19,128 research outputs found
Nanoscale Structure and Elasticity of Pillared DNA Nanotubes
We present an atomistic model of pillared DNA nanotubes (DNTs) and their
elastic properties which will facilitate further studies of these nanotubes in
several important nanotechnological and biological applications. In particular,
we introduce a computational design to create an atomistic model of a 6-helix
DNT (6HB) along with its two variants, 6HB flanked symmetrically by two double
helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double
helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation
trajectories in the presence of explicit water and ions shows that these
structures are stable and well behaved in all three geometries. Hydrogen
bonding is well maintained for all variants of 6HB DNTs. We calculate the
persistence length of these nanotubes from their equilibrium bend angle
distributions. The values of persistence length are ~10 {\mu}m, which is 2
orders of magnitude larger than that of dsDNA. We also find a gradual increase
of persistence length with an increasing number of pillars, in quantitative
agreement with previous experimental findings. To have a quantitative
understanding of the stretch modulus of these tubes we carried out
nonequilibrium Steered Molecular Dynamics (SMD). The linear part of the force
extension plot gives stretch modulus in the range of 6500 pN for 6HB without
pillars which increases to 11,000 pN for tubes with three pillars. The values
of the stretch modulus calculated from contour length distributions obtained
from equilibrium MD simulations are similar to those obtained from
nonequilibrium SMD simulations. The addition of pillars makes these DNTs very
rigid.Comment: Published in ACS Nan
Compact phases of polymers with hydrogen bonding
We propose an off-lattice model for a self-avoiding homopolymer chain with
two different competing attractive interactions, mimicking the hydrophobic
effect and the hydrogen bond formation respectively. By means of Monte Carlo
simulations, we are able to trace out the complete phase diagram for different
values of the relative strength of the two competing interactions. For strong
enough hydrogen bonding, the ground state is a helical conformation, whereas
with decreasing hydrogen bonding strength, helices get eventually destabilized
at low temperature in favor of more compact conformations resembling
-sheets appearing in native structures of proteins. For weaker hydrogen
bonding helices are not thermodynamically relevant anymore.Comment: 5 pages, 3 figures; revised version published in PR
Monte Carlo study of cooperativity in homopolypeptides
©1992 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/9412/1DOI:10.1063/1.463317A discretized model of globular proteins is employed in a Monte Carlo study of the helix-coil transition of polyalanine and the collapse transition of polyvaline. The present lattice realization permits real protein crystal structures to be represented at the level of 1 A resolution. Furthermore, the Monte Carlo dynamic scheme is capable of moving elements of assembled secondary and supersecondary structure. The potentials of mean force for the interactions are constructed from the statistics of a set of high resolution x-ray structures of nonhomologous proteins. The cooperativity of formation of ordered structures is found to be larger when the major contributions to the conformational energy of the low temperature states come from hydrogen bonds and short range conformational propensities. The secondary structure seen in the folded state is the result of an interplay between the short and long range interactions. Compactness itself, driven by long range, nonspecific interactions, seems to be insufficient to generate any appreciable secondary structure. A detailed examination of the dynamics of highly helical model proteins demonstrates that all elements of secondary structure are mobile in the present algorithm, and thus the folding pathways do not depend on the use of a lattice approximation. Possible applications of the present model to the prediction of protein 3D structures are briefly discussed
Electron Transfer in Proteins
Electron-transfer (ET) reactions are key steps in a diverse array of biological transformations ranging from photosynthesis to aerobic respiration. A powerful theoretical formalism has been developed that describes ET rates in terms of two parameters: the nuclear reorganization [lambda] energy (1) and the electronic-coupling strength (HAB). Studies of ET reactions in ruthenium-modified proteins have probed [lambda] and HAB in several metalloproteins (cytochrome c, myoglobin, azurin). This work has shown that protein reorganization energies are sensitive to the medium surrounding the redox sites and that an aqueous environment, in particular, leads to large reorganization energies. Analyses of electronic-coupling strengths suggest that the efficiency of long-range ET depends on the protein secondary structure: [beta]sheets appear to mediate coupling more efficiently than [alpha]-helical structures, and hydrogen bonds play a critical role in both
Energetic Components of Cooperative Protein Folding
A new lattice protein model with a four-helix bundle ground state is analyzed
by a parameter-space Monte Carlo histogram technique to evaluate the effects of
an extensive variety of model potentials on folding thermodynamics. Cooperative
helical formation and contact energies based on a 5-letter alphabet are found
to be insufficient to satisfy calorimetric and other experimental criteria for
two-state folding. Such proteinlike behaviors are predicted, however, by models
with polypeptide-like local conformational restrictions and
environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press
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