We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles (NPs). The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the aminoacids via a central force that depends on the nanoparticle size. The proposed methodology is used to predict the adsorption energies for six common human blood plasma proteins on hydrophobic charged or neutral nanoparticles of different sizes as well as the preferred orientation of the molecules upon adsorption. Our approach allows one to rank the proteins by their binding affinity to the nanoparticle, which can be used for predicting the composition of the NP-protein corona. The predicted ranking is in good agreement with known experimental data for protein adsorption on surfaces.

1.
M.
Monopoli
,
C.
Aberg
,
A.
Salvati
, and
K. A.
Dawson
,
Nat. Nanotechnol.
7
,
779
(
2012
).
2.
I.
Lynch
,
K. A.
Dawson
, and
S.
Linse
,
Sci. Signaling
2006
,
pe14
.
3.
T.
Cedervall
,
I.
Lynch
,
S.
Lindman
,
T.
Berggard
,
E.
Thulin
,
H.
Nilsson
,
K. A.
Dawson
, and
S.
Linse
,
Proc. Natl. Acad. Sci. U. S. A.
104
,
2050
(
2007
).
4.
S.
Lindman
,
I.
Lynch
,
E.
Thulin
,
H.
Nilsson
,
K. A.
Dawson
, and
S.
Linse
,
Nano Lett.
7
,
914
(
2007
).
5.
L.
Allen
,
M.
Tosetto
,
I.
Miller
,
D.
O’Connor
,
S.
Penney
,
I.
Lynch
,
A.
Keenan
,
S.
Pennington
,
K.
Dawson
, and
W.
Gallagher
,
Biomaterials
27
,
3096
(
2006
).
6.
P.
Kamath
,
A.
Fernandez
,
F.
Giralt
, and
R.
Rallo
,
Curr. Top. Med. Chem.
15
,
1930
(
2015
).
7.
O. V.
Salata
,
J. Nanobiotechnol.
2
,
3
(
2004
).
8.
M.
Rahman
,
M.
Ahmad
,
I.
Kazmi
,
S.
Akhter
,
M.
Afzal
,
G.
Gupta
, and
V. R.
Sinha
,
Curr. Drug Discovery Technol.
9
,
319
(
2012
).
9.
Z.
Wang
,
G.
Niu
, and
X.
Chen
,
Pharm. Res.
31
,
1358
(
2014
).
10.
C.
Roecker
,
M.
Poetzl
,
F.
Zhang
,
W. J.
Parak
, and
G. U.
Nienhaus
,
Nat. Nanotechnol.
4
,
577
(
2009
).
11.
P. M.
Kelly
,
C.
Aberg
,
E.
Polo
,
A.
O’Connell
,
J.
Cookman
,
J.
Fallon
,
Z.
Krpetic
, and
K. A.
Dawson
,
Nat. Nanotechnol.
10
,
472
(
2015
).
12.
J. C.
Silva
,
M. V.
Gorenstein
,
G.-Z.
Li
,
J. P. C.
Vissers
, and
S. J.
Geromanos
,
Mol. Cell. Proteomics
5
,
144
(
2006
).
13.
S.
Ritz
,
S.
Schoettler
,
N.
Kotman
,
G.
Baier
,
A.
Musyanovych
,
J.
Kuharev
,
K.
Landfester
,
H.
Schild
,
O.
Jahn
,
S.
Tenzer
, and
V.
Mailaender
,
Biomacromolecules
16
,
1311
(
2015
).
14.
S.
Winzen
,
S.
Schoettler
,
G.
Baier
,
C.
Rosenauer
,
V.
Mailaender
,
K.
Landfester
, and
K.
Mohr
,
Nanoscale
7
,
2992
(
2015
).
15.
P.
del Pino
,
B.
Pelaz
,
Q.
Zhang
,
P.
Maffre
,
G. U.
Nienhaus
, and
W. J.
Parak
,
Mater. Horiz.
1
,
301
(
2014
).
16.
G.
Brancolini
,
D. B.
Kokh
,
L.
Calzolai
,
R.
Wade
, and
S.
Corni
,
ACS Nano
6
,
9863
(
2012
).
17.
F.
Ding
,
S.
Radic
,
R.
Chen
,
P.
Chen
,
N.
Geitner
,
J.
Brown
, and
P.
Ke
,
Nanoscale
5
,
9162
(
2013
).
18.
S.
Khan
,
A.
Gupta
, and
C.
Nandi
,
J. Phys. Chem. Lett.
4
,
3747
(
2013
).
19.
F.
Tavanti
,
A.
Pedone
, and
M. C.
Menziani
,
New J. Chem.
