25 research outputs found
Computational DNA binding studies of (â)-epigallocatechin-3-gallate
<p>The catechin family of molecules that are present in the leaves of green tea has been under investigation since the antioxidant and anti-inflammatory properties of tea were discovered. Among multiple proposed therapeutic targets of these molecules, the direct interaction with nucleic acids has been proposed and experimentally observed but without clear knowledge about the potential binding modes between these ligands and DNA. One of these catechin structures, (â)-epigallocatechin gallate (EGCG), has three aromatic rings that could interact with double-stranded DNA via terminal base-pair stacking, intercalation, or through groove binding. Using enhanced sampling techniques and molecular dynamics simulations, we have found a stable complex between the EGCG ligand and DNA through intercalation of the trihydroxybenzoate aromatic ring and an ApC step. Moreover, we have calculated the absorption spectra of four possible binding modes and compared these to absorption profiles reported in the literature, and explored the possible DNA sequence preference for the EGCG ligand to bind. Our results suggest that an intercalative mode of interaction through the major groove is possible between the EGCG ligands and DNA with apparently very little DNA sequence selectivity.</p
In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study
The
use of functionalized calix- and thia-calixÂ[<i>n</i>]Âarenes
is proposed as the basis for our <i>in silico</i> design
of a suitable drug carrier for the tyrosine kinase inhibitor,
Imatinib. Their mutual electronic properties and interaction energies, <i>E</i><sub>int</sub>, were assessed with the use of Density Functional
Theory (DFT) methods under the NBODel methodology. Three structural
variables for the host molecules were considered: R = {SO<sub>3</sub>H (<b>1</b>), <i>t</i>-Bu (<b>2</b>), <i>i</i>-Pr (<b>3</b>), COOH (<b>4</b>), (CH<sub>2</sub>)<sub>2</sub>OH (<b>5</b>), (CH<sub>2</sub>)<sub>2</sub>NH<sub>2</sub> (<b>6</b>)}; <i>b</i> = {CH<sub>2</sub>,
S}; <i>n</i> = {5, 6, 8}, and two possible orientations
for the insertion of Imatinib within the macrocycle cavity: pyridine
moiety pointing inward (<i>N1</i>) and piperazine pointing
inward (<i>N2</i>). In total, we explored 72 different assemblies.
Initial molecular mechanics geometry optimizations with the UFF potential
were undertaken for every hostâguest complex, with further
optimization at the B97D/6-31GÂ(<i>d</i>,<i>p</i>) level of theory. Using the same optimized structures, Molecular
Dynamics (MD) simulations were carried out on all 72 assemblies using
the General Amber Force Field and the AMBER 12 MD package. Electronic
parameters were fitted using the RESP method, and the complexes were
run for 100 ns. Potential of mean force was obtained for the most
stable systems using umbrella sampling and the Weighted Histogram
Analysis Method. CalixÂ[<i>n</i>]Âarenes families <b>1</b> and <b>5</b> (R = SO<sub>3</sub>H and (CH<sub>2</sub>)<sub>2</sub>OH, respectively) with <i>n</i> = 6 constitute the
most promising candidates to become drug carriers within our parameter
space due to their more negative <i>E</i><sub>int</sub> values
and increased flexibility to allow the inclusion of the drug
Exploring potentially alternative non-canonical DNA duplex structures through simulation
<p>Hopkins proposed an alternative and chirally distinct family of double-stranded DNA (dsDNA) models that have antiparallel chains with 5â˛â3Ⲡsenses opposite to those of the right-handed WatsonâCrick (WC) family. Termed configuration II, this family of dsDNA models contains both right-handed (II-R) and left-handed (II-L) forms, with Z-DNA as an example of the latter. Relative interstrand binding energies for six DNA duplex models, two each of configuration I-R (standard WC canonical B-DNA), II-R, and II-L for the duplex d(CGCGAATTCGCG), have been estimated under identical conditions using MM-PBSA analysis from molecular dynamics trajectories using three different AMBER force fields. These simulations support the stereo chemical soundness of configuration II dsDNA forms. Recent force fields (Barcelona Supercomputing Center [BSC] [bsc1] and Olomouc 2015 [OL15]) successfully render stable II-L structures, whereas the previous force field, bsc0, generated stable II-R structures, although with an energy difference between II-R and II-L of âź30âkcal/mol.</p> <p>Communicated by Ramaswamy H. Sarma</p
Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations
Long
time scale molecular dynamics (MD) simulations of biological systems
are becoming increasingly commonplace due to the availability of both
large-scale computational resources and significant advances in the
underlying simulation methodologies. Therefore, it is useful to investigate
and develop data mining and analysis techniques to quickly and efficiently
extract the biologically relevant information from the incredible
amount of generated data. Wavelet analysis (WA) is a technique that
can quickly reveal significant motions during an MD simulation. Here,
the application of WA on well-converged long time scale (tens of Îźs)
simulations of a DNA helix is described. We show how WA combined with
a simple clustering method can be used to identify both the physical
and temporal locations of events with significant motion in MD trajectories.
