Chemistry Reference
In-Depth Information
to fold into the native state. It has been shown that searching for the ground states
for an HP sequence is an NP-complete problem [
8
,
9
].
The lattice proteins with which we shall deal are of nanoscale dimensions and
hence are at the interface between biology and surface nanoscience. In this chapter
we shall review numerical studies of lattice proteins with different sequences and
also describe our large-scale Monte Carlo studies of several different HP proteins,
both in free space and in contact with an attractive surface.
7.2 Background
7.2.1 The HP Model
In proteins, 20 amino acids are commonly found and they serve as the basic “build-
ing blocks” [
10
]. Each amino acid contains an amino group (
−
NH
2
) and a car-
boxylic acid group (
-carbon atom. Amino
acids are covalently bonded together by a peptide bond between the amino group
of one amino acid and the carboxyl group of another. This forms the linear, rigid
backbone of the protein. The only difference that distinguishes the amino acids is
the side chain to which the
−
COOH), both are bonded to the same
α
-carbon is attached. Side chains can be acidic, basic,
uncharged polar, or non-polar. The first three types are basically hydrophilic, and
the non-polar type is hydrophobic. Hence, the amino acids are classified according
to the types of their side chains.
Amino acids interact with one another or with the environment through non-
covalent bonds: ionic bonds, hydrogen bonds, and van der Waals forces. In an
aqueous environment, hydrophobic amino acids are forced to group together in
order to minimize the disturbance on the hydrogen-bonded networks of water [
11
].
Hydrophobic residues held together in this manner have been regarded as being
“pulled” by their own attraction, the so-called hydrophobic bonds, although it orig-
inates from the repulsive force by the water molecules. Such a hydrophobic interac-
tion is believed to be the most significant factor that governs the structure of proteins
[
12
,
13
].
The hydrophobic-polar (HP) lattice model [
14
] was proposed to capture the
hydrophobic effect in protein folding. In this model, the protein is represented as a
self-avoiding chain of beads (i.e., coarse-grained representations of the amino acid
residues) on a rigid lattice. Amino acids are classified into two types: hydrophobic
(H) and polar (P), and an attractive interaction
α
acts only between non-bonded
0). Different sequences of
H and P monomers are used to “match” different proteins, and several sequences
which have been deemed “benchmarks” have been studied extensively by a variety
of methods with varying success. Some benchmark sequences are listed in Table
7.1
.
If a surface is added additional couplings between monomers and the surface must
be included. In the case of a hydrophobic surface, an additional energy
HH
=−
1
,
HP
=
PP
=
neighboring H residues (i.e.,
HS
is won
if an H is adjacent to the surface.
