Copyright WILEY-VCH Verlag GmbH & Co. KGaA, 69469 Weinheim, Germany, 2013.
Supporting Information
On the Electron Transfer through Geobacter sulfurreducens PilA Protein
Nikolai Lebedev*, Syed Mahmud, Igor Griva, Anders Blom, Leonard M. Tender
Table S1. Transmission eigenvalues for main conductive channels in PilA fragments
Fragment 1
Transmission energy = +3.80 eV
Eigenvalues:
1.558338e-02
5.537715e-11
5.063178e-12
Transmission energy = -4.36 eV
Eigenvalues:
5.843808e-05
2.736846e-08
9.330608e-11
Transmission energy = -4.79 eV
Eigenvalues:
8.136470e-02
2.805728e-07
5.254400e-08
Fragment 2
Transmission energy = +3.60 eV
Eigenvalues:
7.052580e-01
3.309871e-07
3.355569e-08
Transmission energy = +2.97 eV
Eigenvalues:
4.771211e-02
5.693065e-10
5.896611e-11
Transmission energy = -4.89 eV
Eigenvalues:
2.591024e-01
1.023903e-09
2.217945e-14
Fragment 3
Transmission energy = +4.05 eV
Eigenvalues:
1.449451e-02
1.805128e-09
8.013476e-11
Transmission energy = +2.92 eV
Eigenvalues:
3.658953e-03
5.214895e-09
1.307387e-12
Transmission energy = -3.90 eV
Eigenvalues:
3.104484e-05
1.871108e-08
3.584779e-10
Fragment 1:
Structure
(Dipole=46.9283 Debye)
Fragment 2:
Structure
(Dipole= 63.2240 Debye)
Fragment 3:
Structure
(Dipole=94.0446 Debye)
LUMO (+0.32eV)
LUMO (-5.52eV)
LUMO (-3.09eV)
HOMO (-1.45eV)
HOMO (-7.00eV)
HOMO (-3.32 eV)
Figure S1A. Molecular Structures, dipole moments, locations of HOMOs and LUMOs and their
energies (in parentheses) for fragments 1, 2, and 3 calculated using B3LYP functional with 631G(d) basis set. The protons presence and location are as if the fragments are at neutral pH: the
side carboxylic groups of aspartates and glutamates are considered to be deprotonated (charge 1) and side amino groups of arginines and lysines are considered as protonated (charge +1).
Fragment 1:
Structure
(Dipole=52.7458 Debye)
Fragment 2:
Structure
(Dipole= 70.3374 Debye)
Fragment 3:
Structure
(Dipole=100.2383 Debye)
LUMO (-0.085 eV)
LUMO (-5.76 eV)
LUMO (-3.51 eV)
HOMO (-2.02 eV)
HOMO (-7.16 eV)
HOMO (-3.74 eV)
Figure S1B. Molecular Structures, dipole moments, locations of HOMOs and LUMOs and their
energies (in parentheses) for fragments 1, 2, and 3 calculated using B3LYP functional with
LanL2DZ basis set. The protons presence and location are as if the fragments are at neutral pH:
the side carboxylic groups of aspartates and glutamates are considered to be deprotonated
(charge -1) and side amino groups of arginines and lysines are considered as protonated (charge
+1).
Fragment 1:
Structure
(Dipole=95.6132 Debye)
Fragment 2:
Structure
(Dipole=107.4924 Debye)
Fragment 3:
Structure
(Dipole=121.5887 Debye)
LUMO (-1.30 eV)
LUMO (-5.41 eV)
LUMO (-3.18 eV)
HOMO (-1.41 eV)
HOMO (-5.31 eV)
HOMO (-3.32 eV)
Figure S1C. Molecular Structures, dipole moments, locations of HOMOs and LUMOs and their
energies (in parentheses) for fragments 1, 2, and 3 with protonated (charged) N- and C-terminal
end groups calculated using B3LYP functional with 6-31G(d) basis set. The protons presence
and location are as if the fragments are at neutral pH: the side carboxylic groups of aspartates
and glutamates are considered to be deprotonated (charge -1) and side amino groups of arginines
and lysines are considered as protonated (charge +1).
