Table 2.

Energy terms in an Ising for contiguous blocks of helices in a consensus TPR of eight helices (four repeats).

# folded helices	microstate	Internal: −RTHΣsi	Neighbor interaction: −RTJΣsisi+1	Ends: +RTJ(s1 + sn)	bGTotal (kcal/mol)	bStepwise ΔGi→j (kcal/mol)	bOverall ΔG0→j (kcal/mol)
0	−−−−−−−−	+8RTH	−7RTJ	−2RTJ	+RT(8H−9J)	n.a.	0
1	−−−−+−−−	+6RTH	−3RTJ	−2RTJ	+RT(6H−5J)	−2RTH+4RTJ	+2.33
2	−−−−++−−	+4RTH	−3RTJ	−2RTJ	+RT(4H−5J)	−2RTH	0.16
3	−−−+++−−	+2RTH	−3RTJ	−2RTJ	+RT(2H−5J)	−2RTH	−2.01
4	−−++++−−	0	−3RTJ	−2RTJ	−5RTJ	−2RTH	−4.18
5	−−+++++−	−2RTH	−3RTJ	−2RTJ	+RT(−2H−5J)	−2RTH	−6.35
6	−++++++−	−4RTH	−3RTJ	−2RTJ	+RT(−4H−5J)	−2RTH	−8.52
7	−+++++++	−6RTH	−5RTJ	0	+RT(−6H−5J)	−2RTH	−10.69
8	++++++++	−8RTH	−7RTJ	2RTJ	+RT(−8H−5J)	−2RTH	−12.86

H and J parameters from 1D Ising lattice treatment of Kajandar et al [42]. H represents the internal energy of a single lattice site, neglecting interaction terms with neighbors and ends, where helical (+) and unfolded (−) states have energies of +RTH and −RTH, respectively. In the Ising formalism, in which fictitious end-spins are included, H is closely related to the propagation energy (−2RTH; see entries in stepwise ΔG_i→j column). J captures interactions between adjacent sites, with a value −RTJ when adjacent sites are both helix (++) or both unfolded (−−), and +RTJ when they are in different states (+− or −+). J also captures interactions between the end sites (here positions 1 and 8) and sites off the end of the chain (fictitious positions 0 and 9) in (−) states. In the absence of denaturant, H=1.83 and J=1.9.

^bFree energies are evaluated at 298.15K.