Research
Interests
The Structure and Interactions of Small
Peptides
By
definition, a sense peptide is one whose sequence is coded for by the
nucleoside sequence (read 5’→3’) of the sense strand of DNA. The
complimentary peptide, in its strictest definition, is that which is coded for
by the nucleoside sequence (also read 5’→3’) of the complimentary strand
of DNA. Mekler was the first to suggest that sense and complimentary (or
anti-sense) peptides might be able interact on the basis of the specific
recognition of complimentary amino acid pairs [1]. The possible far-reaching
ramifications of these interactions have recently been the subject of a
comprehensive review by Heal et al. [2]. Despite the large body of
evidence presented therein that the sense/anti-sense interactions play an
important role in an extraordinarily diverse number of biological processes,
the interaction itself is still poorly understood at a fundamental level.
In
order to characterize the fundamental aspects of the sense/anti-sense
interactions, several experimental groups mentioned above have attempted to
measure the interactions in the context of some specific sense/anti-sense
peptide pairs. For example, by means of
nuclear magnetic resonance and mass spectrometric techniques, attempts have
been made to quantify the interactions between Met-enkephalin
(Tyr-Gly-Gly-Phe-Met) and its complimentary peptide (Ile-Pro-Pro-Lys-Tyr) as
defined by molecular recognition theory.
To
supplement the experiments and provide explanations for the measured data, I
have been performing classical molecular dynamics simulations on the above
peptides in isolation as well as in a system where they can potentially
interact.
[1] Mekler, L. B. Biofizika
1969, 14, 581.
[2] Heal, J. R.; Roberts,
G. W.; Raynes, J. G.; Bhakoo, A.; Miller, A. D. ChemBioChem 2002, 3, 136.
.