Page 256 - Handbook Of Multiphase Flow Assurance

Molecular modeling 255

The winter flounder polypeptide sequence of the aminoacids in standard nomenclature is:

DTASDAAAAAALTAANAAAAAKLTADNAAAAAAATAA,

where the letters represent D—aspartic acid, T—threonine, A—alanine, S—serine, L—leucine,
N—asparagine, and K—lysine.
The structures of these aminoacids can be found in every recent organic chemistry text-
book. These structures are described in Table 10.8. The VC-713 polymer chain was built as a
repeating sequence of monomers present in the real polymer:

−
−(vinylpyrrolidonevinylcaprolactamDMAEMA ) −.
−
x
The molecules were then transferred from the 486 PC to the IBM workstation in Brookhaven
format. PVP and PVCap chains were also 9 repeat units long. Fig. 10.20 shows polymer struc-
tures. These polymers were built using the SYBYL’ program.
The studied macromolecule and the crystal surface were read into SYBYL’. Charges for
water molecules in the crystal and for the macromolecules were computed using the method
by Pullman (Berthod and Pullman, 1965). Macromolecule was equilibrated in vacuo. Periodic
boundary conditions were set up around the system, and a lattice of the intermolecular po-
tential energy field was precalculated for various relative positions of the macromolecule and
the crystal surface. Six variables define a position and orientation of the rigid polymer chain
in space. Docking of macromolecules on the crystal surface was performed by varying the
x, y, z, Θ and Φ variables for the macromolecule. Coordinates x, y and z specify the center of
the macromolecule relative to the crystal surface, Θ is the angle between the center line of the

TABLE 10.8 Structure of aminoacids composing the winter flounder polypeptide.
General aminoacid formula:

Aminoacid R radical
D aspartic acid CH 2 CO 2 H
T threonine

A alanine CH 3
S serine CH 2
L leucine CH 2 CH(CH 3 ) 2
N asparagine CH 2 CONH 2
K lysine (CH 2 ) 4 NH 2