. Author manuscript; available in PMC: 2020 Aug 24.

Published in final edited form as: Biopolymers. 2017 Mar;107(3):10.1002/bip.22995. doi: 10.1002/bip.22995

Table 1.

The β-cap optimization process as it applies to loop closure.

Entry #	System	Loop Length	Sequence cap – β-strand – loop – β-strand – cap’	ΔG_U (kJ/mol)	Fraction Folded (χ_F)^c
Entry #	System	Loop Length	Sequence cap – β-strand – loop – β-strand – cap’	280 K	300K	320K
1		10	Ac-WVTI - G₃GKKGG₃ - KKIWTG-NH₂	− 2.2	--	<0.10
2		10		+ 3.2	--	0.49
3	B2	2	Ac-WITVTI - GG - KKIRVWTG-NH₂	+ 9.0	0.96	0.91
4	B2	4	Ac-WITVTI – GGGG - KKIRVWTG-NH₂	+ 2.9	0.72	0.58
5	B2	10	Ac-WITVTI - G₃GKKGG₃ - KKIRVWTG-NH₂	+ 2.1	0.57	0.35
6	B4	10	Ac-WITVRIW-G₃GKKGG₃-WKTIRVWTG-NH₂	+ 7.3	0.93	0.85
7	B4	4^a	Ac-WITVRIW - SNGK - WKTIRVWTG-NH₂	> 10	0.99	0.99
8	C2 R1H	10	HWITVTI - G₃GKKGG₃ – KKIRVWE	+ 3.8	0.75	0.57
9	C2	2	RWITVTI - GG - KKIRVWE	> 11	0.99	0.99
10	C2	4	RWITVTI - GGGG - KKIRVWE	+ 5.8	0.88	0.74
11	C2	10	RWITVTI - (G₃GKK)GG₃ - KKIRVWE	+ 5.0	0.84	0.59
12	C2	16	RWITVTI - (G₃GKK)₂GG₃ - KKIRVWE	+ 2.1	0.56	0.38
13	C2	22	RWITVTI - (G₃GKK)₃GG₃ - KKIRVWE	− 1.7	0.29	0.25
14	C4	4^a	RWITVRIW - IGGK - WKTIRVWE	> 11	0.99	0.99
15	C4	10	RWITVRIW - G₃GKKGG₃ - WKTIRVWE	> 10	0.98	0.95
16	C4	16	RWITVRIW- (G₃GKK)₂GG₃ -WKTIRVWE	+ 8.6	0.97	0.92
16Y		16	RWITVRIY- (G₃GKK)₂GG₃ -WKTIRVWE	+ 7.1	0.96	0.89
17	C4	22	RWITVRIW- (G₃GKK)₃GG₃ -WKTIRVWE	+ 5.5^b	0.84^b	0.61^b
18	C4	28	RWITVRIW- (G₃GKK)₄GG₃ -WKTIRVWE	+ 4.0^b	0.77^b	0.45^b

Loop size could be considered 4 or 2 residues since the outer residues of a turn are part of the β-strand.

Fraction folded values estimated by CD, values by NMR not possible due to line broadening.

Fraction folded values represent an average of multiple CSDs (further explained in the Supporting Information) the agreement of these values provides an error of ~0.04 when the mole fraction-folded was in the χ_F = 0.90 range. In the χ_F = 0.35 – 0.90 range, the agreement over the multiple probes provides an error of ~0.08.