Structural Plasticity and Functional Dynamics of Pigeon Cryptochrome 4 as Avian Magnetoreceptor

Cryptochromes (CRYs) are key flavoproteins involved in biological processes such as circadian rhythm regulation and magnetoreception. Type IV CRYs have been identified as primary candidates for avian magnetoreception. However, their structural flexibility, particularly within the cryptochrome C-terminal extension (CCE) and phosphate-binding loop (PBL), remains poorly understood. In this study, we employed temperature replica exchange molecular dynamics (T-REMD) simulations combined with advanced dimensionality reduction techniques, including autoencoder and time-lagged independent component analysis (t-ICA), to explore the conformational space of Columba livia cryptochrome 4 (ClCRY4), as the only available crystal structure of Type IV CRYs to date. By using Drosophila cryptochrome (dCRY) as a reference structure, we assessed the reliability of T-REMD sampling in capturing key states of ClCRY4. Our results indicate that the CCE region of ClCRY4 displays unique conformational dynamics and cooperative interactions with the PBL, highlighting the need for further investigation. The clustering analysis of ClCRY4 conformations revealed multiple structural states, underscoring the functional significance of its intrinsically disordered regions (IDRs). This study provides a novel computational approach for studies of CRYs dynamics, through which the modeling of one CRY with full structure could be used to benchmark the computational study of another CRY only with partial structural information available.