Modeling of Protein⁻Protein Interactions in Cytokinin Signal Transduction.

Dmitry V Arkhipov,Georgy A Romanov,Sergey N Lomin,Ekaterina M Savelieva,Dmitry I Osolodkin,Yulia A Myakushina

doi:10.3390/ijms20092096

Abstract

The signaling of cytokinins (CKs), classical plant hormones, is based on the interaction of proteins that constitute the multistep phosphorelay system (MSP): catalytic receptors—sensor histidine kinases (HKs), phosphotransmitters (HPts), and transcription factors—response regulators (RRs). Any CK receptor was shown to interact in vivo with any of the studied HPts and vice versa. In addition, both of these proteins tend to form a homodimer or a heterodimeric complex with protein-paralog. Our study was aimed at explaining by molecular modeling the observed features of in planta protein–protein interactions, accompanying CK signaling. For this purpose, models of CK-signaling proteins’ structure from Arabidopsis and potato were built. The modeled interaction interfaces were formed by rather conserved areas of protein surfaces, complementary in hydrophobicity and electrostatic potential. Hot spots amino acids, determining specificity and strength of the interaction, were identified. Virtual phosphorylation of conserved Asp or His residues affected this complementation, increasing (Asp-P in HK) or decreasing (His-P in HPt) the affinity of interacting proteins. The HK–HPt and HPt–HPt interfaces overlapped, sharing some of the hot spots. MSP proteins from Arabidopsis and potato exhibited similar properties. The structural features of the modeled protein complexes were consistent with the experimental data.

Highlights

Cytokinins (CKs) are low molecular weight phytohormones that regulate a plethora of physiological processes in higher plants [1,2] (Figure S1)
We present an in silico investigation of all types of protein–protein interactions involved in CK signaling
The ability of CK receptors to give rise to heterodimers together with homodimers in vivo was consistent with a high conservation of interface residues, especially in the sensor module dimerization interface, and with a high level of complementarity in hydrophobicity and electrostatic potential

Summary

Introduction

Cytokinins (CKs) are low molecular weight phytohormones that regulate a plethora of physiological processes in higher plants [1,2] (Figure S1). Plants use a modified prokaryotic two-component system (TCS), referred to as multistep phosphorelay (MSP), to transduce CK signal (Figure 1). This plant signaling system involves three main types of proteins. The first one is the multi-domain transmembrane CK receptor protein, hybrid sensor histidine kinase (HK). Its extracytosolic part facing the endoplasmic reticulum (ER) lumen or apoplast [3] represents the sensor module (SM), which includes dimerization interface, PAS (Per-Arnt-Sim) and PAS-like domains [4,5]. Transmembrane (TM) regions are represented by two to five α-helical stretches depending on receptor type [5]. The cytosolic part of the receptor includes the catalytic module, which consists of

Methods

Results

Conclusion