Replica exchange molecular dynamics (REMD) (42) was adopted here to achieve native (equilibrium) structures within the time scales accessible to molecular dynamics simulation. REMD is an efficient approach to studying folding and aggregation of proteins since it allows the system to overcome energy barriers and local minima corresponding to non-native structures of proteins (43) and assists the progress of identifying the native (equilibrium) protein structures from the amino acid sequence. The simulation protocol for identifying the nanostructure of spider silk proteins has been described previously by Keten and Buehler (32, 40), and see also the flow chart in fig. S7. Assemblies of short segments of MaSp1 and MaSp2 proteins of dragline silk of N. clavipes spider (38, 39) were studied. The sample sequence of MaSp1 is


Bolded regions refer to β-sheet–rich regions (crystal domains). Models include 15 antiparallel strands. Both models were simulated in the presence of water.

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