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normal Amyloid Fibril formation

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9 years 10 months ago #3866 by ngandhiau
Amyloid Fibril formation was created by ngandhiau
Hi List,

On Martini website, parameters files are available for amyloid fibril formation. This work is originally reported in the paper entitled "Protofibrillar Assembly Toward the Formation of Amyloid Fibrils:, J Phys Chem Letters, 2011.

I am bit confused with the methodology reported in this paper. Have they used ElNeDyn force-field with a force constant of 1000 KJ/mol/nm2 or they have used Martini+elastic network?

Any insight on the method is appreciated.

Many thanks,
Neha

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9 years 10 months ago #3870 by Clement
Replied by Clement on topic Amyloid Fibril formation

An elastic network, ElNeDyn,(45) was used to preserve the structure of the two β-sheets independently, that is, the sheets have their own network. In the spirit of the ElNeDyn approach, the extent of the network (0.9 nm) and its strength (1000 kJ/mol) were tuned to reproduce the dynamics of the protofibril in the atomistic simulations (see the Supporting Information for detail). The elastic network also preserves the twist of the protofibrils, which was found stable for cross-β structures in solution.(46)


ElNeDyn was used on each monomer forming the fibril (i.e. no elastic bonds between monomers in a fibril, each monomer has its own independent ElNeDyn network).

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  1. Force Fields
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