Balalab-skku

N2S

							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_I)	ln(k_u)	ln(k_u) (25°C)	β_T	pH	Temp (°C)	Folding type	ln(k_f)	Comments
1	Apomyoglobin (Whale) [1]	1A6N	α	Globin-like	151	153	6.2	5	N2S	1.1	4.5	NA	-3.8	5.5	0.72	—	—	—	—
2	Pit1 [2]	1AU7 (103–160)	α	DNA/RNA-binding 3-helical bundle	58	63	5.5	25.0	N2S	9.7		12.6	5.5		0.74	—	—	—	—
3	4-helix bundle protein FRB [3]	1AUE (Chain B: 2022–2115)	α	Four-helical up-and-down bundle	94	95	7.5	10	N2S	5.4	6.7	NA	-5.2	-1.0	0.83	— —	— —	—	— 6.0	Both the AG and our datasets adopted the same reference [3]. The ACPro and our datasets reported the same ln(k_f) value, but the Garbuzynskiy dataset reported a different value.
4	IM7 [4]	1AYI (1–86)	α	HIV-1 gp41 fragments	86	86	7.0	10	N2S	5.7	6.9	8.0	-0.84	3.0	0.90	—	25	2S	7.2	The ln(k_f) value reported in the AG dataset was based on the 2S model [5]. However, the N2S nature of this protein is well established [4], so that our reported value is based on the N2S model.
5	Apomyoglobin (Horse) [6]	1DWR (1–152)	α	Globin-like	152	153	6.0	26	N2S	2.9	2.9	5.3	NA		NA	NA	Na	NA	NA	The value of ln(k_I) was taken from the rate constant of the fast phase of the bi-phasic refolding kinetics reported.
6	Engrailed Homeodomain [7]	1ENH	α	DNA/RNA-binding 3-helical bundle	54	54	5.7	25.0	N2S	10.6		NA	7.6		0.83	—	—	—	—
7	FF domain from human HYPA/FBP11 [8]	1UZC (3–71)	α	3-Helical bundle	69	71	5.7	25	N2S	8.0		9.9	3.4		0.91	— —	— 10	—	— 7.6	The same experimental group reported the ln(k_f) values at 25°C [8] and at 10°C [9]. The ACPro and our datasets reported the value at 25°C, but the Garbuzynskiy dataset reported the value at 10°C.
8	ACBP (Bovine) [10]	1NTI	α	Acyl-CoA binding protein-like	86	86	5.3	26	N2S	6.5	6.4	9.3	-2.7	-2.9	0.70	—	25	2S	6.96	The ln(k_f) value reported in the AG dataset was based on the 2S model [5]. However, the N2S nature of this protein is well established [10], so that our reported value is based on the N2S model.
9	Phage 434 Cro [11]	2CRO (1–65)	α	Lambda repressor-like DNA-binding domains	65	71	6.0	20	N2S	3.7	4.0	NA	-0.39	0.54	0.91	— —	— —	—	5.35 —	Both the AG and our datasets adopted the same reference [11]. The Garbuzynskiy and our datasets reported the same ln(k_f) value, but the ACPro dataset reported a different value.
10	X domain of Measles Virus protein [12]	1OKS	α	Immunoglobulin/albumin-binding domain-like	49	49	7.2	25	N2S	6.2		8.6	4.5		0.84	NA	NA	NA	NA
11	Barstar [13]	1BTA	α/β	Barstar-like	89	90	7	25	N2S	3.5		NA	-2.3		NA	8	—	—	3.47	We have adopted the data from reference [13], which is more updated than reference [14] adopted by the AG dataset.
12	Apoflavodoxin (Anabaena) [15]	1FTG (2–169)	α/β	Flavodoxin-like	168	169	7.0	25.0	N2S	2.3		3.4	-3.0		0.55	— —	— —	2S	— 2.8	The ln(k_f) value reported in the AG dataset was based on the 2S model [16]. However, the N2S nature of this protein is well established [15], so that our reported value is based on the N2S model. Moreover, the intermediate (I) is mostly off-pathway.
