6 research outputs found
Engineering Gold Nanoparticle Interaction by PAMAM Dendrimer
Bare faceted gold nanoparticles (AuNPs)
have a tendency to aggregate
through a preferred attachment of the [111] surfaces. We have used
fully atomistic classical molecular dynamics simulations to obtain
a quantitative estimate of this surface interaction using umbrella
sampling (US) at various temperatures. To tune this surface interaction,
we use polyamidoamine (PAMAM) dendrimer to coat the gold surface under
various conditions. We observe a spontaneous adsorption of the protonated
as well as nonprotonated PAMAM dendrimer on the AuNP surface. The
adsorbed dendrimer on the nanoparticle surface strongly alters the
interaction between the nanoparticles. We calculate the interaction
between dendrimer-coated AuNPs using US and show how the interaction
between two bare faceted AuNPs can be tuned as a function of dendrimer
concentration and charge (pH-dependent). With appropriate choice of
the dendrimer concentration and charge, two strongly interacting AuNPs
can be made effectively noninteracting. Our simulation results demonstrate
a strategy to tune the nanoparticle interaction, which can help in
engineering self-assembly of such nanoparticles
PAMAM Dendrimer–Drug Interactions: Effect of pH on the Binding and Release Pattern
Understanding the dendrimer–drug interaction is
of great
importance to design and optimize the dendrimer-based drug delivery
system. Using atomistic molecular dynamics (MD) simulations, we have
analyzed the release pattern of four ligands (two soluble drugs, namely,
salicylic acid (Sal), l-alanine (Ala), and two insoluble
drugs, namely, phenylbutazone (Pbz) and primidone (Prim)), which were
initially encapsulated inside the ethylenediamine (EDA) cored polyamidoamine
(PAMAM) dendrimer using the docking method. We have computed the potential
of mean force (PMF) variation with generation 5 (G5)-PAMAM dendrimer complexed with
drug molecules using umbrella sampling. From our calculated PMF values,
we observe that soluble drugs (Sal and Ala) have lower energy barriers
than insoluble drugs (Pbz and Prim). The order of ease of release
pattern for these drugs from G5 protonated PAMAM dendrimer was found
to be Ala > Sal > Prim > Pbz. In the case of insoluble drugs
(Prim
and Pbz), because of larger size, we observe much nonpolar contribution,
and thus, their larger energy barriers can be reasoned to van der
Waals contribution. From the hydrogen bonding analysis of the four
PAMAM–drug complexes under study, we found intermolecular hydrogen
bonding to show less significant contribution to the free energy barrier.
Another interesting feature appears while calculating the PMF profile
of G5NP (nonprotonated)-PAMAM–Pbz and G5NP (nonprotonated)-PAMAM–Sal
complex. The PMF was found to be less when the drug is bound to nonprotonated
dendrimer compared to the protonated dendrimer. Our results suggest
that encapsulation of the drug molecule into the host PAMAM dendrimer
should be carried out at higher pH values (near pH 10). When such
complex enters the human body, the pH is around 7.4 and at that physiological
pH, the dendrimer holds the drug tightly. Hence the release of drug
can occur at a controlled rate into the bloodstream. Thus, our findings
provide a microscopic picture of the encapsulation and controlled
release of drugs in the case of dendrimer-based host–guest
systems
Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures
DNA three-way junctions (TWJs) are important intermediates
in various
cellular processes and are the simplest of a family of branched nucleic
acids being considered as scaffolds for biomolecular nanotechnology.
