Citrate stabilized gold nanoparticles interfere with amyloid fibril formation: D76N and ΔN6 β2-microglobulin variants

Abstract

Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the structure and function of affected organs. Different kind of interactors can interfere with the formation of protein dimers and multimers in solution. A very special class of interactors are nanoparticles thanks to the extremely efficient extension of their interaction surface. In particular citrate-coated gold nanoparticles (cit-AuNPs) were recently investigated with amyloidogenic protein β2-microglobulin (βm). Here we present the computational studies on two challenging models known for their enhanced amyloidogenic propensity, namely ΔN6 and D76N βm naturally occurring variants, and disclose the role of cit-AuNPs on their fibrillogenesis. The proposed interaction mechanism lies in the interference of the cit-AuNPs with the protein dimers at the early stages of aggregation, that induces dimer disassembling. As a consequence, natural fibril formation can be inhibited. Relying on the comparison between atomistic simulations at multiple levels (enhanced sampling molecular dynamics and Brownian dynamics) and protein structural characterisation by NMR, we demonstrate that the cit-AuNPs interactors are able to inhibit protein dimer assembling. As a consequence, the natural fibril formation is also inhibited, as found in experiment.

The Early Phase of β2-Microglobulin Aggregation: Perspectives From Molecular Simulations

“…The terminal regions are more relevant under acidic conditions while the BC, DE and EF loops gain importance as structural interface elements at physiological pH. The participation of the N terminus (Thr4 and Pro5) and BC loop (His31) was recently reported in interfaces of dimers of Asp76Asn obtained by docking simulations ( Cantarutti et al, 2017 ; Brancolini et al, 2018 ).…”

“…Furthermore, since the number of replicas increases markedly with system’s size, the use of RE-MD is limited to the study of oligomerization of small peptide fragments ( Nishino et al, 2005 ; Liang et al, 2007 , 2008 ; Wei et al, 2007 ; De Simone and Derreumaux, 2010 ; Nishikawa et al, 2019 ). In the case of β2m, MD simulations have been used to study the dynamics of the native monomer ( Ma and Nussinov, 2003 ; Deng et al, 2006 ; Fogolari et al, 2011 ; Chandrasekaran and Rajasekaran, 2016 ), the oligomerization process of selected amyloidogenic β2m peptide sequences ( Liang et al, 2007 ; Zheng et al, 2008 ; Fang et al, 2009a ), and provide complementary information to that obtained through in vitro experiments ( Gumral et al, 2013 ; Chong et al, 2015 ; Torbeev et al, 2015 ; Camilloni et al, 2016 ; Hall et al, 2016 ; Brancolini et al, 2018 ). Another enhanced sampling scheme is the so-called metadynamics ( Laio and Parrinello, 2002 ).…”

“…In particular, docking methods based on a rigid-body representation allow for efficient sampling of the conformational space ( Norel et al, 1994 , 1995 , 1999 ; Benyamini et al, 2003 , 2005 ; Kozakov et al, 2006 ; Krobath et al, 2012 ). The scoring function used in protein-protein docking can be based on shape complementarity only ( Lawrence and Colman, 1993 ; Norel et al, 1994 , 1995 , 1999 ; Krobath et al, 2012 ), or consider the other main drivers of protein-protein association, which are hydrophobic and electrostatic interactions ( Dominguez et al, 2003 ; Fernandez-Recio et al, 2003 ; Gray et al, 2003 ; Mendoza et al, 2010 , 2011 ; Cantarutti et al, 2017 ; Brancolini et al, 2018 ; Loureiro et al, 2019 ). Some docking methodologies also include restraints derived from experiments ( Dominguez et al, 2003 ; Karamanos et al, 2014 ; Hall et al, 2016 ); this is the case of HADDOCK, which is available as a webserver ( Dominguez et al, 2003 ; de Vries et al, 2010 ).…”

Functional Electrospun Phospholipid Nano-microfibers

“…T-REMD is used to allow a more extensive search of dimeric conformational minima in the Free Energy Surface. We employ a total of 32 replicas, covering a temperature range 290-320 K [48][49][50]. The adopted protocol yields an aggregated simulation time of 640 ns.…”

“…Due to the intrinsically limited time scale accessible to classical MD, the parallel tempering in the form of replica exchange molecular dynamics (REMD) is also performed, following previous protocol simulation of our group [48][49][50]; in particular, such simulations are applied to dimers exhibiting the most extended dimeric interface (D76N and ΔN6). REMD involves multiple independent simulations at different temperatures (T-REMD), during which running replicas periodically attempt an exchange in temperature space [51][52][53].…”