Biomedical Engineering Reference
In-Depth Information
from the Protein Data Bank
http://www.rcsb.org
) of the native state and any
subscript 0 signifies a value taken from the native state. The potential is given by
X
X
X
r
.r
r
0
/
2
.
0
/
2
V
C˛
.
x
;
x
0
/
D
C
C
D
F
D
.
0
/
bonds
angles
backbone
NC
NC
r
ij
12
X
X
C
C.r
ij
;r
ij
C
0
/
C
;
(2)
contacts
non
contacts
where the dihedral potential F
D
is,
1
2
Œ1
F
D
./
D
Œ1
cos./
C
cos.3/:
(3)
The coordinates
x
describe a configuration of the ˛-carbons, with the bond lengths
to nearest neighbors r , three body angles , four body dihedrals , and distance
between atoms i and j given by r
ij
. C denotes the contact potentials given to
the native contacts (see Sect.
3.2.3
). Protein contacts that are separated by less
than 3 residues are neglected. Excluded volume is maintained by a hard wall
interaction giving the residues an apparent radius of
NC
E
4
˚
A.Thenativebiasis
D
provided by using the parameters from the native state
x
0
. Setting the energy scale
E
k
B
T
D
1, the coefficients are given the homogeneous values:
r
D
100,
D
40,
D
D
C
D
NC
D
.
3.2.2
All-Atom Model
The AA potential is quite similar to the C
˛
potential, although representing the AA
geometry requires some additional terms. In the AA model, all heavy (nonhydrogen)
atoms are explicitly represented as beads of unit mass, so each interaction is now
between atoms as opposed to residues. Bonds, angles, and dihedrals therefore have
their traditional chemical meanings. In each residue, there is an additional backbone
dihedral and, except for glycine, many side chain dihedrals. Improper dihedrals
maintain backbone chirality and, when necessary, side chain planarity. The AA
potential V
AA
is
X
X
X
r
.r
r
0
/
2
.
0
/
2
.
0
/
2
V
AA
.
E
E
x
;
x
0
/
D
C
C
bonds
angles
impropers=planar
X
X
C
BB
F
D
.
0
/
C
SC
F
D
.
0
/
backbone
sidechains
NC
NC
r
ij
12
X
X
C
C.r
ij
;r
i
0
/
C
C
:
(4)
contacts
non
contacts
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