HMGB1-Carbenoxolone Interactions: Dynamics Insights from Combined Nuclear Magnetic Resonance and Molecular Dynamics

The interplay of protein dynamics and molecular recognition is of
fundamental importance in biological processes. Atomic-resolution
insights into these phenomena may provide new opportunities for drug
discovery. Herein, we have combined NMR relaxation experiments and
residual dipolar coupling (RDC) measurements with molecular dynamics
(MD) simulations to study the effects of the anti-inflammatory drug
carbenoxolone (CBNX) on the conformational properties and on the
internal dynamics of a subdomain (box A) of high-mobility group B
protein (HMGB1). (15)N relaxation data show that CBNX binding enhances
the fast pico- to nanosecond motions of a loop and partially removes the
internal motional anisotropy of the first two helices of box A. Dipolar
wave analysis of amide RDC data shows that ligand binding induces
helical distortions. In parallel, increased mobility of the loop upon
ligand binding is highlighted by the essential dynamics analysis (EDA)
of MD simulations. Moreover, simulations detect two possible
orientations for CBNX, which induces two possible conformations of helix
H3, one being similar to the free form and the second one causing a
partial helical distortion. Finally, we introduce a new approach for the
analysis of the internal coordination of protein residues that is
consistent with experimental data and allows us to pinpoint which
substructures of box A are dynamically affected by CBNX. The
observations reported here may be useful for understanding the role of
protein dynamics in binding at atomic resolution.