Fragment 1:
Fragment 2:
Fragment 3:
+5.00 eV
+4.84 eV
+4.54 eV
+4.37 eV
+4.22 eV
4
+4.02 eV
+3.60 eV
+4.16 eV
4
+3.80 eV
+3.60 eV
+4.84 eV
+4.76 eV
+4.05 eV
4
+3.19 eV
+2.97 eV
+3.10 eV
+2.92 eV
2
2
Energy (E-Ef), eV
2
Energy (E-Ef)
Energy (E-Ef) , eV
+0.77 eV
0
-2
0
0
-2
-2
-4
-4
-3.01 eV
-3.71 eV
-3.42 eV
-4
-4.01 eV
0.00
0.05
-4.89 eV
-4.83 eV
0.10 0.15 0.20 0.25
Tranmission Efficiency
-4.32 eV
-4.56 eV
-4.90 eV-4.96 eV
-4.52 eV
-4.35 eV
-4.79 eV
0.0
0.30
-3.78 eV
-3.94 eV
0.0
0.2
0.4
0.6
Transmission Efficiency
0.1
0.2
0.3
0.4
Transmission Efficiency
0.5
Figure S2. Electron transmission spectra for fragment 1, fragment 2, and fragment 3 calculated
for the molecules with uncharged peptide N- and C-terminal ends (HN0- and –COOH0) by using
LDA approximation with PZ functional (blue); with protonated (charged) peptide ends (H3N+and –COO-) by using LDA approximation with PZ functional (red); and with protonated
(charged) peptide ends (H3N+- and –COO-) by using GGA approximation with PBE functional
(green). All calculations are done at zero bias voltage.
Fragment 2:
Fragment 3:
0
0
-1
-1
-1
-2
Veff,eV
0
Veff,eV
Veff, eV
Fragment 1:
-2
-2
-3
-3
-3
-4
-4
-4
0.0
0.2
0.4
0.6
Z coordinate
0.8
1.0
0.0
0.2
0.4
0.6
Z coordinate
0.8
1.0
0.0
0.2
0.4
0.6
Z coordinate
0.8
Figure S3. Profiles of effective potential projected to Z coordinate for fragment 1, fragment 2,
and fragment 3 calculated for the molecules with uncharged peptide N- and C-terminal ends
(HN0- and –COOH0) by using LDA approximation with PZ functional (blue); with protonated
(charged) peptide ends (H3N+- and –COO-) by using LDA approximation with PZ functional
(red); and with protonated (charged) peptide ends (H3N+- and –COO-) by using GGA
approximation with PBE functional (green). All calculations are done at zero bias voltage.
1.0
Fragment 2, Conformation #1:
Fragment 2, Conformation #4:
Structure
Structure
+3.60 eV
+3.61 eV
+2.97 eV
+3.09 eV
4.89 eV
-4.78 eV
Figure S4. Molecular structures and spatial distribution of conductive eigenstates at energies
+3.61, +3.09 and -4.78 eV in fragments 2 in conformation #4 compared to conformation #1.
0.0
0.1
Transmission Efficiency
0.2
0.3
0.4
0.5
0.6
0.7
Transmission Efficiency
0.2
0.4
0.6
0.0
+4.96 eV
+4.93 eV
+4.96 eV
+4.93 eV
+4.54 eV
4
+4.11 eV +3.99 eV
4
Transmission Efficiency
0.2
0.4
0.6
0.0
+4.54 eV
+4.11 eV +3.99 eV
4
+3.94 eV
+3.60 eV
+3.94 eV
+3.60 eV
+3.19 eV
+2.97 eV
+3.19 eV
+2.97 eV
2
+0.77 eV
0
Energy (E-Ef) , eV
2
Energy (E-Ef) , eV
Energy (E-Ef), eV
2
0
+0.77 eV
0
-2
-2
-2
-4
-4
-4
-4.89 eV
-4.78 eV
-4.78 eV
-4.89 eV
Figure S5. Electron transmission spectra (ETS) of fragment 2 in conformation #1 (red) and
conformation #4 (blue).
Conformation #1
CIAIPQFSAYRVKAYNSA
Conformation #4
CIAIPQFSAYRVKAYNSA
Conformation #4 vs. #1
CIAIPQFSAYRVKAYNSA
Figure S6. Profile of effective potential projected to Z coordinate for PilA central part (fragment
2) in conformation #1 (red) conformation #4 (blue). The amino acid sequence is shown above the
profiles.
+4.96 eV
+3.99 eV
+3.94 eV
+4.93 eV
-4.78eV
+4.11 eV
Figure S7. Electron transfer paths for transmission bands at +4.96, +4.93, +4.11, +3.99, +3.94,
and -4.78 eV for fragment 2 in conformation #4.