13	HIV-1 RNase H [17]	1HRH (427–556)	α/β	Ribonuclease H-like motif	130	134	5.5	25	N2S	0.88		NA	-2.5		0.64	NA	NA	NA	NA
14	N-PGK (Bacillus stearothermophilus) [18]	1PHP (1–175)	α/β	Phosphoglycerate kinase	175	175	7.5	25	N2S	2.3		NA	-3.5		0.84	—	—	—	—
15	C-PGK (Bacillus stearothermophilus) [19]	1PHP (186–394)	α/β	Phosphoglycerate kinase	209	209	7.2	25	N2S	-4.0		NA	-9.3		0.51	— —	— —	—	−3.44 —	The Garbuzynskiy and our datasets have adopted the data from reference [19], which is more updated than reference [18] adopted by the ACPro dataset.
16	DHFR [20]	1RA9	α/β	Dihydrofolate reductase-like	159	159	7.8	15	N2S	-0.37	0.86	1.5	-5.2	-0.29	0.92	— —	— —	—	NA −3.20	We have adopted the data from reference [20], which is more updated than reference [21] adopted by the AG dataset.
17	Trp-synthase α-subunit (Escherichia coli) [22]	1WQ5	α/β	TIM β/α-barrel	268	268	7	25	N2S	-2.1		NA	-8.9		NA	—	—	—	—
18	RNase H (Escherichia coli) [23]	2RN2	α/β	Ribonuclease H-like motif	155	155	5.5	25	N2S	-0.3		NA	-11.4		0.80	— —	— —	—	0.0095 0.1	We have adopted the data from reference [23] although the AG datasets adopted the data from reference [24], because the ln(k_f) value reported in reference [24] is not the value in H₂O but in D₂O.
19	CheY [25]	3CHY	α/β	Flavodoxin-like	128	129	7.0	25	N2S	1.0		NA	-4.4		0.70	—	—	—	—
20	Apoflavodoxin (Desulfovibrio desulfuricans) [26]	3F6R (2–148)	α/β	Flavodoxin-like	147	148	7	20	N2S	3.5	4.0	NA	-5.8	-3.6	0.88	—	—	—	—
21	sIGPS (Sulfolobus solfataricus) [27]	1IGS (27–248)	α/β	TIM β/α-barrel	222	222	7.8	25	N2S	-4.5		NA	-13.9		0.79	NA —	NA —	NA —	NA —
22	RNase H (Chlorobaculum tepidum) [28]	3H08	α/β	Ribonuclease H-like motif	146	146	5.5	25	N2S	1.6		NA	-13.6		NA	NA —	NA —	NA —	NA —
23	HisF [29]	1THF	α/β	TIM β/α-barrel	253	253	7.5	25	N2S	-3.2		-1.4	-29.7		NA	NA	NA	NA	NA
24	GFP [30]	1B9C (4–230)	α+β	GFP-like	227	238	7.5	25.0	N2S	-2.6		0.78	-23.5		NA	— NA	— NA	— NA	−1.59 NA	Although both the ACPro and our datasets adopted the data from the same reference [30], the ln(k_f) value reported is different between the two datasets. Because this protein exhibited multiple parallel pathways of folding, we reported the averaged k_f value obtained by the equation: k_f = Σfiki where fi and ki are the fractional amplitude and the observed rate constant, respectively, of the i^th pathway of folding. On the other hand, the ACPro dataset reported the value of the major pathway of folding. The ln(k_u) was taken from reference [31].
25	Barnase [32]	1BNI (3–110)	α+β	Microbial ribonucleases	108	110	7.5	25	N2S	2.7		NA	-12.2		0.64	6.3	—	—	2.56	We have adopted the data from reference [32], which is more updated than reference [33] adopted by the AG dataset.