39
,
2474
(
2015
).
20.
P.
Vilaseca
,
K.
Dawson
, and
G.
Franzese
,
Soft Matter
9
,
6978
(
2013
).
21.
M.
Bellion
,
L.
Santen
,
H.
Mantz
,
H.
Hoehl
,
A.
Quinn
,
A.
Nagel
,
C.
Gilow
,
C.
Weitenberg
,
Y.
Schmitt
, and
K.
Jacobs
,
J. Phys.: Condens. Matter
20
,
404226
(
2008
).
22.
M.
Oberle
,
C.
Yigit
,
S.
Angioletti-Uberti
,
J.
Dzubiella
, and
M.
Ballauff
,
J. Phys. Chem. B
119
,
3250
(
2015
).
23.
M.
Rabe
,
D.
Verdes
, and
S.
Seeger
,
Adv. Colloid Interface Sci.
162
,
87
(
2011
).
24.
V.
Tozzini
,
Curr. Opin. Struct. Biol.
15
,
144
(
2005
).
25.
S.
Takada
,
Curr. Opin. Struct. Biol.
22
,
130
(
2012
).
26.
W. G.
Noid
,
J. Chem. Phys.
139
,
090901
(
2013
).
28.
T.
Bereau
and
M.
Deserno
,
J. Chem. Phys.
130
,
235106
(
2009
).
29.
S.
Miyazawa
and
R.
Jernigan
,
J. Mol. Biol.
256
,
623
(
1996
).
30.
Y.
Kim
,
C.
Tang
,
G.
Clore
, and
G.
Hummer
,
Proc. Natl. Acad. Sci. U. S. A.
105
,
12855
(
2008
).
31.
Y.
Kim
and
G.
Hummer
,
J. Mol. Biol.
375
,
1416
(
2008
).
32.
S.
Wei
and
T.
Knotts
,
J. Chem. Phys.
139
,
095102
(
2013
).
33.
M.
Agashe
,
V.
Raut
,
S.
Stuart
, and
R.
Latour
,
Langmuir
21
,
1103
(
2005
).
34.
Y.
Sun
,
W.
Welsh
, and
R.
Latour
,
Langmuir
21
,
5616
(
2005
).
35.
D.
Kokh
,
S.
Corni
,
P.
Winn
,
M.
Hoefling
,
K.
Gottschalk
, and
R.
Wade
,
J. Chem. Theory Comput.
6
,
1753
(
2010
).
36.
A.
Lesniak
,
A.
Campbell
,
M. P.
Monopoli
,
I.
Lynch
,
A.
Salvati
, and
K. A.
Dawson
,
Biomaterials
31
,
9511
(
2010
).
37.
H.
Limbach
,
A.
Arnold
,
B.
Mann
, and
C.
Holm
,
Comput. Phys. Commun.
174
,
704
(
2006
).
38.
W.
Chen
,
H.
Huang
,
C.
Lin
,
F.
Lin
, and
Y.
Chan
,
Langmuir
19
,
9395
(
2003
).
39.
S.
Yu
,
X.
Xu
,
C.
Yigit
,
M.
van der Giet
,
W.
Zidek
,
J.
Jankowski
,
J.
Dzubiella
, and
M.
Ballauff
,
Soft Matter
11
,
4630
(
2015
).
40.
S.
Lacerda
,
J.
Park
,
C.
Meuse
,
D.
Pristinski
,
M.
Becker
,
A.
Karim
, and
J.
Douglas
,
ACS Nano
4
,
365
(
2010
).
42.
C. A.
LeDuc
,
L.
Vroman
, and
E. F.
Leonard
,
Ind. Eng. Chem. Res.
34
,
3488
(
1995
).
43.
J.
Ortega-Vinuesa
and
R.
Hidalgo-Alvarez
,
Biotechnol. Bioeng.
47
,
633
(
1995
).
44.
M.
Holmberg
and
X.
Hou
,
Langmuir
25
,
2081
(
2009
).
45.
N.
Ben-Tal
,
B.
Honig
,
C. K.
Bagdassarian
, and
A.
Ben-Shaul
,
Biophys. J.
79
,
1180
(
2000
).
46.
S.
Köhler
,
F.
Schmid
, and
G.
Settanni
,
PLOS Comput. Biol.
11
,
e1004346
(
2015
).
47.
E.
Brandt
and
A. P.
Lyubartsev
,
Biophys. J.
106
,
208a
(
2014
).
48.
E.
Brandt
and
A. P.
Lyubartsev
,
J. Phys. Chem. C
119
,
18126
(
2015
).
You do not currently have access to this content.