Balalab-skku

2S

							Present dataset										AG dataset
No.	Protein short name	PDB	Class	Fold	L_pdb	L	pH	Temp (°C)	Folding type	ln(k_f)	ln(k_f) (25°C)		ln(k_u)	ln(k_u) (25°C)		β_T	pH	Temp (°C)	Folding type	ln(k_f)	Comment
1	Arc repressor [1]	1ARR_mod (1–106)	α	Ribbon-helix-helix	106	125	7.5	25	2S	9.2			0.34			0.78	— NA	— NA	— NA	— NA	The folding experiments were carried out for the monomeric form of Arc repressor. 1ARR_mod indicates the PDB coordinates of the monomeric form, and the amino-acid residue number was renumbered accordingly.
2	TRF1 (Human) [2]	1BA5	α	DNA/RNA-binding 3-helical bundle	53	53	5.7	25.0	2S	5.9			1.2			0.90	—	—	—	—
3	R16 [3]	1CUN (7–112)	α	Spectrin repeat-like	106	116	7.0	25.0	2S*	4.8			-6.0			0.63	—	—	—	—
4	R17 [3]	1CUN (113–219)	α	Spectrin repeat-like	107	116	7.0	25.0	2S	3.4			-7.8			0.61	—	—	—	—
5	FADD [4]	1E41_ (93–192)	α	DEATH domain	100	100	7.0	25.0	2S	6.9			-3.2			0.76	—	—	—	—
6	RAP1 (Human) [2]	1FEX	α	DNA/RNA-binding 3-helical bundle	59	59	5.7	25.0	2S	8.2			2.9			0.82	—	—	—	—
7	c-Myb [2]	1IDY	α	DNA/RNA-binding 3-helical bundle	54	54	5.7	25.0	2S	8.7			1.7			0.79	—	—	—	—
8	Im9 [5]	1IMQ	α	Acyl carrier protein-like	86	93	7.0	25	2S	7.33			-1.87			0.95	—	—	—	—
9	V1sE (Borrelia burgdorferi) [5]	1L8W (Chain B: 29–335)	α	Variable surface antigen VlsE	307	338	7.0	20	2S	2.0	3.6	3.6	-8.5	-5.0	-5.2	0.64	—	25	—	—	According to Maxwell et al. [5], the V1sE data were adopted from reference [6], where the measurement temperature was 20°C. Hence, we reported 20°C as the measurement temperature, although the AG dataset reported 25°C.
10	λ-Repressor [5]	1LMB (6–85)	α	Lambda repressor-like DNA-binding domains	80	80	8	25	2S	10.4			3.2			0.72	—	—	—	—
11	PAB [7]	1PRB (7–53)	α	Immunoglobulin/albumin-binding domain-like	47	47	7.0	74.5	2S	13.8	14.3	NA	9.9	4.7	NA	NA	— NA	— NA	— NA	— NA
12	Protein YjbJ [5]	1RYK	α	SAM domain-like	69	89	7.0	25	2S	9.1			4.5			0.58	—	—	—	—
13	IGBPA [8]	1SS1 (2–60)	α	Immunoglobulin/albumin-binding domain-like	59	60	5.5	25.0	2S	11.5			3.2			0.83	— 5.0	— 37.0	—	— 11.7	The ACPro and our datasets have adopted the data from reference [8], which is more updated than reference [9] adopted by the Garbuzynskiy dataset.
14	ACBP (Yeast) [10]	1ST7	α	Acyl-CoA binding protein-like	86	86	5.3	5	2S	8.5	10.9	10.8	-6.4	-3.0	-2.8	0.60	—	—	N2S	—	This protein was classified as a N2S protein in the AG dataset, but our dataset classified the protein as a 2S protein, because the authors of reference [10] did not observe any intermediates during kinetic refolding.
15	R15 [3]	1U4Q (1662–1771)	α	Spectrin repeat-like	110	116	7.0	25.0	2S	11.0			0.26			0.65	—	—	—	—
16	HP-35 (Chicken) [11]	1VII (42–76)	α	Villin headpiece domain	35	35	4.9	27	2S	12.3	12.3	NA	7.1	7.0	NA	NA	5.3 NA	49.9 NA	—	12.6 NA	Both the ACPro and our datasets have adopted the data from reference [11], which reports the ln(k_f) values at 27 and 49.9°C. We adopted the data at 27°C, while the ACPro dataset adopted those at 49.9°C.
17	PSBD (Bacillus stearothermophilus) [12]	1W4E	α	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	45	45	5.5	25	2S	10.2			3.0			0.65	7.9 NA	41 NA	—	9.69 NA	We have adopted the data from reference [12], which is more updated than reference [13] adopted by the AG dataset.