26	p16INK4a [34]	2A5E (9–156)	α+β	β-Hairpin-α-hairpin repeat	148	148	7.5	25	N2S	3.5		NA	-0.22		0.89	—	—	—	—
27	N-HypF [35]	1GXT (4–91)	α+β	Ferredoxin-like	88	91	5.5	28	N2S	4.4	4.3	NA	-3.9	-4.7	NA	—	—	—	—
28	Monellin [36]	1FA3	α+β	β-β-α Zinc fingers	96	97	7	25	N2S	4.1		NA	-10.8		0.89	NA	NA	NA	NA	Because this protein exhibited multiple parallel pathways of folding, we reported the averaged k_f value obtained by the equation shown in the comment of entry number 24.
29	T4 Lysozyme [24]	1L63 (1–162)	α+β	Lysozyme-like	162	164	6.0	25.0	N2S	3.7		NA	-12.3		NA	—	—	—	4.1	Although the ACPro and our dataset adopted the data from the same reference [24], the ln(k_f) value reported is different between the two datasets. The ACPro dataset reported the value based on the 2S model, however, our value is based on N2S model.
30	B1 domain of protein G (Streptococcal sp. group G) [37]	1PGB	α+β	Ubiquitin-like	56	57	5	20	N2S	6.4	6.6	7.7	-2.0	-1.2	0.85	7.5	25	2S	6.3	The ln(k_f) value reported in the AG dataset was based on the 2S model [5]. However, the N2S nature of this protein is well established [37], so that our reported value is based on the N2S model. The value was measured in the presence of 0.4 M sodium sulfate [37].
31	p13suc1 [38]	1PUC_mod (2–102)	α+β	Cell cycle regulatory proteins	101	114	7.5	25	N2S	4.2		NA	-4.0		0.80	—	—	—	—	1PUC_mod indicates the monomeric form of p13suc1, and its coordinates were kindly given by J. Schymkowitz [39].
32	Ubiquitin [40]	1UBQ	α+β	Ubiquitin-like	76	76	5.0	25	N2S	5.3		7.3	-6.7		0.65	—	—	2S	7.33	The ln(k_f) value reported in the AG dataset was based on the 2S model [5]. However, the N2S nature of this protein is well established [40], so that our reported value is based on the N2S model. Moreover, the ln(k_u) was taken from the following reference [41].
33	Villin 14T [42]	2VIL	α+β	Gelsolin-like	126	126	5	37	N2S	4.2	4.0	NA	-2.4	-6.9	0.78	4.1 4.1	25 —	—	11.9 5.0	We have adopted the data from reference [42], which is more updated than reference [43] adopted by the AG dataset.
34	β-Lactamase (Staphylococcus aureus) [44]	3BLM	α+β	β-Lactamase/transpeptidase-like	257	257	7.0	25	N2S	-6.6		NA	-10.8		0.79	NA	NA	NA	NA
35	ACYP (Sulfolobus solfataricus) [45]	2BJD (12–101)	α+β	Ferredoxin-like	90	101	5.5	37	N2S	1.7	1.6	NA	-12.0	-15.2	0.66	NA	NA	NA	NA
36	UCH-L3 [46]	1UCH (5–230)	α+β	Cysteine proteinases	226	230	7.6	25	N2S	-2.6		NA	-6.9		0.72	NA	NA	NA	NA
37	Ubq-UIM [47]	2KDI	α+β	NA	114	114	7.4	25	N2S	2.3		NA	-9.9		NA	NA	NA	NA	NA
38	Frataxin (Human) [48]	1EKG	α+β	N domain of copper amine oxidase-like	119	130	7.0	25	N2S	3.5		NA	-8.9		0.72	NA	NA	NA	NA
39	β-Lactamase (Bacillus licheniformis) [49]	4BLM (31–291)	α+β	β-Lactamase/transpeptidase-like	261	265	7.0	20	N2S	-4.7	-3.9	NA	-13.6	-9.6	0.73	— NA	— NA	— NA	−1.24 NA	Although the ACPro and our dataset adopted the data from the same reference [49], the ln(k_f) value reported is different between the two datasets. The ACPro dataset reported the value based on the 2S analysis using the kinetic folding data between 0.6 and 2 M guanidinium chloride, whereas our reported value is based on the N2S analysis using the data below 0.4 M guanidinium chloride.
