Question

How does the protein motion change on changing force constant in md simulation?

Answer 1

Protein motion plays several fundamental roles in protein function, from transmitting the flow of energy and allosteric signals to shuttling a protein via biased routes on the energy landscape for folding and catalysis (Miyashita et al., 2003). The timescales of protein motion span from picosecond to seconds, and the length scales range from local Angstrom motion to nanometer global motion (McCammon, 1984). Understanding nanoscale protein motions is essential, for thermal fluctuations on fast timescales, such as on picosecond to nanosecond timescales, ultimately inspire and dictate the kinetics of large conformational changes necessary for protein function (Bu et al., 2000, 2001, 2005; Lindorff-Larsen et al., 2005; Ishikawa et al., 2008).