18	PSBD (Pyrobaculum aerophilum) [14]	1W4J	α	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	51	51	5.7	25	2S	12.3			6.3			0.80	—	—	—	—
19	Rd-apocyt b562 [15]	1YYJ	α	Designed single chain four-helix bundle	106	106	5.2	25	2S	8.4			-7.5			0.47	— NA	— NA	— NA	— NA
20	De novo bundle a3d [16]	2A3D	α	Designed single chain three-helix bundle	73	73	2.6	25	2S	12.2			7.8			NA	— NA	44 NA	—	12.50 NA	Both the ACPro and our datasets have adopted the data from reference [16], which reports the ln(k_f) values at 25 and 44°C. We adopted the data at 25°C, while the ACPro dataset adopted those at 44°C.
21	C-NPM1 [17]	2LLH (19–70)	α	DNA binding protein chaperone	52	52	7.0	10	2S	7.0	7.9	8.1	1.1	2.6	2.1	0.74	NA	NA	NA	NA
22	BBL [18]	2WXC	α	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	47	47	7.0	25	2S	11.7			7.6			0.72	—	10	—	11.2	The same experimental group reported the ln(k_f) values at 25°C [18] and 10°C [19]. We adopted the data at 25°C, but the AG dataset adopted those at 10°C. It has also been reported that BBL exhibits down-hill folding without a significant free-energy barrier, depending on solution conditions [71, 72].
23	SAP domain of THO1 [20]	2WQG	α	LEM/SAP HeH motif	51	51	6.0	20	2S	8.5	8.8	8.8	4.1	4.6	4.6	0.67	NA	NA	NA	NA
24	KIX domain [21]	1KDX (586–666)	α	Kix domain of CBP (creb binding protein)	80	86	7.2	20	2S	7.8	8.2	8.3	2.6	3.5	3.1	0.79	NA	NA	NA	NA
25	RNase HII (Thermococcus kodakaraensis) [22]	1IO2	α/β	Ribonuclease H-like motif	213	228	9.0	50	2S	-0.25	-1.4	-1.5	-16.8	-29.8	-28.5	0.66	NA	NA	NA	NA
26	Myotrophin [23]	2MYO	α+β	β-Hairpin-alpha-hairpin repeat	118	118	7.5	25	2S*	4.8			-5.3			0.47	NA —	NA —	NA N2S	NA —	This protein is classified as a N2S protein in the Garbuzynskiy dataset. Since the intermediate is a high-energy state not significantly populated during folding, it is classified as a 2S protein in our dataset.
27	Urm1 [5]	2QJL	α+β	β-Grasp (ubiquitin-like)	99	101	7.0	25	2S	2.6			3.3			0.57	— NA	— NA	— NA	— NA
28	ACYP2 (Horse) [5]	1APS	α+β	Ferredoxin-like	98	99	7.0	25	2S	-1.6			-9.0			0.24	—	—	—	—
29	FKBP12 [5]	1D6O	α+β	FKBP-like	107	107	7.0	25	2S	1.6			-8.1			0.70	—	—	—	—
30	NTL9 [5]	1DIV (1–56)	α+β	MbtH/L9 domain-like	56	56	7.0	25	2S	6.55			0.1			0.72	—	—	—	—
31	CTL9 [5, 24]	1DIV (58–149)	α+β	Ribosomal protein L9 C-domain	92	92	8.0	25	2S	3.3			-7.9			0.69	—	—	—	—
32	CksHs1 (Human) [25]	1DKT (5–76)	α+β	Cell cycle regulatory proteins	72	79	7.5	10	2S	4.5	5.8	5.2	-2.7	-0.6	1.2	0.31	NA	NA	NA	NA
33	LysM domain [26]	1E0G	α+β	LysM domain	48	64	7.0	10.5	2S	7.0	7.9		2.2	3.5	3.3	0.69	—	—	—	—
34	U1A [5]	1FHT (2–97)	α+β	Ferredoxin-like	96	102	7.0	25	2S	4.6			-11.7			0.53	—	—	—	—
35	HPr [27]	1HDN	α+β	HPr-like	85	85	7.0	20	2S	2.7	3.3		-6.2	-5.3	-5.3	0.64	—	—	—	—
36	TM1083 [5]	1J5U	α+β	MTH1598-like	124	124	7.0	25	2S	6.9			-5.3			0.64	— NA	— NA	— NA	— NA
37	Ribosomal protein L23 (Thermus thermophilus) [5]	1N88	α+β	Ribosomal proteins S24e, L23 and L15e	96	96	7.0	25	2S	2.0			-3.9			0.75	—	—	—	—
38	ADAh2 [5]	1O6X	α+β	Ferredoxin-like	81	81	7.0	25	2S	6.8			-0.42			0.74	—	—	—	—
