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

ABSTRACT: 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 (?2m) that displays an aggressive aggregation propensity. Here we investigate the dynamics of ?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 ?2m. The destabilization of the outer strands of D76N ?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.

SUBMITTER: Le Marchand T

PROVIDER: S-EPMC5916882 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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

Le Marchand Tanguy T de Rosa Matteo M Salvi Nicola N Sala Benedetta Maria BM Andreas Loren B LB Barbet-Massin Emeline E Sormanni Pietro P Barbiroli Alberto A Porcari Riccardo R Sousa Mota Cristiano C de Sanctis Daniele D Bolognesi Martino M Emsley Lyndon L Bellotti Vittorio V Bellotti Vittorio V Blackledge Martin M Camilloni Carlo C Pintacuda Guido G Ricagno Stefano S

Nature communications 20180425 1

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 destab ...[more]

PMID: 29695721

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Project description:Profilin-1 (PFN1) is a 140-amino-acid protein with two distinct binding sites-one for actin and one for poly-L-proline (PLP). The best-described function of PFN1 is to catalyze actin elongation and polymerization. Thus far, eight DNA mutations in the PFN1 gene encoding the PFN1 protein are associated with human amyotrophic lateral sclerosis (ALS). We and others recently showed that two of these mutations (Gly118Val or G118V and Cys71Gly or C71G) cause ALS in rodents. In vitro studies suggested that Met114Thr and Thr109Met cause the protein to behave abnormally and cause neurotoxicity. The mechanism by which a single amino acid change in human PFN1 causes the degeneration of motor neurons is not known. In this study, we investigated the structural perturbations of PFN1 caused by each ALS-associated mutation. We used molecular dynamics simulations to assess how these mutations alter the secondary and tertiary structures of human PFN1. Herein, we present our in silico data and analysis on the effect of G118V and T109M mutations on PFN1 and its interactions with actin and PLP. The substitution of valine for glycine reduces the conformational flexibility of the loop region between the α-helix and β-strand and enhances the hydrophobicity of the region. Our in silico analysis of T109M indicates that this mutation alters the shape of the PLP-binding site and reduces the flexibility of this site. Simulation studies of PFN1 in its wild type (WT) and mutant forms (both G118V and T109M mutants) revealed differential fluctuation patterns and the formation of salt bridges and hydrogen bonds between critical residues that may shed light on differences between WT and mutant PFN1. In particular, we hypothesize that the flexibility of the actin- and PLP-binding sites in WT PFN1 may allow the protein to adopt slightly different conformations in its free and bound forms. These findings provide new insights into how each of these mutations in PFN1 might increase its propensity for misfolding and aggregation, leading to its dysfunction.

Dataset Information

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

Publications

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

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