from pico to nano: biofunctionalization of cube-octameric ...supplemental information this journal...

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This journal is © The Royal Society of Chemistry [year] Journal Name, [year], [vol], 00–00 | 0

From Pico to Nano: Biofunctionalization of Cube-octameric

Silsesquioxanes by Peptides and Miniproteins

Sebastian Fabritz,‡ Sebastian Hörner,‡ Doreen Könning, Martin Empting, Michael Reinwarth, Christian Dietz, Bernhard Glotzbach, Holm Frauendorf,

Harald Kolmar* and Olga Avrutina

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Electronic Supplemental Information

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Fig. S1: HR-MS spectrum of 2.


Fig. S3: ATR-IR spectrum of 2.


Fig. S5: (a) 1H-NMR of 2, (b) 1H-NMR of 3. 15

Fig. S6: (a) 29Si-NMR of 2, (b) 29Si-NMR of 3, the NMR spectra were base-line corrected using MestReNova.

Fig. S7: AFM image of aggregated and randomly distributed COSS particles 1.

Fig. S8: (a) proposed structure of reaction intermediates in the synthesis of 6. (b) ESI-MS spectrum of the reaction mixture after 30 min.

Fig. S9: (a) unprotected aminooxy COSS particle, (b) periodate oxidized p4, (c) possible conjugation products 4.

Fig. S10: LC-MS monitoring of the synthesis of 4: analysis after overnight reaction. 20

Fig. S11: Synthesis of 4: deconvoluted ESI MS spectrum of the reaction mixture.

Fig. S12: 3D representation (sticks) of compound 4.


Fig. S14: LC-MS monitoring of the synthesis of 5: analysis after overnight reaction.

Fig. S15: Synthesis of 5: deconvoluted ESI MS spectrum of the reaction mixture. 25





Fig. S20: LC-MS monitoring of the synthesis of 7: analysis after overnight reaction. 30





Fig. S25: (a) unprotected aminooxy COSS particle, (b) periodate oxidized p9, (c) possible conjugation products 9. 35



40

Electronic Supplementary Material (ESI) for Organic & Biomolecular ChemistryThis journal is © The Royal Society of Chemistry 2012



Fig. S3: ATR-IR spectrum of 2




Fig. S5: (a) 1H-NMR of 2, (b) 1H-NMR of 3.




Fig. S6: (a) 29Si-NMR of 2, (b) 29Si-NMR of 3, the NMR spectra were base-line corrected using MestReNova. 5




5

Fig. S7: AFM image of aggregated and randomly distributed COSS particles 1.

10

15

20



This journal is © The Royal Society of Chemistry [year]

a 5

b

10

Fig. S8: (a) proposed structure of reaction intermediates

15

Royal Society of Chemistry [year] Journal Name

proposed structure of reaction intermediates in the synthesis of 6. (b) ESI-MS spectrum of the reaction mixture

Journal Name, [year], [vol], 00–00 | 8

reaction mixture after 30 min.




I P R G D Y R K G COOH

O

O

IPRGDYRKGCOOH

O

O

ON

IPRGDYRKGCOOH

O

O

O

N

IPRGDYRKGCOOH

O

O

O

N

IPRGDYRKGCOOH

O

O

O

Si Si

Si Si

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

NN

N

NN

N N

N

O

O

N

O

O N

OO

NO

ON

O

ON


O


O


O


O

O

ONH2

O

O

NH2

O

O

NH2

O

O

Si Si

Si Si

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

NH

NH

NH

NHN

H

NH NH

NH

O

O

NH2

O

O NH2

OO

NH2

OONH

2

O

ONH

2

Molecular Weight =1117.24Molecular Formula =C48H76N16O15

Molecular Weight =1465.93Molecular Formula =C40H88N16O28Si8

HeptaconjugateMolecular Weight =9160.49Molecular Formula =C376H606N128O126Si8

HexaconjugateMolecular Weight =8061.27Molecular Formula =C328H532N112O112Si8

PentaconjugateMolecular Weight =6962.04Molecular Formula =C280H458N96O98Si8

TetraconjugateMolecular Weight =5862.82Molecular Formula =C232H384N80O84Si8

TriconjugateMolecular Weight =4763.60Molecular Formula =C184H310N64O70Si8

DiconjugateMolecular Weight =3664.37Molecular Formula =C136H236N48O56Si8

MonoconjugateMolecular Weight =2565.15Molecular Formula =C88H162N32O42Si8

OctaconjugateMolecular Weight =10259.72Molecular Formula =C424H680N144O140Si8

a b

c

d





Fig. S12: 3D representation (sticks) of compound 4. The model was generated using the YASARA structure package. 5

