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Molecular Design of Biological and Nano-Materials 233

Figure 8.4 (See color insert following page 302) Two distinct classes of self-assembling peptide construction
motifs are shown here. (a) The first class belongs to amphiphilic peptides that form well-ordered nanofibers. These
peptides have two distinctive sides, one hydrophobic and the other hydrophilic. The hydrophobic side forms a double
sheet inside of the fiber and hydrophilic side forms the outside of the nanofibers that interact with water molecules
and they can form extremely high water content hydrogel, containing as high as 99.9% water. At least three types of
molecules can be made, with , þ, /þ on the hydrophilic side. (b) The second class of self-assembling peptide
belongs to surfactant-like molecules. These peptides have a hydrophilic head and a hydrophobic tail, much like lipids
or detergents. They sequester their hydrophobic tail inside of micelle, vesicles or nanotube structures and expose
their hydrophilic heads to water. At least three kinds of molecules can be made, with , þ, /þ heads.

hydrophilic side (Zhang and Altman, 1999; Zhang, 2002). The second class of self-assembling
peptide belongs to a surfactant-like molecule (Vauthey et al., 2002; Santoso et al., 2002; von
Maltzahn et al., 2003). These peptides have a hydrophilic head and a hydrophobic tail, much like
lipids or detergents. They sequester their hydrophobic tail inside of micelle, vesicles or nanotube
structures and expose their hydrophilic heads to water. As in the previous case, at least three kinds of
molecules can be made, with , þ, /þ heads.
The first class includes: ‘‘Peptide Lego’’ that forms well-ordered nanofiber scaffolds and can be
used not only for 3-D tissue cell culture but also for regenerative medicine, namely to promote
healing and replacing damaged tissues. The second class includes peptide surfactants and deter-
gents that can be used not only for drug, protein and gene deliveries, but also for solubilizing,
stabilizing, and crystallizing membrane proteins. Membrane proteins are crucial for biological
energy conversations, cell–cell communications, specific ion channels and pumps including our
senses, sight, hearing, smell, taste, touch, and temperature sensing.
Like bricks and architectural construction units, these designed peptide construction motifs are
structurally simple, versatile for a wide spectrum of applications.

8.4 CHEMICAL COMPLEMENTARITY AND STRUCTURAL COMPATIBILITY
THROUGH NONCOVALENT WEAK INTERACTIONS

Molecular self-assembly, by definition, is the spontaneous organization of numerous molecules
under thermodynamic and kinetic conditions into structurally well-defined and rather stable
arrangements through a number of noncovalent interactions. These molecules undergo self-asso-
ciation forming hierarchical structures. The ribosome is one of the most sophisticated molecular
machines nature has ever remarkably self-assembled (Figure 8.5). It has more than 50 different
kinds of proteins and 3 different size and functional RNAs, all through weak interactions to form
the remarkable assembly line (Stillman, 2002). The other molecular machines include the photo-
systems I and II that collect photos to convert into electrons in order to produce energy needed for
nearly all living systems on Earth (Barber, 1992).
Molecular self-assembly is mediated by weak, noncovalent bonds — notably hydrogen bonds,
ionic bonds (electrostatic interactions or salt bridges), hydrophobic interactions, van der Waals
interactions, and water-mediated hydrogen bonds. Although these bonds are relatively insignificant
in isolation, when combined together as a whole, they govern the structural conformation of all
biological macromolecules and influence their interaction with other molecules (Pauling, 1960).
The water-mediated hydrogen bond is especially important for living systems as all biological
materials interact with water (Ball, 2001).