Loop dynamics govern MALT1 activation revealed by integrative AlphaFold, MD, and NMR analysis

Abstract

Abstract Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a central regulator of immune signalling, yet how its conformational dynamics govern activation remains poorly understood. Here, we integrate NMR relaxation measurements, molecular dynamics simulations, and ensemble modelling to characterise the solution-state behaviour of the catalytic core MALT1(PCASP–Ig3) 339−719 under different ionic conditions. Under low-salt conditions, all simulations converge to a dominant inactive ensemble characterised by inward rotation of residue W580 and coordinated rearrangements of regulatory loops, indicating that the inactive state is energetically favoured in solution. At intermediate ionic strength, reversible loop motions permit transient access to active-like conformations, whereas high-salt conditions suppress loop dynamics and trap the protein in its functional starting conformational basin. Comparison with experimental NMR relaxation data identifies the low-salt inactive ensemble as the best representation of solution-state dynamics, revealing stable hydrophobic cores and loop-localised conformational plasticity. Together, these results support ionic strength as a key determinant for MALT1 conformational equilibria in solution and suggest how coordinated loop dynamics regulate access to catalytically competent states. This provides a dynamic framework for future structure-based modulation of MALT1 activity.