30,017 research outputs found
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.
The conformational pathways and the free energy variations for base opening into the major and minor grooves of a B-DNA duplex are studied using umbrella sampling molecular dynamics simulations. We compare both GC and AT base pair opening within a double-stranded d(GAGAGAGAGAGAG). d(CTCTCTCTCTCTC) oligomer, and we are also able to study the impact of opening on the conformational and dynamic properties of DNA and on the surrounding solvent. The results indicate a two-stage opening process with an initial coupling of the movements of the bases within the perturbed base pair. Major and minor groove pathways are energetically comparable in the case of the pyrimidine bases, but the major groove pathway is favored for the larger purine bases. Base opening is coupled to changes in specific backbone dihedrals and certain helical distortions, including untwisting and bending, although all these effects are dependent on the particular base involved. Partial opening also leads to well defined water bridging sites, which may play a role in stabilizing the perturbed base pairs
Ab initio RNA folding
RNA molecules are essential cellular machines performing a wide variety of
functions for which a specific three-dimensional structure is required. Over
the last several years, experimental determination of RNA structures through
X-ray crystallography and NMR seems to have reached a plateau in the number of
structures resolved each year, but as more and more RNA sequences are being
discovered, need for structure prediction tools to complement experimental data
is strong. Theoretical approaches to RNA folding have been developed since the
late nineties when the first algorithms for secondary structure prediction
appeared. Over the last 10 years a number of prediction methods for 3D
structures have been developed, first based on bioinformatics and data-mining,
and more recently based on a coarse-grained physical representation of the
systems. In this review we are going to present the challenges of RNA structure
prediction and the main ideas behind bioinformatic approaches and physics-based
approaches. We will focus on the description of the more recent physics-based
phenomenological models and on how they are built to include the specificity of
the interactions of RNA bases, whose role is critical in folding. Through
examples from different models, we will point out the strengths of
physics-based approaches, which are able not only to predict equilibrium
structures, but also to investigate dynamical and thermodynamical behavior, and
the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure
DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism
Inverted repeat (IR) sequences in DNA can form non-canonical cruciform
structures to relieve torsional stress. We use Monte Carlo simulations of a
recently developed coarse-grained model of DNA to demonstrate that the
nucleation of a cruciform can proceed through a cooperative mechanism. Firstly,
a twist-induced denaturation bubble must diffuse so that its midpoint is near
the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must
be large enough to allow one of the arms to form a small number of hairpin
bonds. Once the first arm is partially formed, the second arm can rapidly grow
to a similar size. Because bubbles can twist back on themselves, they need
considerably fewer bases to resolve torsional stress than the final cruciform
state does. The initially stabilised cruciform therefore continues to grow,
which typically proceeds synchronously, reminiscent of the S-type mechanism of
cruciform formation. By using umbrella sampling techniques we calculate, for
different temperatures and superhelical densities, the free energy as a
function of the number of bonds in each cruciform along the correlated but
non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat
Sampling rare switching events in biochemical networks
Bistable biochemical switches are ubiquitous in gene regulatory networks and
signal transduction pathways. Their switching dynamics, however, are difficult
to study directly in experiments or conventional computer simulations, because
switching events are rapid, yet infrequent. We present a simulation technique
that makes it possible to predict the rate and mechanism of flipping of
biochemical switches. The method uses a series of interfaces in phase space
between the two stable steady states of the switch to generate transition
trajectories in a ratchet-like manner. We demonstrate its use by calculating
the spontaneous flipping rate of a symmetric model of a genetic switch
consisting of two mutually repressing genes. The rate constant can be obtained
orders of magnitude more efficiently than using brute-force simulations. For
this model switch, we show that the switching mechanism, and consequently the
switching rate, depends crucially on whether the binding of one regulatory
protein to the DNA excludes the binding of the other one. Our technique could
also be used to study rare events and non-equilibrium processes in soft
condensed matter systems.Comment: 9 pages, 6 figures, last page contains supplementary informatio
Anharmonic Torsional Stiffness of DNA Revealed under Small External Torques
DNA supercoiling plays an important role in a variety of cellular processes.
The torsional stress related with supercoiling may be also involved in gene
regulation through the local structure and dynamics of the double helix. To
check this possibility steady torsional stress was applied to DNA in the course
of all-atom molecular dynamics simulations. It is found that small static
untwisting significantly reduces the torsional persistence length () of
GC-alternating DNA. For the AT-alternating sequence a smaller effect of the
opposite sign is observed. As a result, the measured values are similar
under zero stress, but diverge with untwisting. The effect is traced to
sequence-specific asymmetry of local torsional fluctuations, and it should be
small in long random DNA due to compensation. In contrast, the stiffness of
special short sequences can vary significantly, which gives a simple
possibility of gene regulation via probabilities of strong fluctuations. These
results have important implications for the role of local DNA twisting in
complexes with transcription factors.Comment: 8 pages, 5 figures, to appear in Phys. Rev. Let
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.
The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3'-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3'-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation
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