Right- and Left-Handed
Helices, What is in between?
Interconversion of Helical Structures of Alternating Pyridinedicarboxamide/<i>m</i>‑(phenylazo)azobenzene Oligomers
Peng Tao
Jon R. Parquette
Christopher M. Hadad
10.1021/ct2009335.s002
https://acs.figshare.com/articles/media/Right_and_Left_Handed_Helices_What_is_in_between_Interconversion_of_Helical_Structures_of_Alternating_Pyridinedicarboxamide_i_m_i_phenylazo_azobenzene_Oligomers/2461234
Some unnatural polymers/oligomers have been designed
to adopt a
well-defined, compact, three-dimensional folding capability. Azobenzene
units are common linkages in these oligomer designs. Two alternating
pyridinedicarboxamide/<i>m</i>-(phenylazo)Âazobenzene oligomers
that can fold into both right- and left-handed helices were studied
computationally in order to understand their dynamical properties.
Helical structures were shown to be the global minima among the many
different conformations generated from the Monte Carlo simulations,
and extended conformations have higher potential energies than compact
ones. To understand the interconversion process between right- and
left-handed helices, replica-exchange molecular dynamic (REMD) simulations
were performed on both oligomers, and with this method, both right-
and left-handed helices were successfully sampled during the simulations.
REMD trajectories revealed twisted conformations as intermediate structures
in the interconversion pathway between the two helical forms of these
azobenzene oligomers. This mechanism was observed in both oligomers
in current study and occurred locally in the larger oligomer. This
discovery indicates that the interconversion between helical structures
with different handedness goes through a compact and partially folded
structure instead of globally unfold and extended structure. This
is also verified by the nudged elastic band (NEB) calculations. The
temperature weighted histogram analysis method (T-WHAM) was applied
on the REMD results to generate contour maps of the potential of mean
force (PMF). Analysis showed that right- and left-handed helices are
equally sampled in these REMD simulations. In large oligomers, both
right- and left-handed helices can be adopted by different parts of
the molecule simultaneously. The interconversion between two helical
forms can occur in the middle of the helical structure and not necessarily
at the termini of the oligomer.
2016-02-20 04:09:45
right
NEB
oligomer
PMF
helical forms
helice
histogram analysis method
conformation
REMD
interconversion
Monte Carlo simulations