We also show that WA can not only distinguish and quantify the locations
and time scales of significant motions, but by changing the maximum
time scale of WA a more complete characterization of these motions
can be obtained. This allows motions of different time scales to be
identified or ignored as desired
Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA
An
experimentally well-studied model of RNA tertiary structures
is a 58mer rRNA fragment, known as GTPase-associating center (GAC)
RNA, in which a highly negative pocket walled by phosphate oxygen
atoms is stabilized by a chelated cation. Although such deep pockets
with more than one direct phosphate to ion chelation site normally
include magnesium, as shown in one GAC crystal structure, another
GAC crystal structure and solution experiments suggest potassium at
this site. Both crystal structures also depict two magnesium ions
directly bound to the phosphate groups comprising this controversial
pocket. Here, we used classical molecular dynamics simulations as
well as umbrella sampling to investigate the possibility of binding
of potassium versus magnesium inside the pocket and to better characterize
the chelation of one of the binding magnesium ions outside the pocket.
The results support the preference of the pocket to accommodate potassium
rather than magnesium and suggest that one of the closely binding
magnesium ions can only bind at high magnesium concentrations, such
as might be present during crystallization. This work illustrates
the complementary utility of molecular modeling approaches with atomic-level
detail in resolving discrepancies between conflicting experimental
results
Refinement of the SugarâPhosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and BâDNA
Z-DNA
duplexes are a particularly complicated test case for current
force fields. We performed a set of explicit solvent molecular dynamics
(MD) simulations with various AMBER force field parametrizations including
our recent refinements of the Îľ/Îś and glycosidic torsions.
None of these force fields described the ZI/ZII and other backbone
substates correctly, and all of them underpredicted the population
of the important ZI substate. We show that this underprediction can
be attributed to an inaccurate potential for the sugarâphosphate
backbone torsion angle β. We suggest a refinement of this potential,
β<sub>OL1</sub>, which was derived using our recently introduced
methodology that includes conformation-dependent solvation effects.
