Biomedical Engineering Reference
In-Depth Information
RADA16-I peptide can form stable b-sheet structure in water (Fig.
11
). Thus,
they not only form the intermolecular hydrogen bonding on the peptide backbones
but they also have two distinctive sides, one hydrophobic with array of overlapping
alanines (Fig.
11
, green color sandwiched inside), similar as found in silk fi broin or
spider silk assemblies (Pauling
1960
). The other side of the backbones has nega-
tively charged (−) aspartic acids represented as red and positively charged (+) argi-
nines represented as blue. The alanines form packed hydrophobic interactions in
water; during sonication, the hydrophobic interaction could be disrupted mechani-
cally. However, these hydrophobic cohesive ends could fi nd each other quickly in
water since the exposure of hydrophobic alanine arrays to water is energetically
unfavorable. Since the hydrophobic alanines interaction is non-specifi c, they can
slide diffuse along the nanofi ber. The same sliding diffusion phenomenon was also
observed in nucleic acids where polyA and polyU form complementary base pair-
ings that can slide diffuse along the chains (Rich and Davies
1956
; Felsenfeld et al.
1957
). If, however, the bases are heterogonous, containing G, A, T, C, the bases
cannot undergo sliding diffusion. Likewise, if the hydrophobic side of the peptides
does not always contain alanine, such as valine and isoleucine, it would become
more diffi cult for sliding diffusion to occur due to structure constraint.
On the charged side, both positive and negative charges are packed together
through intermolecular ionic interactions in a checkerboard manner (looking from
the top). Likewise, the collectively complementary positive and negative ionic interac-
tions may also facilitate the reassembly. Similar to restriction-digested DNA fragments,
these nanofi ber fragments could form various assemblies: blunt, semi-protruding
and protruding ends. The fragments with semi-protruding and various protruding
ends as well as blunt ends can reassemble readily through hydrophobic and ionic
interactions.
Fig. 11
A proposed molecular sliding diffusion model for dynamic reassembly of self-assembling
RADA16-I peptides. When the peptides form stable b-sheets in water, they form intermolecular
hydrogen bonds along the peptide backbones. The b-sheets have two distinctive sides, one hydro-
phobic with an array of alanines and the other with negatively charged aspartic acids and positively
charged arginines. These peptides form anti-parallel b-sheet structures. The alanines form overlap
packed hydrophobic interactions in water. On the charged sides, both positive and negative charges
are packed together through intermolecular ionic interactions in a checkerboard-like manner.
These nanofi ber fragments can form various assemblies similar to restriction-digested DNA frag-
ments: (
a
) blunt ends; (
b
) semi-protruding ends; (
c
) These fragments with protruding ends could
reassemble readily through hydrophobic interactions; (
d
) The fragments with semi-protruding and
various protruding ends; (
e
) These fragments can reassemble readily. (
Bottom
) A proposed molec-
ular sliding diffusion model for dynamic reassembly of self-assembling a single peptide nanofi ber
consisting thousands of individual peptides. When the fragments of nanofi ber fi rst meet, the hydrophobic
sides may not fi t perfectly but with gaps (original state). However, the non-specifi c hydrophobic inter-
actions permit the nanofi ber to slide diffusion (sliding diffusion) along the fi ber in either direction
that minimizes the exposure of hydrophobic alanines and eventually fi ll the gaps (fi nal state). For
clarity, these b-sheets are not presented as twisted strands. Color code:
green
alanines;
red
negatively
charged aspartic acids;
blue
positively charged arginines
