteins upon adsorption to AuNPs or to determine the exposed amino-acid residues of the hard corona that drive the acquisition of dynamic soft coronas. We anticipate that the combined use of simulation and experimental methods to characterize biomolecule-nanoparticle interactions, as demonstrated here, will become increasingly necessary as the complexity of such target systems grows.

Original languageEnglish (US)
Pages (from-to)6856-6866
Number of pages11
JournalACS nano
Volume13
Issue number6
DOIs
StatePublished - Jun 25 2019

Bibliographical note

Funding Information:
This work was supported by the National Science Foundation (NSF) under the Center for Sustainable Nanotechnology, CHE-1503408. The CSN is part of the Centers for Chemical Innovation Program. The computing resources necessary for this research were provided in part by the NSF through XSEDE resources provided by Comet (TG-CTS090079) and by the Maryland Advanced Research Computing Center (MARCC). E.J.T. would like to thank Dr. LeeAnn Higgins, Todd Markowski, and Dr. Yingchun Zhao for assistance with mass spectrometry and Mike Fealey for assistance with CD analysis.

Funding Information:
This work was supported by the National Science Foundation (NSF) under the Center for Sustainable Nanotechnology, CHE- 1503408. The CSN is part of the Centers for Chemical Innovation Program. The computing resources necessary for this research were provided in part by the NSF through XSEDE resources provided by Comet (TG-CTS090079) and by the Maryland Advanced Research Computing Center (MARCC). E.J.T. would like to thank Dr. LeeAnn Higgins, Todd Markowski, and Dr. Yingchun Zhao for assistance with mass spectrometry and Mike Fealey for assistance with CD analysis.

Publisher Copyright:
Copyright © 2019 American Chemical Society.

Keywords

  • Cytochrome c
  • Gold nanoparticle
  • Lysine modification
  • Mass spectrometry
  • Molecular dynamics simulations
  • Protein footprinting

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