Paper Citing NAMD - Abstract
Hsin, Jen; Schulten, Klaus
Improved Resolution of Tertiary Structure Elasticity in Muscle Protein
BIOPHYSICAL JOURNAL, 100:L22-L24, FEB 16 2011
Rearrangement of tertiary structure in response to mechanical force (termed tertiary structure elasticity) in the tandem Ig chain is the first mode of elastic response for muscle protein titin. Tertiary structure elasticity occurs at low stretching forces (few tens of pN), and was described at atomic resolution in a recent molecular dynamics study, in which an originally crescent-shaped six-Ig chain was stretched into a linear chain. However, the force-extension profile that resulted from this explicit solvent simulation was dominated by the hydrodynamic drag force, and effects of tertiary structure elasticity only manifested for stretching forces above 20 pN. Here we report a slow pulling 100-ns simulation (along with other auxiliary simulations), in which hydrodynamic drag force is seen to reduce to near 0 pN, such that tertiary structure elasticity could be characterized over a 0-200 pN range. Statistical mechanical analysis showed that the stretching velocity was sufficiently low such that the protein remained significantly relaxed during the major part of its extension.
