Title: Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1

Abstract

DORN1 (also known as P2K1) is a plant receptor for extracellular ATP, which belongs to a large gene family of legume-type (L-type) lectin receptor kinases. Extracellular ATP binds to DORN1 with strong affinity through its lectin domain, and the binding triggers a variety of intracellular activities in response to biotic and abiotic stresses. However, information on the tertiary structure of the ligand binding site of DORN1is lacking, which hampers efforts to fully elucidate the mechanism of receptor action. Available data of the crystal structures from more than 50 L-type lectins enable us to perform an in silico study of molecular interaction between DORN1 and ATP. In this study, we employed a computational approach to develop a tertiary structure model of the DORN1 lectin domain. A blind docking analysis demonstrated that ATP binds to a cavity made by four loops (defined as loops A B, C and D) of the DORN1 lectin domain with high affinity. In silico target docking of ATP to the DORN1 binding site predicted interaction with 12 residues, located on the four loops, via hydrogen bonds and hydrophobic interactions. The ATP binding pocket is structurally similar in location to the carbohydrate binding pocket of the canonical L-typemore » lectins. However, four of the residues predicted to interact with ATP are not conserved between DORN1 and the other carbohydrate-binding lectins, suggesting that diversifying selection acting on these key residues may have led to the ATP binding activity of DORN1. Finally, the in silico model was validated by in vitro ATP binding assays using the purified extracellular lectin domain of wild-type DORN1, as well as mutated DORN1 lacking key ATP binding residues.« less

Authors:

Nguyen, Cuong The ;

• Search DOE PAGES for author "Nguyen, Cuong The"
• Search DOE PAGES for ORCID "0000-0002-8700-9598"

Tanaka, Kiwamu ;

• Search DOE PAGES for author "Tanaka, Kiwamu"
• Search DOE PAGES for ORCID "0000-0001-5045-560X"

Cao, Yangrong; Cho, Sung-Hwan; Xu, Dong; Stacey, Gary

Publication Date:

Thu Sep 01 00:00:00 EDT 2016

Research Org.:

Univ. of Missouri, Columbia, MO (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Rural Development Administration, Republic of Korea

OSTI Identifier:

1346609

Alternate Identifier(s):

OSTI ID: 1393423

Grant/Contract Number:  

FG02-08ER15309; FG02-02ER15309

Resource Type:

Published Article

Journal Name:

PLoS ONE

Additional Journal Information:

Journal Name: PLoS ONE Journal Volume: 11 Journal Issue: 9; Journal ID: ISSN 1932-6203

Publisher:

Public Library of Science

Country of Publication:

United States

Language:

English

Subject:

60 APPLIED LIFE SCIENCES; Lectins; Sequence alignment; Crystal Structure; Multiple alignment calculation; sequence databases; carbohydrates; binding analysis; sequence similarity searching