40	CD2.d1 [50]	1HNG (2–98)	β	Immunoglobulin-like β-sandwich	97	98	7.0	25	N2S	1.8		NA	-5.7		NA	—	—	2S —	—	Both the AG and our datasets adopted the same reference [50]. The Garbuzynskiy and our datasets classified the folding type as the N2S type according to the reference, but the ACPro dataset classified it as the 2S type.
41	IL-1β [51]	1I1B (3–153)	β	β-Trefoil	151	153	7.0	25	N2S	-4.0		1.4	-11.1		0.93	— NA	NA NA	— NA	— NA	The ln(k_u) was taken from reference [52].
42	TI I27 [53]	1TIT	β	Immunoglobulin-like β-sandwich	89	89	7.4	25	N2S	3.6		NA	-7.6		0.94	—	—	— 2S	—	Both the AG and our datasets adopted the same reference [53]. The ACPro and our datasets classified the folding type as the N2S type according to the reference, but the Garbuzynskiy dataset classified it as the 2S type.
43	10FNIII [54]	1TTG	β	Immunoglobulin-like β-sandwich	94	94	5.0	25	N2S	5.5		NA	-8.4		NA	—	—	—	—	The ln(k_u) value was obtained by extrapolation to zero denaturant by using the second-order polynomial of the denaturant (GuSCN) activity. The ln(k_f) value was based on the linear extrapolation along GuHCl concentration [55].
44	CRABPI (Mouse) [56]	1CBI	β	Lipocalins	136	137	8.0	25	N2S	-3.2		2.6	-9.2		0.72	NA —	NA —	NA —	NA —
45	CRBPII (Rat) [56]	1OPA (1–133)	β	Lipocalins	133	134	8.0	25	N2S	1.4		7.6	-6.3		0.79	NA —	NA —	NA —	NA —
46	IFABP [57]	1IFC	β	Lipocalins	131	131	7.3	20	N2S	4.3	4.7	7.6	-5.1	-3.1	0.69	NA 8.0	NA 25	—	NA 3.40	We have adopted the data from reference [57], which is more updated than reference [56] adopted by the Garbuzynskiy dataset.
47	Carbonic anhydrase II (Bovine) [58]	1V9E	β	Carbonic anhydrase	259	260	8.0	20	N2S	-4.4	-3.6	-2.4	-23.6	-19.6	NA	—	—	—	—
48	CRABPII (Mouse) [59]	2FS6	β	Lipocalins	137	137	8.0	25	N2S	2.3		4.7	-5.7		0.83	NA	NA	NA	NA
49	Pseudoazurin [60]	1ADW	β	Cupredoxin-like	123	123	7.0	15	N2S	0.69	1.6	NA	-3.5	0.2	0.90	— NA	— NA	— NA	— NA	The experiments were carried out in the presence of 0.5 M Na2SO4.
50	SNase [61]	2PQE	β	OB-fold	149	149	6.0	20.0	N2S	2.2	2.7	4.9	-6.3	-4.0	NA	5.3	15	—	2.34	We adopted reference [61], but the AG dataset adopted another reference [62]. Because this protein exhibited multiple parallel pathways of folding, we reported the averaged k_f value obtained by the equation shown in the comment of entry number 24. Moreover, the ln(k_u) was estimated from the chevron plot for the P47T/P117G mutant (pH 7.0 and 20°C) [63]
51	BABP (Human) [64]	5L8I (3–127)	β	Lipocalins	125	128	8.0	25	N2S	0.64		2.7	-8.6		0.70	NA	NA	NA	NA
52	IL-33 [65]	2KLL	β	NA	160	160	6.5	25	N2S	-1.4		NA	-12.3		0.82	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 nine subdivisions: 1) pH, 2) Temperature, 3) folding type, 4) the ln(k_f) reported, 5) the ln(k_f) value after the temperature correction, 6) the logarithmic rate constant of formation of a folding intermediate, ln(k_I), when the value is available in the literature (only for N2S proteins), 7) the ln(k_u) value reported, 8) the ln(k_u) value after the temperature correction and 9 ) 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.

References:

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