39	raf RBD [28]	1RFA (56–130)	α+β	β-Grasp (ubiquitin-like)	75	75	7.0	25.0	2S	7.7			-3.0			0.75	—	—	—	8.36	We have adopted the data from reference [28], which is more updated than reference [5] adopted by the AG dataset.
40	Ribosomal protein S6 (Thermus thermophilus) [5]	1RIS (1–97)	α+β	Ferredoxin-like	97	101	7.0	25	2S	6.1			-8.3			0.69	—	—	—	—
41	Src SH2 [5]	1SPR (2–104)	α+β	SH2-like	103	110	7.0	25	2S	8.7			-3.5			0.83	—	—	—	—
42	NBR1-PB1 [29]	2BKF (1–85)	α+β	β-Grasp (ubiquitin-like)	85	100	5.0	25	2S*	6.2			-5.6			0.71	NA	NA	NA	NA
43	Ribosomal protein S6 (Aquifex aeolicus) [30]	2J5A (3–108)	α+β	Ferredoxin-like	106	110	6.3	25	2S	7.3			-10.9			0.74	NA	NA	NA	NA
44	B1 domain of protein L (Finegoldia magna) [5]	2PTL (18–77)	α+β	β-Grasp (ubiquitin-like)	62	79	7.0	25	2S	4.1			-3.3			0.75	—	—	—	—
45	ACYP1 (Human) [31]	2VH7 (5–98)	α+β	Ferredoxin-like	94	98	5.5	28	2S	0.84	0.72		-6.5	-7.1	-7.0	0.72	—	—	—	—
46	CI2 [5]	3CI2	α+β	CI-2 family of serine protease inhibitors	64	64	7.0	25	2S	5.8			-10.3			0.58	—	—	—	—
47	Apocytochrome b₅ hydrophilic domain [32]	1EHB (3–84)	α+β	Cytochrome b5-like heme/steroid binding domain	82	104	7.0	10.0	2S	3.0	4.5		-1.4	1.1		0.70	—	—	—	—
48	Frataxin (Yeast) [33]	2GA5	β	N domain of copper amine oxidase-like	123	123	7.0	25	2S	5.4			-3.1			0.71	NA	NA	NA	NA	The refolding kinetics were measured in the presence of stabilizing ions (0.4 M sodium sulfate)
49	IκBα [34]	1NFI (67–206)	β	Common fold of diphtheria toxin/transcription factors/cytochrome f	140	140	7.5	25	2S*	1.8			-5.6			0.072	NA	NA	NA	NA
50	Sso7d [35]	1C8C	β	SH3-like barrel	64	64	6.1	20	2S	7.0	7.2	7.3	-3.2	-2.6	-2.6	0.63	—	—	—	—
51	CheW (Thermotoga maritima) [5]	1K0S	β	OB-fold	151	151	7.0	25	2S	7.4			-12.1			0.64	—	—	—	—
52	CyPA (Escherichia coli) [36]	1LOP	β	Cyclophilin-like	164	164	7.0	20	2S	6.6	7.4	7.3	-10.4	-8.6	-8.3	0.57	—	—	—	—
53	Protein S (N-terminal domain) [37]	1PRS (1–88)	β	𝛾-Crystallin-like	88	88	7.0	20	2S	3.0	3.5	3.5	-9.4	-8.4	-8.4	0.62	—	—	—	—
54	Protein S (C-terminal domain) [37]	1PRS (91–173)	β	𝛾 -Crystallin-like	83	91	7.0	20	2S	-2.0	-1.6	-1.5	-9.3	-8.4	-8.9	0.84	—	—	—	—
55	CspB (Bacillus caldolyticus) [38]	1C9O	β	OB-fold	66	66	7.0	25	2S	7.2			-0.45			0.93	—	—	—	—
56	CspB (Bacillus subtilis) [38]	1CSP	β	OB-fold	67	67	7.0	25	2S	6.5			2.3			0.91	—	—	—	—
57	Cold shock-like protein (Thermotoga maritima) [38]	1G6P	β	OB-fold	66	68	7.0	25	2S	6.3			-4.0			0.86	—	—	—	—
58	FBP28 WW domain [39]	1E0L	β	WW domain-like	37	37	6.5	10.0	2S	10.1	10.7	10.8	5.8	6.8	6.6	0.71	7	25	—	10.62	We reported the data for the wild-type protein [39], while the AG dataset reported those for the W30A mutant [40].
59	Prototype WW domain [40]	1E0M	β	WW domain-based designs	37	38	7.0	25.0	2S	8.9			7.1			0.64	—	—	—	—
60	Hisactophilin [41]	1HCD	β	β-Trefoil	118	118	6.7	20.0	2S	1.3	1.6		-9.9	-9.5		0.73	7.7 7.7	— —	N2S	4.6 4.0	We have adopted the data from reference [41], which is more updated than reference [42] adopted by the AG dataset.
61	Abp1 SH3 [5]	1JO8	β	SH3-like barrel	58	68	7.0	25	2S	2.5			-2.7			0.88	—	—	—	—	There is some evidence for the presence of a folding intermediate for a mutant of abp1 SH3, characterized by relaxation dispersion NMR [43]. However, the intermediate was not highly populated under strongly native folding conditions, so that the folding type of this protein was classified as the 2S.
