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European Biophysics Journal

, Volume 44, Issue 6, pp 433–436 | Cite as

Erratum to: Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

  • Mattia RoccoEmail author
  • Olwyn Byron
Erratum
  • 630 Downloads

Erratum to: Eur Biophys J DOI 10.1007/s00249-015-1042-9

In the original publication of the article, the minus sign is omitted in the last two entries of the last column “BEST Heur” in Table 2. Similar error is also found in Table 3, in the fifth entry under Column 7. The correct version of both Tables 2 and 3 are given for your reading:
Table 2

Proteins used for the comparison, with their PDB code, molecular weight (mol. wt.), partial specific volume (\( \bar{v}_{{(20,{\text{w}})}} \)), experimental sedimentation coefficient (±SD) (\( s_{{(20,{\text{w}})}}^{0} \) expt.) taken from the literature (Ref.), and percent difference between the computed and experimental \( s_{{(20,{\text{w}})}}^{0} \) values (Δ % \( s_{{(20,{\text{w}})}}^{0} \) comp.) for each of the different methods used. The horizontal line between entries 13 and 14 separates monomeric from multimeric solution forms

#

Proteina

PDB

Mol. wt.

\( \bar{v}_{{(20,{\text{w}})}} \) b cm3/g

\( s_{{(20,{\text{w}})}}^{0} \) expt.c S

Ref.d

Δ % \( s_{{(20,{\text{w}})}}^{0} \) comp.

SoMo SMI

SoMo Zeno

SoMo ov Zeno

AtoB G5 SMI

AtoB G2 SMI

HP auto

BEST man

BEST heur

1

Cytochrome c

1HRC

12,357.5

0.724

2.00 ± 0.04*

2,3

−21.0

−14.2

−16.3

−23.5

−23.0

−17.5

−18.1

−17.8

2

Ribonuclease A

8RAT

13,683.8

0.709

2.00 ± 0.03 

2e

−3.0

−4.0

−6.5

−5.0

−4.0

−10.0

−10.4

−10.4

3

α-Lactalbumin

1A4Vf

15,784.7

(0.718)

1.76 ± n.a.*

3e

+13.6

+12.6

+9.4

+10.8

+10.8

0.0

+5.7

+5.6

4

Lysozyme

1AKI

14,306.7

(0.716)

1.88 ± 0.02

2e

+5.9

+5.1

+2.4

+3.2

+4.3

−2.7

−1.8

−1.6

5

Myoglobin apo

2V1 K

17,568.3

0.743

2.05 ± n.a.

3e

−1.0

−1.9

−4.6

−3.9

−3.4

−6.3

−6.7

−6.8

6

Soybean trypsin inh.

1AVU

19,962.8

(0.735)

2.29 ± n.a.

4

−2.6

−3.8

−5.7

−4.4

−3.9

−4.4

−8.7

−8.8

7

β-Trypsin

1TPO

23,335.9

(0.724)

2.54 ± 0.02

5

+6.3

+5.6

+2.4

+3.5

+3.9

−1.2

−0.5

−0.5

8

Trypsinogen

1TGN

23,182.7

0.73

2.48 ± 0.01 

5

+7.7

+5.1

+2.0

+4.8

+5.6

−1.6

−0.9

−0.9

9

α-Chymotrypsin (mon)

4CHA

25,236.5

(0.733)

2.59 ± 0.02 

6

+3.1

+3.0

+0.8

+1.5

+1.5

−3.5

−2.8

−2.7

10

Chymotrypsinogen A

2CGA

25,659.0

(0.732)

2.56 ± 0.03 

3e

+6.6

+6.3

+4.1

+4.7

+5.5

−0.8

+0.4

+0.2

11

Carbonic anhydrase B

2CAB

28,820.5

0.73

3.01 ± 0.19 

7–10

+1.0

−1.5

−3.9

−1.7

−1.0

−6.3

−6.0

−6.0

12

Pepsin

4PEP

34,588.6

(0.723)

