Molecular modeling of cytochrome b5 with a single
cytochrome c-like thioether linkage
Ying-Wu Lina, b*, Yi-Mou Wuc, Li-Fu Liaoa, Chang-Ming Niea
a
School of Chemistry and Chemical Engineering, University of South China,
Hengyang 421001, China
b
State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing
210093, China
c
Institute of Pathogenic Biology, University of South China, Hengyang 421001,
China
Supporting Information
Topology file of residue HOBC defined for oxidized C-type heme with one thioether
linkage and bis-His coordination:
PRES HOBC
-0.50 !-0.73 ! Patch for HEME to C-type Cytochrome b5 links.
! Patch residues must be 1:HSD, 2:HSD, 3:CYS (C-terminal), and
! 4:HEMO.
! Modified by Ying-Wu Lin 10/3/2011 to include charge
! redistribution and to be a single patch.
GROUP
ATOM 1CB
!
CT2
-0.09 !-0.22 !
ATOM 1ND1 NR1
-0.36 !-0.61 !
1HD1 1HE1
|
ATOM 1HD1 H
0.32 ! 0.45 !
1HB1
ATOM 1CG
-0.05 ! 0.32 !
|
CPH1
GROUP
!
0.25 ! 0.24 !
ATOM 1HE1 HR1
0.13 ! 0.27 !
ATOM 1NE2 NR2
-0.70 ! -0.51 !
ATOM 1CD2 CPH1
0.22 !-0.04 !
ATOM 1HD2 HR3
0.10 ! 0.16 !
DELETE ANGLE 4NA 4FE 4NC
/
||
! -1CB-1CG
ATOM 1CE1 CPH2
/
1ND1-1CE1
|
||
\\
1HB2
||
1CD2-1NE2
|
1HD2
\
4FE-
4NB 4FE 4ND
BOND 1NE2 4FE
ANGLE 1CD2 1NE2 4FE
1CE1 1NE2 4FE
ANGLE 1NE2 4FE
1NE2 4FE
4NC
1NE2 4FE 4NA
1NE2 4FE 4NB
4ND
IMPR 1NE2 1CD2 1CE1 4FE !add impr for heme/his planarity
IC 1CD2 1NE2 4FE
4NA
0.0000
0.0000
0.0000
0.0000
0.0000
IC 1CD2 1NE2 4FE
4NB
0.0000
0.0000
0.0000
0.0000
0.0000
S1
IC 1CD2 1NE2 4FE
4NB
0.0000
0.0000
0.0000
0.0000
0.0000
IC 1CD2 1NE2 4FE
4NB
0.0000
0.0000
0.0000
0.0000
0.0000
IC 1CE1 1NE2 4FE
4NA
0.0000
0.0000
0.0000
0.0000
0.0000
! Heme to Histidine portion of patch
GROUP
ATOM 2CB
!
CT2
-0.09 !-0.22 !
ATOM 2ND1 NR1
-0.36 !-0.61 !
2HD1
|
ATOM 2HD1 H
0.32 ! 0.45 !
ATOM 2CG
-0.05 ! 0.32 !
CPH1
GROUP
!
2HB1
|
/
2ND1-2CE1
/
||
! -2CB-2CG
ATOM 2CE1 CPH2
0.25 ! 0.24 !
|
ATOM 2HE1 HR1
0.13 ! 0.27 !
2HB2
ATOM 2NE2 NR2
-0.70 !-0.51 !
ATOM 2CD2 CPH1
0.22 !-0.04 !
ATOM 2HD2 HR3
0.10 ! 0.16 !
DELETE ANGLE 4NA 4FE 4NC
2HE1
||
\\
||
2CD2-2NE2
|
\
2HD2
4FE-
4NB 4FE 4ND
BOND 2NE2 4FE
ANGLE 2CD2 2NE2 4FE
2CE1 2NE2 4FE
ANGLE 2NE2 4FE
2NE2 4FE
4NC
2NE2 4FE 4NA
2NE2 4FE 4NB
4ND
IMPR 2NE2 2CD2 2CE1 4FE !add impr for heme/his planarity
IC 2CD2 2NE2 4FE
4NA
0.0000
0.0000
0.0000
0.0000
0.0000
IC 2CD2 2NE2 4FE
4NB
0.0000
0.0000
0.0000
0.0000
0.0000
IC 2CD2 2NE2 4FE
4NB
0.0000
0.0000
0.0000
0.0000
0.0000
IC 2CD2 2NE2 4FE
4NB
0.0000
0.0000
0.0000
0.0000
0.0000
IC 2CE1 2NE2 4FE
4NA
0.0000
0.0000
0.0000
0.0000
0.0000
!(C-terminal) Heme to Cysteine (Thioether bond) portion of patch
GROUP
!
ATOM 3CB
CT2
ATOM 3SG
S
0.07 ! -3CB-3SG-4CAC-0.23 !
DELETE ATOM 3HG1
BOND 3SG 4CAC
ANGLE 3CB 3SG
4CAC
ANGLE 3SG 4CAC 4C3C
ANGLE 3SG 4CAC 4CBC
ANGLE 3SG 4CAC 4HAC
DIHEDRAL 3CB 3SG 4CAC 4C3C
DIHEDRAL 3CB 3SG 4CAC 4CBC
DIHEDRAL 3CB 3SG 4CAC 4HAC
DIHEDRAL 3CA 3CB 3SG
4CAC
DIHEDRAL 3HB1 3CB 3SG
4CAC
DIHEDRAL 3HB2 3CB 3SG
4CAC
S2
-1
(deg.cm .dmol )
9
Wild Type cyt b5
6
2
N57C cyt b5
3
[Theta] x 10
4
0
-3
-6
-9
200
210
220
230
Wavelength (nm)
240
250
Fig. S1 Circular dichroism (CD) spectra of WT cyt b5 and N57C cyt b5 in the
oxidized state collected at 25 C from 190 to 250 nm (0.1 cm path length) with a
Jasco model J720 spectropolarimeter. The protein concentration was 25 μM, dissolved
in 100 mM sodium phosphate buffer at pH 7.0. (The experiment was performed by
Y.-W. Lin in Prof. Zhong-Xian Huang’s group at Fudan University, China).
S3
a
b
N57C cyt b5
X-ray:1cyo
c
d
NMR:1hko
DS cyt b5
Fig. S2 Ramachandran plots of amino acids for modeling structure of bovine N57C
cyt b5 (a), X-ray structure of cyt b5 (PDB entry 1cyo) (b), NMR structure of cyt b5
(PDB entry 1hko, model 1) (c), and modeling structure of DS cyt b5 (d), as separately
by dashed line. The horizontal and vertical axes are phi and psi, respectively. Protein
residues are mapped to the Ramachandran diagram with yellow squares. The most
allowed regions of Ramachandran space are colored blue; partially allowed regions
are colored green.
S4