62	CAfn2 [44]	1K85	β	Immunoglobulin-like β-sandwich	88	88	5.0	25	2S	1.4			-7.1			0.62	—	—	—	—
63	hbLBD [45]	1K8M (1–87)	β	Barrel-sandwich hybrid	87	93	7.5	22.0	2S	-0.94	-0.71	-0.73	-8.0	-7.5	-7.4	0.55	— —	— —	—	−0.71 —	Both the AG and our datasets adopted the same reference (90). Our reported ln(k_f) value is identical with that of the Garbuzynskiy dataset, but the ACPro dataset reports a different value.
64	PDZ3 from PSD-95 [46]	1TP3 (309–401)	β	PDZ domain-like	93	93	2.85	25	2S*	3.0			-3.4			0.56	—	—	N2S	—	This protein is classified as a N2S protein in the AG dataset. Since the intermediate is a high-energy state not significantly populated during folding, it is classified as a 2S protein in our dataset.
65	YAP 65 WW domain [41]	1K9Q	β	WW domain-like	40	40	7.0	25.0	2S	8.4			6.7			0.78	—	—	—	—
66	GW1 of Internalin B [5]	1M9S (391–466)	β	SH3-like barrel	76	85	7.0	25	2S	4.0			-1.7			0.69	—	—	—	—
67	CspA [47]	1MJC	β	OB-fold	69	69	7.0	25	2S	5.3			1.4			0.94	—	—	—	—
68	Pin WW domain [48]	1PIN (6–39)	β	WW domain-like	34	34	7.0	39.5	2S	9.4	9.2	NA	6.2	5.2	NA	NA	—	—	—	—
69	PI3 SH3 [49]	1PNJ (3–84)	β	SH3-like barrel	82	82	7.2	25	2S	-0.69			-7.2			0.57	—	20	—	−1.04	There is some evidence for initial non-specific chain collapse during the refolding of the PI3 SH3 domain [49]. However, there is no cooperative transition between the collapsed and the unfolded states, indicating that the collapsed state may belong to the unfolded species, and hence, the folding of PI3 SH3 was classified as the 2S type. In the presence of a stabilizing salt (0.5 M sodium sulfate), however, the folding behavior of PI3 SH3 changed from the 2S to the N2S type with a stable folding intermediate [50].
70	MTCP1 oncogene product P13 [51]	1QTU (1–115)	β	Oncogene products	115	117	7.0	21	2S	-0.36	0.08	0.17	-11.1	-10.1	-10.5	0.76	— —	— —	—	— 0.0	Both the AG and our datasets adopted the same reference [51]. Our reported ln(k_f) value is identical with that of the ACPro dataset, but the Garbuzynskiy dataset reports a different value.
71	FGF-1 (Human) [52]	1RG8	β	β-Trefoil	137	140	6.60	25	2S	1.3			-7.1			0.93	NA	NA	NA	NA
72	Fyn SH3 [5]	1AVZ (Chain C: 85–141)	β	Regulatory factor Nef	57	78	7.0	25	2S	4.9			-4.3			0.75	—	—	—	—	There is some evidence for the presence of a low-populated folding intermediate for Fyn SH3 mutants characterized by relaxation dispersion NMR [53, 54]. However, the intermediate was not highly populated under strongly native folding conditions, and the stopped-flow kinetics of refolding were well represented by a 2S model [55]. The folding of Fyn SH3 was thus classified as the 2S type.
73	α-spectrin SH3 [5]	1SHG (6–62)	β	SH3-like barrel	57	62	7.0	25	2S	1.1			-4.8			0.80	—	—	—	—	There are reports suggesting the presence of the intermediate species in α-spectrin SH3 [56]. However, the majority of the folding reaction under native folding conditions is well represented by the 2S mechanism.
