Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity

Tanguy Le Marchand (1) , Matteo de Rosa (2) , Nicola Salvi (3) , Benedetta Maria Sala (2) , Loren B Andreas (1) , Emeline Barbet-Massin (1) , Pietro Sormanni (4) , Alberto Barbiroli (5) , Riccardo Porcari (6) , Cristiano Sousa Mota (7) , Daniele de Sanctis (7) , Martin Bolognesi (2, 8) , Lyndon Emsley (1) , Vittorio Bellotti (6) , Martin Blackledge (3) , Carlo Camilloni (2) , Guido Pintacuda (1) , Stefano Ricagno (2)

1 Biological Solid-State NMR Methods - Méthodes de RMN à l'état solide en biologie
2 Dipartimento di Bioscienze [Milano]
3 IBS - UMR 5075 - Institut de biologie structurale
4 Department of Chemistry [Cambridge, UK]
5 Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente
6 Wolfson Drug Discovery Unit
7 ESRF - European Synchrotron Radiation Facility
8 UNIMI - Università degli Studi di Milano = University of Milan

Spontaneous aggregation of folded and soluble native proteins in vivo is still a poorly understood process. A prototypic example is the D76N mutant of beta-2 microglobulin (beta 2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of beta 2m by X-ray crystallography, solid-state NMR, and molecular dynamics simulations to unveil the effects of the D76N mutation. Taken together, our data highlight the presence of minor disordered substates in crystalline beta 2m. The destabilization of the outer strands of D76N beta 2m accounts for the increased aggregation propensity. Furthermore, the computational modeling reveals a network of interactions with residue D76 as a keystone: this model allows predicting the stability of several point mutants. Overall, our study shows how the study of intrinsic dynamics in crystallo can provide crucial answers on protein stability and aggregation propensity. The comprehensive approach here presented may well be suited for the study of other folded amyloidogenic proteins.

Keywords: NMR CHEMICAL-SHIFTS; PROTON-DETECTED NMR; RATIONAL DESIGN; AMYLOID FIBRILS; PROTEIN; STATE; RELAXATION; MODEL; ASSIGNMENT; BACKBONE

Domains: Life Sciences [q-bio]

Tanguy Le Marchand, Matteo de Rosa, Nicola Salvi, Benedetta Maria Sala, Loren B Andreas, et al.. Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity. Nature Communications, 2018, 9, pp.1658-1-1658-11. ⟨10.1038/s41467-018-04078-y⟩. ⟨hal-01859528⟩