The new potential significantly increases the stability of the dominant
ZI backbone substate and improves the overall description of the Z-DNA
backbone. It also has a positive (albeit small) impact on another
important DNA form, the antiparallel guanine quadruplex (G-DNA), and
improves the description of the canonical B-DNA backbone by increasing
the population of BII backbone substates, providing a better agreement
with experiment. We recommend using β<sub>OL1</sub> in combination
with our previously introduced corrections, ξΜ<sub>OL1</sub> and Ď<sub>OL4</sub>, (the combination being named OL15) as
a possible alternative to the current β torsion potential for
more accurate modeling of nucleic acids
Assessing the Current State of Amber Force Field Modifications for DNA
The utility of molecular
dynamics (MD) simulations to model biomolecular
structure, dynamics, and interactions has witnessed enormous advances
in recent years due to the availability of optimized MD software and
access to significant computational power, including GPU multicore
computing engines and other specialized hardware. This has led researchers
to routinely extend conformational sampling times to the microsecond
level and beyond. The extended sampling time has allowed the community
not only to converge conformational ensembles through complete sampling
but also to discover deficiencies and overcome problems with the force
fields. Accuracy of the force fields is a key component, along with
sampling, toward being able to generate accurate and stable structures
of biopolymers. The Amber force field for nucleic acids has been used
extensively since the 1990s, and multiple artifacts have been discovered,
corrected, and reassessed by different research groups. We present
a direct comparison of two of the most recent and state-of-the-art
Amber force field modifications, bsc1 and OL15, that focus on accurate
modeling of double-stranded DNA. After extensive MD simulations with
five test cases and two different water models, we conclude that both
modifications are a remarkable improvement over the previous bsc0
force field. Both force field modifications show better agreement
when compared to experimental structures. To ensure convergence, the
DrewâDickerson dodecamer (DDD) system was simulated using 100
independent MD simulations, each extended to at least 10 Îźs,
and the independent MD simulations were concatenated into a single
1 ms long trajectory for each combination of force field and water
model. This is significantly beyond the time scale needed to converge
the conformational ensemble of the internal portions of a DNA helix
absent internal base pair opening. Considering all of the simulations
discussed in the current work, the MD simulations performed to assess
and validate the current force fields and water models aggregate over
14 ms of simulation time. The results suggest that both the bsc1 and
OL15 force fields render average structures that deviate significantly
less than 1 Ă
from the average experimental structures. This
can be compared to similar but less exhaustive simulations with the
CHARMM 36 force field that aggregate to the âź90 Îźs time
scale and also perform well but do not produce structures as close
to the DDD NMR average structures (with root-mean-square deviations
of 1.3 Ă
) as the newer Amber force fields. On the basis of these
analyses, any future research involving double-stranded DNA simulations
using the Amber force fields should employ the bsc1 or OL15 modification
Transitions of Double-Stranded DNA Between the A- and BâForms
The structure of
double-stranded DNA (dsDNA) is sensitive to solvent
conditions. In solution, B-DNA is the favored conformation under physiological
conditions, while A-DNA is the form found under low water activity.
The A-form is induced locally in some proteinâDNA complexes,
and repeated transitions between the B- and A-forms have been proposed
to generate the forces used to drive dsDNA into viral capsids during
genome packaging. Here, we report analyses on previous molecular dynamics
(MD) simulations on B-DNA, along with new MD simulations on the transition
from A-DNA to B-DNA in solution. We introduce the A-B Index (ABI),
a new metric along the A-B continuum, to quantify our results. When
A-DNA is placed in an equilibrated solution at physiological ionic
strength, there is no energy barrier to the transition to the B-form,
which begins within about 1 ns. The transition is essentially complete
within 5 ns, although occasionally a stretch of a few base pairs will
remain A-like for up to âź10 ns. A comparison of four sequences
with a range of predicted A-phobicities shows that more A-phobic sequences
make the transition more rapidly than less A-phobic sequences. Simulations
on dsDNA with a region of roughly one turn locked in the A-form allow
us to characterize the A/B junction, which has an average bend angle
of 20â30°. Fluctuations in this angle occur with characteristic
times of about 10 ns
Oxazinin A, a Pseudodimeric Natural Product of Mixed Biosynthetic Origin from a Filamentous Fungus
A racemic,
prenylated polyketide dimer, oxazinin A (<b>1</b>), was isolated
from a novel filamentous fungus in the class Eurotiomycetes,
and its structure was elucidated spectroscopically. The pentacyclic
structure of oxazinin A (<b>1</b>) is a unique combination of
benzoxazine, isoquinoline, and a pyran ring. Oxazinin A (<b>1</b>) exhibited antimycobacterial activity and modestly antagonized transient
receptor potential (TRP) channels
TNF signaling is affected in HeLa cells treated with Cas II-gly favoring apoptosis rather than differentiation and proliferation.
<p>Image based in an analysis of the gene expression matrix in the IngenuityÂŽ database for Systems Pathways Analysis (IPA) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054664#pone.0054664-Ingenuity1" target="_blank">[28]</a>. Molecules in green are transcriptionally down-regulated whereas molecules in red are transcriptionally over-expressed. Notice the abundance of molecules -such as HMOX1- responding to oxidative stress.</p