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

• Published in: Nature communications Vol. 9; no. 1; pp. 1658 - 11
• Main Authors: Le Marchand, Tanguy, de Rosa, Matteo, Salvi, Nicola, Sala, Benedetta Maria, Andreas, Loren B., Barbet-Massin, Emeline, Sormanni, Pietro, Barbiroli, Alberto, Porcari, Riccardo, Sousa Mota, Cristiano, de Sanctis, Daniele, Bolognesi, Martino, Emsley, Lyndon, Bellotti, Vittorio, Blackledge, Martin, Camilloni, Carlo, Pintacuda, Guido, Ricagno, Stefano
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.04.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/470/2284; 631/45/535/1266; 631/45/535/1267; 631/45/535/878; 82/6; Agglomeration; Amyloidogenesis; Amyloidogenic Proteins - chemistry; Amyloidogenic Proteins - genetics; Amyloidogenic Proteins - metabolism; Amyloidosis - genetics; beta 2-Microglobulin - chemistry; beta 2-Microglobulin - genetics; beta 2-Microglobulin - metabolism; Computer applications; Computer simulation; Crystallography; Crystallography, X-Ray; Crystals; Destabilization; Dynamic stability; Humanities and Social Sciences; Humans; Investigations; Life Sciences; Molecular dynamics; Molecular Dynamics Simulation; multidisciplinary; Mutagenesis, Site-Directed; Mutants; Mutation; NMR; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular; Point Mutation; Protein Aggregation, Pathological - genetics; Protein Aggregation, Pathological - pathology; Protein Folding; Protein Stability; Proteins; Science; Science (multidisciplinary); X-ray crystallography; AMYLOID FIBRILS; PROTEIN; PROTON-DETECTED NMR; NMR CHEMICAL-SHIFTS; ASSIGNMENT; STATE; RELAXATION; MODEL; BACKBONE; RATIONAL DESIGN
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-04078-y

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 (β2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of β2m 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 β2m. The destabilization of the outer strands of D76N β2m 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. The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.