Branched nucleic acids are stabilized by divalent cations such as
Mg<sup>2+</sup>, presumably due to condensation and neutralization
of the negatively charged DNA backbone. However, electrostatic screening
effects point to more complex solvation dynamics and a large role
of interfacial waters in thermodynamic stability. Here, we report
extensive computer simulations in explicit water and salt on a model
TWJ and use free energy calculations to quantify the role of ionic
character and strength on stability. We find that enthalpic stabilization
of the first and second hydration shells by Mg<sup>2+</sup> accounts
for 1/3 and all of the free energy gain in 50% and pure MgCl<sub>2</sub> solutions, respectively. The more distorted DNA molecule is actually
destabilized in pure MgCl<sub>2</sub> compared to pure NaCl. Notably,
the first shell, interfacial waters have very low translational and
rotational entropy (i.e., mobility) compared to the bulk, an entropic
loss that is overcompensated by increased enthalpy from additional
electrostatic interactions with Mg<sup>2+</sup>. In contrast, the
second hydration shell has anomalously high entropy as it is trapped
between an immobile and bulklike layer. The nonmonotonic entropic
signature and long-range perturbations of the hydration shells to
Mg<sup>2+</sup> may have implications in the molecular recognition
of these motifs. For example, we find that low salt stabilizes the
parallel configuration of the three-way junction, whereas at normal
salt we find antiparallel configurations deduced from the NMR. We
use the 2PT analysis to follow the thermodynamics of this transition
and find that the free energy barrier is dominated by entropic effects
that result from the decreased surface area of the antiparallel form
which has a smaller number of low entropy waters in the first monolayer
Translocation of Bioactive Molecules through Carbon Nanotubes Embedded in the Lipid Membrane
One
of the major challenges of nanomedicine and gene therapy is the effective
translocation of drugs and genes across cell membranes. In this study,
we describe a systematic procedure that could be useful for efficient
drug and gene delivery into the cell. Using fully atomistic molecular
dynamics (MD) simulations, we show that molecules of various shapes,
sizes, and chemistries can
be spontaneously encapsulated in a single-walled carbon nanotube (SWCNT)
embedded in a 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine
(POPC) lipid bilayer, as we have exemplified with dendrimers, asiRNA,
ssDNA, and ubiquitin protein. We compute the free energy gain by the
molecules upon their entry inside the SWCNT channel to quantify the
stability of these molecules inside the channel as well as to understand
the spontaneity of the process. The free energy profiles suggest that
all molecules can enter the channel without facing any energy barrier
but experience a strong energy barrier (≫<i>k</i><sub>B</sub><i>T</i>) to translocate across the channel.
We propose a theoretical model for the estimation of encapsulation
and translocation times of the molecules. Whereas the model predicts
the encapsulation time to be of the order of few nanoseconds, which
match reasonably well with those obtained from the simulations, it
predicts the translocation time to be astronomically large for each
molecule considered in this study. This eliminates the possibility
of passive diffusion of the molecules through the CNT–nanopore
spanning across the membrane. To counter this, we put forward a mechanical
method of ejecting the encapsulated molecules by pushing them with
other free-floating SWCNTs of diameter smaller than the pore diameter.
The feasibility of the proposed method is also demonstrated by performing
MD simulations. The generic strategy described here should work for
other molecules as well and hence could be potentially useful for
drug- and gene-delivery applications
Differential dynamics of the serotonin<sub>1A</sub> receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation
<p>The serotonin<sub>1A</sub> receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin<sub>1A</sub> receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3 μs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin<sub>1A</sub> receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin<sub>1A</sub> receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.</p
Efficient Dendrimer–DNA Complexation and Gene Delivery Vector Properties of Nitrogen-Core Poly(propyl ether imine) Dendrimer in Mammalian Cells
Dendrimers as vectors for gene delivery
were established, primarily
by utilizing few prominent dendrimer types so far. We report herein
studies of DNA complexation efficacies and gene delivery vector properties
of a nitrogen-core poly(propyl ether imine) (PETIM) dendrimer, constituted
with 22 tertiary amine internal branches and 24 primary amines at
the periphery. The interaction of the dendrimer with pEGFPDNA was
evaluated through UV–vis, circular dichroism (CD) spectral
studies, ethidium bromide fluorescence emission quenching, thermal
melting, and gel retardation assays, from which most changes to DNA
structure during complexation was found to occur at a weight ratio
of dendrimer:DNA ∼ 2:1. The zeta potential measurements further
confirmed this stoichiometry at electroneutrality. The structure of
a DNA oligomer upon dendrimer complexation was simulated through molecular
modeling and the simulation showed that the dendrimer enfolded DNA
oligomer along both major and minor grooves, without causing DNA deformation,
in 1:1 and 2:1 dendrimer-to-DNA complexes. Atomic force microscopy
(AFM) studies on dendrimer-pEGFP DNA complex showed an increase in
the average <i>z</i>-height as a result of dendrimers decorating
the DNA, without causing a distortion of the DNA structure. Cytotoxicity
studies involving five different mammalian cell lines, using [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium
bromide] (MTT) assay, reveal the dendrimer toxicity profile (IC<sub>50</sub>) values of ∼400–1000 μg mL<sup>–1</sup>, depending on the cell line tested. Quantitative estimation, using
luciferase assay, showed that the gene transfection was at least 100
times higher when compared to poly(ethylene imine) branched polymer,
having similar number of cationic sites as the dendrimer. The present
study establishes the physicochemical behavior of new nitrogen-core
PETIM dendrimer–DNA complexes, their lower toxicities, and
efficient gene delivery vector properties