Understanding the regulatory factors of self-assembly processes is a necessity in order to modulate the nano-structures and their properties. Here, the self-assembly mechanism of a peptide-perylenediimide (P-1) conjugate in mixed solvent systems of THF/water is studied and the semiconducting properties are correlated with the morphology. In THF, right handed helical fibers are formed while in 10% THF-water, the morphology changes to nano-rings along with a switch in the helicity to left-handed orientation. Experimental results combined with DFT calculations reveal the critical role of thermodynamic and kinetic factors to control these differential self-assembly processes. In THF, P-1 forms right handed helical fibers in a kinetically controlled fashion. In case of 10% THF-water, the initial nucleation of the aggregate is controlled kinetically. Due to differential solubility of the molecule in these two solvents, elongation of the nuclei into fibers is restricted after a critical length leading to the formation of nano-rings which is governed by the thermodynamics. The helical fibers show superior semi-conducting property to the nano-rings as confirmed by conducting-AFM and conventional I-V characteristics.
A water insoluble peptide-hydrogel that shows unique compartmentalization by not allowing any exchange to and from the hydrogel and can protect enzymes from denaturation.
Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
Understanding
lateral organizations of self-assembled bilayers
is crucial to gain a control on functionally relevant topologies.
We study self-assembled bilayers composed of a surfactant, behenyl
trimethyl ammonium chloride (BTMAC), a cosurfactant, stearyl alcohol
(SA), at a ratio of 2:1 in the presence of water at 283 K employing
subsequent all-atom (AA) and coarse-grained (CG) molecular dynamics
simulations. Differences in initial configurations lead to the formation
of bilayers at ripple or square phases or interdigitated gel phases
of varying trans-leaflet asymmetry. The AA ripple and gel phases are
reproduced well at the CG level using bonded potentials from Boltzmann
inversion of AA canonical sampling and nonbonded potentials from MARTINI.
Inhomogeneous populations of disordered chains with higher per chain
configurational entropy and tilt result in rippling stabilized by
periodic hydrophobic energy barrier and strong interdigitation. Order
parameters of the asymmetric bilayers are sufficiently coupled to
the per chain entropies at both levels of resolutions to serve as
a reflector of the per chain configurational entropy inaccessible
by experiments. Thus, trans-bilayer asymmetry may be a controlling
parameter to induce rippling in a bilayer of industrial importance.
This work will be useful for future investigation on domain-associated
transport and signaling in biomembranes at a low temperature.
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