Transient-state fluctuationlike relation for the driving force on a biomolecule.
In experiments and simulations the force acting on a single biomolecular system has been observed as a fluctuating quantity if the system is driven under constant velocity. We ask the question that is analogous to transient state entropy production and work fluctuation relations whether the force fluctuations observed in the single biomolecular system satisfy a transient state fluctuationlike relation, and the answer is in the affirmative. Using a constant velocity pulling steered molecular dynamics simulation study for protein unfolding, we confirm that the force fluctuations of this single biomolecular system satisfy a transient-state fluctuationlike relation 1/γ(T,v) ln[P(v)(+f)/P(v)(-f)] = f. P(v)(±f) is the probability of positive and negative values of forces f = f · for a given unfolding velocity of magnitude v and the pulling direction n, nis the unit vector of n, and γ(T,v) is a factor that depends on initial equilibrium temperature T and the unfolding velocity. For different unfolding velocities we find that the system in the nonequilibrium pulling region displays substantial negative fluctuation in its unfolding force when velocity decreases. A negative value of force may indicate the emergence of refolding behavior during protein unfolding. We also find that γ(T,v) ~ T(-δ)v(α) and the system relaxation time τ(T,v) ~ T(δ)v(-(1+α), where α and δ are scaling exponents.
The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai 600113, India. mpn@imsc.res.in
M
M
Ponmurugan
Satyavani
S
Vemparala
D001696:Biomechanical Phenomena; D058967:Contactin 1 / Q000737:chemistry*; D019277:Entropy; D055595:Mechanical Phenomena; D056004:Molecular Dynamics Simulation; D011336:Probability; D017434:Protein Structure, Tertiary; D058767:Protein Unfolding
D058967:Contactin 1