Home
Resources
Publications
Structure-based Design and Application of a Nucleotide Coenzyme Mimetic Ligand: Application to the Affinity Purification of Nucleotide Dependent Enzymes

Structure-based Design and Application of a Nucleotide Coenzyme Mimetic Ligand: Application to the Affinity Purification of Nucleotide Dependent Enzymes

Marigianna Marinou, Dimitrios Platis, Farid S Ataya, Evangelia Chronopoulou, Dimitrios Vlachakis, Nikolaos E Labrou

J Chromatogr A. 2018 Feb 2;1535:88-100.

PMID: 29331223

Abstract:

In the present study, a structure-based approach was exploited for the in silico design of a nucleotide coenzyme mimetic ligand. The enzyme formate dehydrogenase (FDH) was employed as a model in our study. The biomimetic ligand was designed and synthesized based on a tryptamine/3-aminopropylphosphonic acid bi-substituted 1,3,5-triazine (Trz) scaffold (Tra-Trz-3APP), which potentially mimics the interactions of NAD+-FDH complex. Molecular docking studies of the biomimetic ligand predicted that it can occupy the same binding site as the natural coenzyme. Molecular modeling and dynamics simulations revealed that the ligand binds in an energetically more stable pose in the FDH binding site, as it adopts a more twisty conformation, compared to the natural coenzyme. Study of the FDH/Tra-Trz-3APP-Sepharose interaction, through adsorption equilibrium studies and site-directed mutagenesis of selected FDH coenzyme binding residues, provided additional experimental evidences of the specificity of the interaction. The Tra-Trz-3APP-Sepharose biomimetic adsorbent was further evaluated towards a range of different dehydrogenases and was exploited for the development of a single-step purification protocol for FDH. The protocol afforded enzyme with high yield and purity, suitable for analytical and industrial purposes.

Chemicals Related in the Paper:

Catalog Number	Product Name	Structure	CAS Number	Price
AP13138335	3-Aminopropylphosphonic acid		13138-33-5	Price

As a specialist in analytical chemical Products, Alfa Chemistry offers consumers a wealth of raw materials and a full range of technologies and services.

QUICK LINKS

HEADQUARTERS

Tel:

Fax:

Email: