Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils – a comparative study using MD simulations of 17–42 residues

Abstract

Extracellular plaques, the hallmark of Alzheimer’s disease brains, consist of insoluble amyloid fibrils that result from the aggregation of amyloid beta peptides. None of the few therapeutic options currently adopted, address the cause of the disease. Instead, they reduce symptom of the disease. Inhibition of aggregation or destabilization of aggregates therefore, emerges as a preferable therapeutic approach. Designing inhibitors or destabilizers demands comprehensive knowledge of the residues of amyloid beta responsible for the phenomenal structural stability of the aggregate. For the purpose, we have compared the effect on structural destabilization of 13 in silico mutations (single and double) with the wild type counterpart of beta-strand-turn-beta-strand motif of the amyloid beta protofibrils by molecular dynamics simulation. Besides the already known salt bridge interaction between K28 and D23, our analyses expose more significant role of K28 as the only positive charge present in the vicinity. Amongst the two consecutive aromatic residues, F19 is involved in stacking interaction; although effect of F20 mutation is more pronounced. Face to face arrangement of A21 and V36 acts as a pillar maintaining the necessary optimum distance between consecutive chains to promote stabilizing interactions. In addition to providing stability to the first beta-strand, large sized negatively charged E22 facilitates salt bridge formation by ensuring fixed relative position of D23 and in turn K28. Likewise, the hydrophobic residues I32 and L34 pack the protofibril core, once again fostering salt bridge interaction. Prospectively, these findings may be compiled for efficient identification or design of scaffolds accountable for protofibril destabilization.

Communicated by Ramaswamy H. Sarma

Keywords:

• Alzheimer’s disease
• aggregation
• salt-bridge
• stacking
• hydrophobic core

Acknowledgements

We gratefully acknowledge the Centre for High Performance Computing for Modern Biology University of Calcutta for providing the computational facility and Dr. Subinit Roy of Saha Institute of Nuclear Physics for allowing us to use ORIGIN 8.0.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors acknowledge Department of Science and Technology, Government of West Bengal (Grant No. 159(Sanc.)/ST/P/S&T/2G-6/2008) and MSD acknowledges University Grant Commission, Ministry of Human Resource Development, Government of India for his fellowship.