The turn less taken: Investigating patterns in β -turn dynamics using large-scale molecular dynamics data

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Abstract

β -turns are among the most common structural motifs in proteins, yet their conformational dynamics and sequence determinants remain incompletely understood. Here we present a data-driven classification and dynamic analysis of β -turn conformations using large-scale molecular dynamics trajectories from the mdCATH database. Clustering of backbone dihedral angles using a cross-bond Ramachandran representation identifies six β -turn types, including a previously uncharacterized hybrid I/I′ cluster that combines geometric features of canonical type I and I′ conformations. Time-resolved analysis indicates that this hybrid state acts as a transient intermediate state of β -turns. Transitions observed in molecular dynamics simulations closely match NMR ensembles and altlocs detected in X-ray crystal structures, with the most dominant exchanges occurring between type I and II, and between type I′ and II′ turns. Sequence analysis shows that each turn type exhibits characteristic amino acid preferences at the central residues ( i + 1 and i + 2). Within these overall preferences, specific residue pairs display distinct biases toward static or dynamic behavior. Targeted in silico substitutions that interchange dynamic- and static-enriched residue pairs shift the conformational behavior of turns accordingly, providing direct support for these sequence-dynamics relationships. Analysis of flanking secondary-structure environments reveals that structural context further modulates turn flexibility, with strand- and coil-associated turns exhibiting higher dynamic propensity than helix-associated turns. Together, these results reveal how sequence composition and structural context jointly shape the conformational landscape of β -turns.

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