74	Src SH3 [5]	1SRL (9–64)	β	SH3-like barrel	56	61	7.0	25	2S	4.4			-1.3			0.71	—	—	—	—	There are reports indicating the presence of an α-helical burst-phase intermediate in the kinetic refolding of src SH3, particularly at acid pH at a low temperature (4°C or lower) in the presence of an anti-freezing agent (ethylene glycol) [57, 58]. Unfortunately, however, there is no quantitative analysis of the src SH3 folding, based on the N2S model under native folding conditions (neutral pH and 25°C), and the previous quantitative analysis of the src SH3 folding was based on the 2S model [5, 59]. We thus temporarily leave the folding-type classification of this protein as the 2S type.
75	Tenascin 3FNIII [60]	1TEN (803–891)	β	Immunoglobulin-like β-sandwich	89	90	5.0	25	2S	1.8			-8.6			0.79	—	20	—	1.06	We have adopted the data from reference [60], which is more updated than reference [61] adopted by the AG dataset.
76	Twitchin [62]	1WIT	β	Immunoglobulin-like β-sandwich	93	93	5.0	20	2S	0.41	0.85	0.90	-8.2	-7.2	-7.4	0.7	—	—	—	—
77	Sho1 SH3 (Yeast) [5]	2VKN (1–66)	β	Membrane protein	66	76	7.0	25	2S	2.1			-2.5			0.68	— NA	— NA	N2S NA	— NA	Both the ACPro and our datasets adopted the same reference [5]. We classified the folding type as the 2S type according to the reference, but the ACPro dataset classified it as the N2S type.
78	9FNIII [63]	1FNF (1325–1415)	β	Immunoglobulin-like β-sandwich	91	91	5.2	25.0	2S	-0.9			NA			0.7	—	—	N2S —	—	Both the AG and our datasets adopted the same reference [63]. The Garbuzynskiy and our datasets classified the folding type as the 2S type according to the reference, but the ACPro dataset classified it as the N2S type.
79	PDZ2 from PTP-BL [64]	1GM1 (9–102)	β	PDZ domain-like	94	94	7.0	25	2S*	1.0			-3.9			0.53	— —	— —	N2S	— 0.8	Both the AG and our datasets adopted the same reference [64]. Our reported ln(k_f) value is identical with that of the ACPro dataset, but the Garbuzynskiy dataset reports a different value. Although this protein is classified as a N2S protein in the AG dataset, the intermediate is a high-energy state, not significantly populated during folding, so that it is classified as a 2S protein in our dataset.
80	SPCp41 [65]	2JMC	β	SH3-like barrel	75	75	7.0	25	2S	3.3			-1.6			0.76	NA	NA	NA	NA
81	FGF-2 (Human) [66]	1FGA (20–143)	β	β-Trefoil	124	153	7.0	25	2S	-1.4			-10.4			0.82	NA	NA	NA	NA
82	PDZ1 from PSD-95 [67]	3ZRT (3–93)	β	PDZ domain-like	91	91	7.4	25	2S*	1.3			-7.3			0.66	NA	NA	NA	NA
83	PDZ2 from PSD-95 [67]	3ZRT (97–189)	β	PDZ domain-like	93	95	5.45	25	2S*	0.3			-6.6			0.51	NA	NA	NA	NA
84	nNOS PDZ [67]	1QAU (14–125)	β	PDZ domain-like	112	132	4.0	25	2S*	1.8			-4.1			0.21	NA	NA	NA	NA
85	Symfoil-4T [68]	3O4B (11–147)	β	β-Trefoil	137	140	6.6	25	2S	4.3			-11.4			0.83	NA	NA	NA	NA
86	Symfoil-1 [68]	3O49	β	β-Trefoil	127	140	6.6	25	2S	1.7			-9.0			0.82	NA	NA	NA	NA
87	Symfoil-4P [68]	3O4D	β	β-Trefoil	126	140	6.6	25	2S	4.9			-13.7			0.84	NA	NA	NA	NA
88	gpW [69]	2L6R	β	gpW/XkdW-like	62	62	6.0	37	2S	10.3	9.9	NA	NA	NA	NA	NA	NA	NA	NA	NA	The protein is a downhill folder, which shows barrier-free folding, and hence the temperature correction is tentative.
89	PDZ2 from SAP97 [70]	2X7Z (311–407)	β	PDZ domain-like	97	97	7.5	25	2S*	0.74			-6.2			0.76	NA	NA	NA	NA

