Table 2 Crosslinks detected within DNAJB6 oligomers and between DNAJB6 and Aβ42.

From: Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface

Precursor mass

Charge

Score

Crosslinked peptides DNAJB6-DNAJB6 a

LysA

LysB

#1–2 b

Distance c (Å)

3101.577

3+

52.9

HASPEDIKKAYR + QVAEAYEVLSDAKK

K20

K60

1

16.6

1708.898

3+

69.4

HASPEDIKK + SDAKK

K20

K60

2

16.6

2012.068

3+

78.3

HASPEDIKK + KSISTSTK

K20

K189

1,2

36.0

1750.981

3+

85.4

HASPEDIKK + KITTK

K20

K202

1,2

29.6

2532.388

3+

56.6

HASPEDIKK + SLTINGKEQLL

K20

K232

2

47.2

2587.334

4+

46.3

WHPDKNPENKEEAER + KLALK

K34

K25

2

12.0

2899.498

4+

57.3

HPDKNPENKEEAER + KITTKR

K34

K202

1

16.5

2116.153

3+

54.6

KQVAEAY + TINGKEQLL

K47

K232

1

36.4

2154.108

3+

57.1

EVLSDAKKR + DIYDKY

K60

K67

1

11.0

2275.082

3+

63.7

GKEGLNGGGGGGSHF + KQVAEAY

K70

K47

1

21.6

2439.121

3+

52.6

GKEGLNGGGGGGSHF + DIYDKY

K70

K67

1

5.4

2812.348

3+

61.4

GKEGLNGGGGGGSHF + VEVEEDGQLKSL

K70

K225

1

28.3

1839.014

4+

72.3

KSISTSTK + KSISTSTK

K189

K189

2,*

—

2506.276

3+

54.6

VEVEEDGQLKSL + HASPEDIKK

K225

K20

1,2

33.1

3360.603

3+

65.2

VEVEEDGQLKSL + WHPDKNPENKEEAER

K225

K34

2

25.4

2371.237

3+

88.8

VEVEEDGQLKSL + EVLSDAKK

K225

K60

2

36.8

2483.232

3+

80.6

VEVEEDGQLKSL + DIYDGYGK

K225

K67

1,2

31.7

2492.265

3+

66.3

VEVEEDGQLKSL + SISTSTKM

K225

K196

1,2

14.5

2072.121

3+

79.5

VEVEEDGQLKSL + KITTK

K225

K202

2

12.3

2853.531

3+

77.8

VEVEEDGQLKSL + SLTINGKEQLL

K225

K232

1,2

16.1

2309.220

3+

67.4

TINGKEQLLR + DIYDKYGK

K232

K67

2

40.7

1198.116

3+

54.2

TINGKEQLL + KITTK

K232

K202

1

25.2

2679.516

3+

79.4

SLTINGKEQLL + TINGKEQLLR

K232

K232

1,2,*

—

Precursor mass

Charge

Score

Crosslinked peptides a Aβ42-DNAJB6

LysA

LysB

  

2437.218

3+

48.8

HDSGYEVHHQKL + KSISTSTK

K16

K189

2

 

2384.301

3+

53.8

EVHHQKL + VEVEEDGQLKSL

K16

K225

2

 

2348.265

3+

81.4

FAEDVGSNKGAIIGLM + KITTK

K28

K202

2

 

3129.674

3+

59.3

FAEDVGSNKGAIIGLM + SLTINGKEQLL

K28

K232

2

 
  1. aCrosslinks with BS3 within DNAJB6 can be either intra-subunit or inter-subunit, except the K189xK189 and K232xK232 crosslinks which must be inter-subunit.
  2. bDatasets are: (#1) duplicate samples with crosslinked DNAJB6 oligomers, (#2) duplicate samples in which DNAJB6 oligomers and Aβ42. Approved MSMS-spectra used to validate the crosslinks are supplied in Fig. S6 (#1, 2). As indicated with asterisk (*), the inter-subunit crosslinks K189-K89 and K232-K232 are validated as inter-subunit also as 14N-15N hybrid crosslinks in a separate dataset with unlabeled (14N) and labeled (15N) DNAJB6, approved MSMS-spectra are supplied in Fig. S7.
  3. cCalculated Cα-Cα distances for crosslinked lysine residues using the pdb file of the DNAJB6 Robetta structural model_5 described in Fig. 1.
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