3.19 ± 0.08 

11

+6.3

+5.5

+3.6

+4.4

+5.0

−0.3

+0.5

+0.4

13

H. serum albumin

1AO6

66,428.6

(0.734)

4.28 ± 0.04

12

+5.1

+5.5

+4.3

+5.1

+5.4

+0.9

+2.8

+2.5

14

Superoxide dismutase

2SOD

31,442.2

(0.718)

3.03 ± 0.05

13

+1.7

+1.6

−0.4

+1.0

+1.0

−3.0

−2.1

−1.9

15

β-Lactoglobulin

1BEB

35,224.7

(0.745)

2.87 ± 0.06

3e

+4.9

+1.8

+0.3

+4.2

+4.2

−2.1

−1.4

−1.4

16

α-Chymotrypsin (dim)

4CHA

50,473.5

(0.733)

3.5 ± 0.02*

14

+18.0

+18.7

+16.8

+16.9

+16.9

+12.3

+13.7

+13.3

17

Triosephosphate isom.

8TIM

52,971.4

(0.742)

3.75 ± 0.05 

15

+7.5

+6.7

+5.4

+6.1

+6.4

+2.9

+3.7

+3.4

18

Hemoglobin CO

1HCO

64,559.7

0.749

4.5 ± n.a.

3e

+4.4

+3.2

+1.9

+3.1

+3.3

−0.7

+2.5

+2.2

19

Citrate synthase

1CTS

97,845.5

0.733

6.1 ± 0.1

2e

+1.1

+3.3

+3.7

+0.2

+0.5

−1.6

+0.6

+0.1

20

Inorganic pyrophosph.

1FAJ

117,339.0

(0.743)

7.01 ± 0.04 

16

−4.6

−4.2

−5.3

−5.1

−5.1

−8.0

−6.5

−5.8

21

G3PD apo

2GD1

143,787.8

(0.742)

7.6 ± 0.15 

3e

+2.2

+2.5

+1.1

+0.9

+1.2

−0.8

0.0

−0.4

22

G3PD holo

1GD1

146,437.7

(0.741)

8.1 ± 0.16 

3e

−1.5

−1.3

−2.7

−2.6

−2.3

−5.2

−3.5

−3.8

23

LDH pig H + NAD

5LDH

148,942.6

(0.746)

7.80 ± 0.08 

3e

+2.8

+2.8

+1.8

+1.7

+1.9

0.0

−0.2

+0.4

24

LDH pig M + NAD

9LDH

149,063.5

(0.745)

7.79 ± 0.08 

3e

+5.6

+5.9

+4.4

+4.1

+4.2

+1.2

+2.6

+2.4

25

Aldolase

1ADO

157,131.2

0.742

7.85 ± 0.05 

3e

+2.5

+1.2

−0.5

+1.9

+2.0

−2.5

−2.7

−2.5

26

Catalase

4BLC

235,775.1

0.73

11.4 ± 0.15

3e

+2.1

+1.3

+0.2

+1.2

+1.5

−5.3

27

β-Galactosidase

1BGL

465,257.6

(0.725)

16.23 ± 0.13

17

+6.0

+6.6

+5.9

+5.4

+3.3

+2.8

   

Mean Δ % monomeric (without * values)

+3.2 ± 4.0

+2.3 ± 4.2

−0.1 ± 4.2

+1.1 ± 4.1

+1.7 ± 4.0

−3.3 ± 3.2

−3.1 ± 4.2

−3.1 ± 4.2

   

Mean Δ % all (without * values)

