Karrikins (KARs)
are a class of smoke-derived seed germination
stimulants with great significance in both agriculture and plant biology.
By means of direct binding to the receptor protein KAI2, the compounds
can initiate the KAR signal transduction pathway, hence triggering
germination of the dormant seeds in the soil. In the research, several
molecular dynamics (MD) simulation techniques were properly integrated
to investigate the binding process of KAR1 to KAI2 and
reveal the details of the whole binding event. The calculated binding
free energy, −7.00 kcal/mol, is in good agreement with the
experimental measurement, −6.83 kcal/mol. The obtained PMF
profile indicates the existence of three intermediate states in the
binding process. The analysis of the simulation trajectories demonstrates
that, in the intermediate structures, KAR1 is stabilized
by some hydrophobic residues (Phe26, Phe134, Leu142, Trp153, Phe157,
Leu160, Phe194), along with several bridging water molecules, and
meanwhile, the significant shifting occurs in the local conformation
of the protein as the ligand’s binding. A series of the residues
(Gln141–Phe157) on the so-called “cap domain”
are proposed to be responsible for capturing the ligand at the initial
stage of the binding. Besides, the changes of the ligand’s
poses are also quantitatively characterized by the proper choice of
the coordinate system. Our work will contribute to the more penetrating
understanding of the ligand binding process and the receptor affinity
difference between several members in the KAR family and help design
new, more effective germination stimulants.