Paper Citing NAMD - Abstract
Gao, M.; Lu, H.; Schulten, K.
Simulated refolding of stretched titin immunoglobulin domains
BIOPHYSICAL JOURNAL, 81:2268-2277, OCT 2001
Steered molecular dynamics (SMD) is used to investigate forced unfolding and spontaneous refolding of immunoglobulin 127, a domain of the muscle protein titin. Previous SMD simulations revealed the events leading to stretch-induced unfolding of 127, the rupture of hydrogen bonds bridging beta -strands A and B, and those bridging beta -strands A' and G, the latter rupture occurring at an extension of similar to 15 Angstrom and preceding the complete unfolding. Simulations are now used to study the refolding of partially unfolded 127 domains. The results reveal that stretched domains with ruptured interstrand hydrogen bonds shrink along the extension direction. Two types of refolding patterns are recognized: for separated beta -strands A' and G, in most simulations five of the six hydrogen bonds between A' and G stably reformed in 2 ns, whereas for separated beta -strands A and B hydrogen bonds seldom reformed in eight 2-ns simulations. The mechanical stability of the partially refolded intermediates has been tested by re-stretching.
