Table 1.
Translational Hydrodynamic Radii for Folded Proteins
| Protein (PDB ID) | M (Da) | Chains | RT,expa (Å) | RT,calc (Å) | % Signed Error | % Error (Jackknifed) | a/bb | Reference(s) |
|---|---|---|---|---|---|---|---|---|
| BPTI (5PTI) | 6518 | 1 | 14.5 | 14.3 | −1.61 | −3.41 | 1.66 | (65) |
| Cytochrome c (1HRC) | 11,703 | 1 | 17.3c | 17.2 | −0.39 | −0.56 | 1.16 | (66, 67, 68) |
| RNase A (8RAT) | 13,692 | 1 | 18.9 | 19.0 | +0.37 | +0.27 | 1.31 | (65) |
| Lysozyme (1AKI) | 14,315 | 1 | 18.6 | 18.5 | −0.54 | −0.75 | 1.51 | (65) |
| LegHb (1LH1) | 16,657 | 1 | 21.4 | 20.2 | −5.72 | −5.86 | 1.43 | (69) |
| Apo-Mb (1MGN) | 17,359 | 1 | 20.8 | 19.9 | −4.19 | −4.52 | 1.35 | (70) |
| Soy TI (1AVU)d | 19,984 | 1 | 22.6 | 21.9 | −3.21 | −3.43 | 1.10 | (71) |
| Trypsinogen (1TGN) | 22,620 | 1 | 22.1 | 22.1 | −0.11 | −0.25 | 1.15 | (72) |
| β-trypsin (1TPO) | 23,124 | 1 | 22.8 | 22.2 | −2.74 | −2.96 | 1.13 | (73) |
| α-chymotrypsin (4CHA)d | 25,041 | 1 | 22.7 | 22.9 | +0.80 | +0.72 | 1.15 | (71) |
| Chymotrypsinogen (2CGA)d | 25,670 | 1 | 22.6 | 23.3 | +2.91 | +2.91 | 1.08 | (74) |
| Carbonic anhydrase (2CAB)d | 28,757 | 1 | 24.1 | 23.9 | −0.71 | −0.84 | 1.36 | (75) |
| Superoxide dismutase (2SOD)d | 31,089 | 2 | 25.9 | 25.8 | −0.58 | −0.73 | 1.59 | (76) |
| Pepsin (4PEP)d | 34,516 | 1 | 24.6 | 26.2 | +6.26 | +6.38 | 1.37 | (77) |
| β-lactoglobulin (1BEB)d | 36,606 | 2 | 27.4 | 27.3 | −0.52 | −0.66 | 1.83 | (78) |
| TPI (8TIM) | 52,996 | 2 | 29.7 | 30.5 | +2.42 | +2.39 | 1.45 | (66) |
| Hb (CO) (1HCO) | 61,942 | 4 | 31.5 | 31.6 | +0.24 | +0.15 | 1.11 | (79) |
| HSA (1AO6) | 66,482 | 1 | 34.0 | 35.1 | +3.21 | +3.21 | 1.49 | (80) |
| Alkaline phosphatase (1ALK) | 94,082 | 2 | 37.6 | 36.5 | −2.94 | −3.10 | 1.67 | (81) |
| Citrate synthase (1CTS)d | 97,835 | 2 | 37.0 | 37.7 | +2.06 | +2.03 | 1.53 | (82) |
| Inorganic PPase (2AU9) | 1,17,361 | 6 | 37.6 | 39.4 | +4.72 | +4.77 | 1.23 | (81) |
| Trp. synth. (1KFK) | 1,38,595 | 4 | 44.4 | 45.8 | +3.11 | +3.11 | 2.20 | (83) |
| Human IgG (1HZH) | 1,433,37 | 4 | 55.1 | 54.9 | −0.37 | −0.44 | 2.07 | (84) |
| Apo-G3PD (2GD1)d | 1,43,743 | 4 | 42.9 | 43.3 | +1.00 | +0.95 | 1.16 | (85) |
| Apo-LDH (5LDH)d | 1,45,749 | 4 | 42.5 | 42.5 | −0.07 | −0.14 | 1.20 | (86) |
| Aldolase (1ADO)d | 1,56,776 | 4 | 47.6c | 47.7 | +0.12 | +0.03 | 1.30 | (87, 88, 89) |
| Holo calalase (4BLC)d | 2,30,321 | 4 | 52.3 | 52.4 | +0.17 | +0.11 | 1.47 | (90) |
| Xanthine oxidase (1FIQ) | 2,67,770 | 6 | 54.5 | 54.5 | −0.14 | −0.21 | 1.78 | (91) |
| β-galactosidase (4V40) | 4,64,490 | 4 | 68.5 | 67.1 | −2.02 | −2.10 | 1.63 | (92) |
| Apoferritin (3AJO) | 5,120,84 | 24 | 67.4 | 64.7 | −4.00 | −4.11 | 1.00 | (93) |
| Urease (3LA4) | 5,397,00 | 6 | 65.8c | 66.6 | +1.26 | +1.23 | 1.13 | (94, 95) |
| GroEL (2CGT) | 8,28,989 | 21 | 82.8 | 86.3 | +4.26 | +4.27 | 1.40 | (96) |
| YMV capsid (1AUY) | 3,456,960 | 60 | 151.2 | 152.4 | +0.28 | +0.28 | 1.06 | (97) |
| mean % signed error | +0.10 | −0.04 | ||||||
Hb, hemoglobin; HSA, human serum albumin; IgG, immunoglobulin G; TI, trypsin inhibitor; TPI, triose phosphate isomerase; Trp. Synth., tryptophan synthase; YMV, Yellow Mosaic Virus.
a
All experimental hydrodynamic coefficients as reported in the references were converted to RT for comparison.
b
Axial ratio of a prolate ellipsoid with volume equal to the initial convex hull volume.
c
Average value of those reported in cited publications.
d
PDB files for these structures provided by Mattia Rocco and Olwyn Byron. Missing residues were modeled as described in (32).