Synthesis, Characterization, and Simulation of Four-Armed Megamolecules

Shengwang Zhou, Peng He, Sonali Dhindwal, Valerie L. Grum-Tokars, Ying Li, Kelly Parker, Justin A. Modica, Reiner Bleher, Roberto Dos Reis, Joshua Zuchniarz, Vinayak P. Dravid, Gregory A. Voth, Benoît Roux, Milan Mrksich*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule"strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a para-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.

Original languageEnglish (US)
Pages (from-to)2363-2372
Number of pages10
JournalBiomacromolecules
Volume22
Issue number6
DOIs
StatePublished - Jun 14 2021

ASJC Scopus subject areas

  • Bioengineering
  • Biomaterials
  • Polymers and Plastics
  • Materials Chemistry

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