Folding of the Protein Domain hbSBD

Abstract

The folding of the alpha-helix domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T(F) = 317.8 +/- 1.95 K and the enthalpy change DeltaH(G) = 19.67 +/- 2.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free-energy landscape as a function of the number of native contacts, and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in branched-chain alpha-ketoacid dehydrogenase.

Structure of the Subunit Binding Domain and Dynamics of the Di-domain Region from the Core of Human Branched Chain α-Ketoacid Dehydrogenase Complex

“…The hbSBD exhibits considerable sequence-dependent variation in dynamics, especially in the loop region. These results are consistent with the lower melting temperature and stability of hbSBD (T m ϭ 318 K and ⌬H G ϭ 20 kcal/mol) compared with hbLBD (T m ϭ 344 K and ⌬H G ϭ 80 kcal/mol) (32)(33)(34). The spatial variation of the dynamics associated with hbSBD can be seen more clearly from the sausage plot shown in Fig.…”

Scaling of hysteresis loop of interacting polymers under a periodic force

“…The equilibrium force-temperature (f − T ) diagram may be obtained by monitoring the energy fluctuation (or the specific heat) with temperature at different forces f [39,40,43]. The peak in the specific heat curve gives the melting temperature at that f , which is consistent with the f − y curve for that temperature T .…”

“…For example, local motion, which involves atomic fluctuation, side chain motion and loop motion, occurs in the length scale of 0.01 to 5Å and the time involved in such a process is of the order of 10 −15 to 10 −12 s. The motion of helix and protein domain belong to the rigid body motion, whose typical length scales are in between 1 to 100Å and time involved in such motion is in between 10 −9 to 10 −6 s. Here, our interest is in the large-scale motion e.g. helix-coil transition, folding-unfolding transition of proteins and coilglobule transition in polymer, which occurs in the length scale more than 5Å and time involved is about 10 −7 to 100 s. Since, such a time scale is not amenable computationally, therefore, we consider a coarse-grained model of a linear polymer chain and impose restrictive interaction among monomers in such a way that it captures some essential properties of different bio-polymers [39][40][41][42][43]. We follow Ref.…”

“…The native topologybased model, turns out to be quite helpful in predicting the mechanism involved in the DNA unzipping and protein unfolding. It also allowed to decipher the free-energy landscapes of bio-polymers [39][40][41][42][43]49].…”

“…Here, F c is defined as − dE dr and the random force Γ is a white noise [38], and is related to the friction coefficient by fluctuation dissipation theorem i.e., < Γ(t)Γ(t ′ ) >= 2ζT δ(t − t ′ ). It may be noted that the friction term used here only influences the kinetics, not the thermodynamic properties [39,40]. The choice of this dynamics keeps temperature (T ) constant throughout the simulation.…”