1. Synthesis, Characterization, and Simulation of Four-Armed Megamolecules
- Author
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Gregory A. Voth, Valerie Grum-Tokars, Reiner Bleher, Shengwang Zhou, Kelly Parker, Benoît Roux, Justin A. Modica, Peng He, Roberto dos Reis, Vinayak P. Dravid, Milan Mrksich, Ying Li, Joshua Zuchniarz, and Sonali Dhindwal
- Subjects
Cutinase ,Polymers and Plastics ,Organophosphonates ,Bioengineering ,02 engineering and technology ,010402 general chemistry ,Crystallography, X-Ray ,01 natural sciences ,Biomaterials ,chemistry.chemical_compound ,Molecular dynamics ,Protein Domains ,Catalytic Domain ,Materials Chemistry ,Molecule ,biology ,Molecular Structure ,Chemistry ,Active site ,Serine hydrolase ,021001 nanoscience & nanotechnology ,Phosphonate ,0104 chemical sciences ,Crystallography ,Covalent bond ,biology.protein ,0210 nano-technology ,Linker - 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.
- Published
- 2021