HYCUD

HYCUD predicts effective rotational correlation times of folded protein domains within flexible multidomain proteins and protein complexes to characterize their hydrodynamic behavior in the presence of long disordered tails and interdomain linkers.

Key Features:

• Prediction of Rotational Correlation Times: Estimates effective rotational correlation times for folded domains in multidomain proteins and protein complexes.
• Focus on Flexible Modular Systems: Accounts for flexibility arising from long disordered tails and interdomain linkers that are prevalent in eukaryotic proteins.
• Application to Intrinsically Disordered Proteins (IDPs): Handles intrinsically disordered proteins and protein complexes that exhibit significant conformational mobility.
• Detection of Molecular Switch Events: Enables identification of molecular switch events mediated by disorder–order transitions in interdomain linkers through changes in rotational correlation times.
• Hydrodynamic–Computational Integration: Integrates hydrodynamic principles with computational predictions to model rotation in flexible systems.
• Implementation: Implemented in Python for computational analysis.

Scientific Applications:

• Structural Biology and Protein Dynamics: Provides quantitative measures of domain rotation to inform structural models and dynamic interpretations.
• Functional Analysis of Proteins: Uses rotational correlation time predictions to relate protein flexibility and interdomain motion to molecular function.
• Molecular Switch Mechanisms: Facilitates study of disorder–order transitions as molecular switches that regulate protein activity and interactions.

Methodology:

Employs a workflow that integrates hydrodynamic principles with computational predictions to model protein rotation in flexible systems, addressing limitations of traditional hydrodynamic methods.