+2.9 ± 3.5

+2.3 ± 3.5

+0.6 ± 3.7

+1.4 ± 3.5

+1.7 ± 3.4

−2.4 ± 3.2

−1.9 ± 3.8

−1.9 ± 3.7

SoMo SoMo models without overlaps, SoMo ov SoMo models with overlaps, AtoB G5 AtoB models generated with a 5 Å grid, AtoB G2 AtoB models generated with a 2 Å grid, SMI hydrodynamic computations with the supermatrix inversion procedure, Zeno hydrodynamic computations using the Zeno method, HP auto HYDROPRO shell models generation and hydrodynamic computations via the SMI method, with the automatic determination of the number of beads in each shell model with a maximum of 2000 beads, BEST man BEST models and hydrodynamic computations, with the manual setting for the determination of minimum and maximum number of plates, BEST heur BEST models and hydrodynamic computations, with the heuristic approach for the determination of minimum and maximum number of plates

aFor the species of origin of the protein considered, see the PDB headers and the literature cited (Ref.). Mon monomer, dim dimer

bThe values in parentheses were calculated by US-SOMO, the other are experimental, taken from the literature

cThe values marked with “*” were not considered when taking the reported mean values

dSee the correspondence between the numbers listed and the references at the end of these table footnotes

eSee references cited within this paper

fCarbohydrate not present in the PDB structure, manually modelled

1Stellwagen (1968); 2Rai et al. (2005); 3Brookes et al. (2010b); 4Rackis et al. (1962); 5Cunningham (1954); 6Ghirlando (2011); 7Armstrong et al. (1966); 8Coleman (1965); 9Nyman (1961); 10Rickli et al. (1964); 11Edelhoch (1957); 12Charlwood (1952); 13Wood et al. (1971); 14Schwert (1949); 15McVittie et al. (1977); 16Wong et al. (1970); 17Sund and Weber (1963)

Table 3

Characteristics and performances of the main hydrodynamic modelling/computational methods discussed in this work

Program (conditions)

Structure check?

NMR?a

Modelling method

Computational method

\( D_{{t\;(20,{\text{w}})}}^{0} \) average Δ %b

\( s_{{(20,{\text{w}})}}^{0} \) average Δ %c

Computing time (minutes) for selected structuresd

1AKI (14 kDa)

1AO6 (66 kDa)

1ADO (160 kDa)

SoMo (with overlaps) in US-SOMO

Yese

Yes

BM, residue to bead

Zeno

−0.2 ± 2.4

−0.6 ± 3.7

0.5

7.8

20.3

AtoB (5 Å grid) in US-SOMO

Yese

Yes

BM, grid

SMI

+0.3 ± 2.4

+1.4 ± 3.5

0.03

1

9

SoMo (no overlaps) in US-SOMO

Yese

Yes

BM, residue to bead

SMI

+1.9 ± 2.5

+2.9 ± 3.5

0.02

0.2

0.5

BEST (manual) in US-SOMO

Yesf

No

BE (2000–6000 plates)

SI

−2.7 ± 2.1

−1.9 ± 3.8

356

100

93

BEST (heuristic) in US-SOMO

Yesf

No

BE (variable # of plates)

SI

−2.8 ± 2.2

−1.9 ± 3.7

170

261

1072

HYDROPRO (WinHydropro)

No

No

Shell BM (≤2000 beads)

SMI

−3.6 ± 3.0

−2.4 ± 3.2

0.3

0.3

0.3

BM bead modelling, BE boundary elements, SMI supermatrix inversion, SI surface integrals

aAutomatic computation and averaging of hydrodynamic parameters possible for multiple structures in NMR-type files

bFor all test proteins listed in Table 1, outliers excluded (±SD)

cFor all test proteins listed in Table 2, outliers excluded (±SD)

dFor the Zeno and SMI methods within US-SOMO (Windows version) and HYDROPRO (WinHydropro), computations were run on an Intel Core i5-3470 3.2 GHz PC with 6 GB RAM, operating under the Windows 7 Professional OS; for BEST within US-SOMO, they were run on the TACC Stampede cluster, and do not include waiting times in the queue (see “Materials and methods”)

eApproximate methods available for non-coded or incomplete residues

fChecks performed but no influence on program execution

Copyright information

© European Biophysical Societies' Association 2015

Authors and Affiliations

  1. 1.Biopolimeri e Proteomica, IRCCS AOU San Martino-IST, Istituto Nazionale per la Ricerca sul CancroGenovaItaly
  2. 2.School of Life Sciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK

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