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Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ

BIOMOLECULES(2020)

Cited 15|Views4
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Abstract
How sequences of intrinsically disordered proteins (IDPs) code for their conformational dynamics is poorly understood. Here, we combined NMR spectroscopy, small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations to characterize the conformations and dynamics of ChiZ1-64. MD simulations, first validated by SAXS and secondary chemical shift data, found scant alpha-helices or beta-strands but a considerable propensity for polyproline II (PPII) torsion angles. Importantly, several blocks of residues (e.g., 11-29) emerge as "correlated segments", identified by their frequent formation of PPII stretches, salt bridges, cation-pi interactions, and sidechain-backbone hydrogen bonds. NMR relaxation experiments showed non-uniform transverse relaxation rates (R(2)s) and nuclear Overhauser enhancements (NOEs) along the sequence (e.g., highR(2)s and NOEs for residues 11-14 and 23-28). MD simulations further revealed that the extent of segmental correlation is sequence-dependent; segments where internal interactions are more prevalent manifest elevated "collective" motions on the 5-10 ns timescale and suppressed local motions on the sub-ns timescale. Amide proton exchange rates provides corroboration, with residues in the most correlated segment exhibiting the highest protection factors. We propose the correlated segment as a defining feature for the conformations and dynamics of IDPs.
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Key words
correlated segment,conformational dynamics,intrinsically disordered protein,molecular dynamics,nuclear magnetic resonance (NMR),protein conformation,small-angle X-ray scattering (SAXS)
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