Reply to Comment on"Criterion that Determines the Foldability of Proteins"
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چکیده
We point out that the correlation between folding times and σ = (T θ − T f)/T θ in protein-like heteropolymer models where T θ and T f are the collapse and folding transition temperatures was already established in 1993 before the other presumed equivalent criterion (folding times correlating with T f alone) was suggested. We argue that the folding times for these models show no useful correlation with the energy gap even if restricted to the ensemble of compact structures as suggested by Karplus and Shakhnovich. In a recent article [1] we (KT) showed that for certain lattice models of proteins the folding times, τ f , correlate extremely well with σ = (T θ − T f)/T θ where T θ and T f are well defined thermodynamic collapse and folding transition temperatures, respectively. We also demonstrated that there is " no useful correlation between folding times and the energy gap between the native conformation and the first excited state " [1]. In response to these results Karplus and Shakhnovich (KS) [2] try to argue (i) that the folding criterion used by KT is " essentially the same as one introduced earlier [3,4] " and (ii) that the energy gap used by KT is not " appropriate ". We take up these two issues separately. In addition, we also show that folding times do not correlate with the energy gap ∆ CS restricted to the ensemble of compact structures as KS [2] desire.
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Comment on"A Criterion that determines foldability of proteins"by D. Klimov and D. Thirumalai (PRL,v.76, p.4070 (1996))
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Criterion that determines the foldability of proteins.
We show, using lattice models of proteins, how the kinetic accessibility of the native state of proteins is encoded in the primary sequence itself. The folding times for various sequences correlate extremely well with the single parameter intrinsic to the sequence, namely, s jTu 2 Tf jyTu where Tu and Tf are the collapse and folding transition temperatures. Fast folding sequences have small v...
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تاریخ انتشار 1996