posted on 2021-01-15, 03:29authored byMaohua Yang, Yegen Tang, Jingwei Weng, Zhijun Liu, Wenning Wang
The d-glucose/d-galactose-binding protein (GGBP)
from Escherichia coli is a substrate-binding
protein (SBP) associated with sugar transport and chemotaxis. It is
also a calcium-binding protein, which makes it unique in the SBP family.
However, the functional importance of Ca2+ binding is not
fully understood. Here, the calcium-dependent properties of GGBP were
explored by all-atom molecular dynamics simulations and Markov state
model (MSM) analysis as well as single-molecule Förster resonance
energy transfer (smFRET) measurements. In agreement with previous
experimental studies, we observed the structure stabilization effect
of Ca2+ binding on the C-terminal domain of GGBP, especially
the Ca2+-binding site. Interestingly, the MSMs of calcium-depleted
GGBP and calcium-bound GGBP (GGBP/Ca2+) demonstrate that
Ca2+ greatly stabilizes the open conformation, and smFRET
measurements confirmed this result. Further analysis reveals that
Ca2+ binding disturbs the local hydrogen bonding interactions
and the conformational dynamics of the hinge region, thereby weakening
the long-range interdomain correlations to favor the open conformation.
These results suggest an active regulatory role of Ca2+ binding in GGBP, which finely tunes the conformational distribution.
The work sheds new light on the study of calcium-binding proteins
in prokaryotes.