Paper Citing NAMD - Abstract
Kouza, Maksim; Hu, Chin-Kun; Zung, Hoang; Li, Mai Suan
Protein mechanical unfolding: Importance of non-native interactions
JOURNAL OF CHEMICAL PHYSICS, 131 Art. No. 215103, DEC 7 2009
Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension Delta R similar to 22 nm in the force-extension curve is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at Delta R similar to 2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4. (C) 2009 American Institute of Physics. [doi:10.1063/1.3272275]