atoms and connectivities an energy minimization procedure was applied. The respective peptide structures

coordinates were fixed. The resulting conjugate 4 was simulated in

Blue: nitrogen, green: silicon, red: oxygen, grey: carbon, hydrogen was left out fo

terminal carboxylic carbons of peptide ligands attached to opposing corners of the COSS cage. The measured values

and 5.61 nm. The resulting average diameter was 6.42 ± 0.6910

15

20

25


. The model was generated using the YASARA structure package. After modelling of the

an energy minimization procedure was applied. The respective peptide structures (compare p4)

was simulated in 0.9 % (m/v) NaCl aq. at pH 7 and 298 K for 0.1 ns using the AMBER03 force field.

Blue: nitrogen, green: silicon, red: oxygen, grey: carbon, hydrogen was left out for clarity. Representative diameters were measured

nds attached to opposing corners of the COSS cage. The measured values were

6.42 ± 0.69 nm.


After modelling of the COSS core

) were attached, and the core

using the AMBER03 force field.

r clarity. Representative diameters were measured as distances of C-

were: 7.21 nm, 6.69 nm, 6.16 nm,




O

ONH2

O

O

NH2

O

O

NH2

O

O

Si Si

Si Si

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

NH

NH

NH

NHN

H

NH NH

NH

O

O

NH2

O

O NH2

OO

NH2

OONH

2

O

ONH

2

LHLSLKF

O

G PCOOH

LHLSLKF

O

G PCOOH

N

LHLSLKF

O

G PCOOHN

LHLSLKF

O

G PCOOH

N

L H L S L K F

O

GP COOHN

L H L S L K F

O

GP COOHN

L H L S L K F

O

GP COOHN

O

O

O

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

NH

NH

NH

NHN

H

NH NH

NH

O

O

N

O

O

OOO

ON

O

O

L H L S L K F

O

GP COOH

L H L S L K F

O

GP COOH

O


Molecular Weight =1067.26Molecular Formula =C51H78N12O13

MonoconjugateMolecular Weight =2515.17Molecular Formula =C91H164N28O40Si8

DiconjugateMolecular Weight =3564.42Molecular Formula =C142H240N40O52Si8

TriconjugateMolecular Weight =4597.65Molecular Formula =C193H314N51O64Si8

TetraconjugateMolecular Weight =5662.92Molecular Formula =C244H392N64O76Si-

PentaconjugateMolecular Weight =6712.16Molecular Formula =C295H468N76O88Si8

HexaconjugateMolecular Weight =7761.41Molecular Formula =C346H544N88O100Si8

HeptaconjugateMolecular Weight =8810.66Molecular Formula =C397H620N100O112Si8

OctaconjugateMolecular Weight =9859.91Molecular Formula =C448H696N112O124Si8

a b

c

d





Fig. S19: (a) unprotected aminooxy COSS particle, (b) periodate oxidized p7, (c) possible conjugation products.




O

ONH2

O

O

NH2

O

O

NH2

O

O

Si Si

Si Si

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

NH

NH

NH

NHN

H

NH NH

NH

O

O

NH2

O

O NH2

OO

NH2

OONH

2

O

ONH

2

O

ONH2

O

O

NH2

O

O

NH2

O

O

Si Si

Si Si

O

O

O

O

O

Si Si

Si Si

O

O

O

O

O

NH

NH

NH

NHN

H

NH NH

NH

O

O

N

O

O N

OO

NH2

OONH

2

O

ONH

2

W G V P K V L R N R R D S D P G A I L G N G YN

O

S

N

O

S

N

O

S

N

O

S

N

O

S

N

O

S

O

N

O

NH2


O

S

N

O

S

N

O

S

N

O

S

N

O

S

N

O

S

O

N

O

NH2


O

S

N

O

S

N

O

S

N

O

S

N

O

S

N

O

S

O

O

N

O

NH2


Molecular Weight =3265.79Molecular Formula =C134H206N44O40S6

MonoconjugateMolecular Weight =4713.70Molecular Formula =C174H292N60O67S6Si8

DiconjugateMolecular Weight =7961.48Molecular Formula =C308H496N104O106S12Si8

a

b

c

d






5




Fig. S25: (a) unprotected aminooxy COSS particle, (b) periodate oxidized p9, (c) possible conjugation products 9. 5




Fig. S26: LC-MS monitoring of the synthesis of


MS monitoring of the synthesis of 9: analysis after overnight reaction.






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