Description of each proteins includes:

Column 1: “No”: serial number.

Column 2: “Protein short name”: includes a reference to the original experimental paper on its folding kinetics.

Column 3: “PDB code”: the protein three-dimensional (3D) structure code according to the PDB. If only a part of the chain was used in the protein folding experiment, it is contained in brackets. If a 3D structure composed of multiple separated chains (eg. A, B, C, and D), we considered a chain that have the highest coverage with L. If the considered chain is other than chain A, it is explicitly mentioned.

Column 4: “Protein structural class”

Column 5: Fold classification by SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/).

Column 6: “L_pdb”: number of folded residues according to the PDB data. If a 3D structure is not continuous (i.e. multiple breaks), we removed only terminal residues (N- and C- terminal) and considered the remaining region as continuous.

Column 7: “L”: number of residues in the protein used in the experimental study.

Column 8: Either the present dataset or our dataset, which contains eight subdivisions: 1) pH, 2) Temperature, 3) folding type (2S: two-state folding, 2S*: two-state folding with a high-energy intermediate), 4) the ln(k_f) reported, 5) the ln(k_f) value after the temperature correction, which has two columns (refer the manuscript for the explaination), 6) the ln(k_u) value reported, 7) the ln(k_u) value after the temperature correction, whcih contain two columns (refer the manuscript for the explaination) and 8) the Tanford β value (β_T)

Column 9: ACPro and Garbuzynskiy (AG) dataset, which contains four subdivisions: 1) pH, 2) temperature, 3) folding type and 4) ln(k_f). If the values provided in the present dataset and the AG dataset were the same, they are represented as “—”. Otherwise, values reported in the AG dataset are represented normally. If the present dataset is unique or had not been previously reported previously, it is represented as “NA”. Note: if the ACPro and Garbuzynskiy sets were identical, we reported those values in a single row. Otherwise, both the ACPro values and the Garbuzynskiy values are listed in the first and second rows, respectively.

Column 10: Comments, including descriptions concerning discrepancies between the present dataset and the AG dataset of specific proteins, where necessary.

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