170 research outputs found
DNA uptake into nuclei: Numerical and analytical results
The dynamics of polymer translocation through a pore has been the subject of
recent theoretical and experimental works. We have considered theoretical
estimates and performed computer simulations to understand the mechanism of DNA
uptake into the cell nucleus, a phenomenon experimentally investigated by
attaching a small bead to the free end of the double helix and pulling this
bead with the help of an optical trap. The experiments show that the uptake is
monotonous and slows down when the remaining DNA segment becomes very short.
Numerical and analytical studies of the entropic repulsion between the DNA
filament and the membrane wall suggest a new interpretation of the experimental
observations. Our results indicate that the repulsion monotonically decreases
as the uptake progresses. Thus, the DNA is pulled in (i) either by a small
force of unknown origin, and then the slowing down can be interpreted only
statistically; (ii) or by a strong but slow ratchet mechanism, which would
naturally explain the observed monotonicity, but then the slowing down requires
additional explanations. Only further experiments can unambiguously distinguish
between these two mechanisms.Comment: 12 pages, 6 figures, submitted to J. Phys. Cond. Ma
Trapping and Wiggling: Elastohydrodynamics of Driven Microfilaments
We present a general theoretical analysis of semiflexible filaments subject
to viscous drag or point forcing. These are the relevant forces in dynamic
experiments designed to measure biopolymer bending moduli. By analogy with the
``Stokes problems" in hydrodynamics (fluid motion induced by that of a wall
bounding a viscous fluid), we consider the motion of a polymer one end of which
is moved in an impulsive or oscillatory way. Analytical solutions for the
time-dependent shapes of such moving polymers are obtained within an analysis
applicable to small-amplitude deformations. In the case of oscillatory driving,
particular attention is paid to a characteristic length determined by the
frequency of oscillation, the polymer persistence length, and the viscous drag
coefficient. Experiments on actin filaments manipulated with optical traps
confirm the scaling law predicted by the analysis and provide a new technique
for measuring the elastic bending modulus. A re-analysis of several published
experiments on microtubules is also presented.Comment: RevTex, 24 pages, 15 eps figs, uses cite.sty, Biophysical
A stitch in time: Efficient computation of genomic DNA melting bubbles
Background: It is of biological interest to make genome-wide predictions of
the locations of DNA melting bubbles using statistical mechanics models.
Computationally, this poses the challenge that a generic search through all
combinations of bubble starts and ends is quadratic.
Results: An efficient algorithm is described, which shows that the time
complexity of the task is O(NlogN) rather than quadratic. The algorithm
exploits that bubble lengths may be limited, but without a prior assumption of
a maximal bubble length. No approximations, such as windowing, have been
introduced to reduce the time complexity. More than just finding the bubbles,
the algorithm produces a stitch profile, which is a probabilistic graphical
model of bubbles and helical regions. The algorithm applies a probability peak
finding method based on a hierarchical analysis of the energy barriers in the
Poland-Scheraga model.
Conclusions: Exact and fast computation of genomic stitch profiles is thus
feasible. Sequences of several megabases have been computed, only limited by
computer memory. Possible applications are the genome-wide comparisons of
bubbles with promotors, TSS, viral integration sites, and other melting-related
regions.Comment: 16 pages, 10 figure
Statics, metastable states and barriers in protein folding: A replica variational approach
Protein folding is analyzed using a replica variational formalism to
investigate some free energy landscape characteristics relevant for dynamics. A
random contact interaction model that satisfies the minimum frustration
principle is used to describe the coil-globule transition (characterized by
T_CG), glass transitions (by T_A and T_K) and folding transition (by T_F).
Trapping on the free energy landscape is characterized by two characteristic
temperatures, one dynamic, T_A the other static, T_K (T_A> T_K), which are
similar to those found in mean field theories of the Potts glass. 1)Above T_A,
the free energy landscape is monotonous and polymer is melted both dynamically
and statically. 2)Between T_A and T_K, the melted phase is still dominant
thermodynamically, but frozen metastable states, exponentially large in number,
appear. 3)A few lowest minima become thermodynamically dominant below T_K,
where the polymer is totally frozen. In the temperature range between T_A and
T_K, barriers between metastable states are shown to grow with decreasing
temperature suggesting super-Arrhenius behavior in a sufficiently large system.
Due to evolutionary constraints on fast folding, the folding temperature T_F is
expected to be higher than T_K, but may or may not be higher than T_A. Diverse
scenarios of the folding kinetics are discussed based on phase diagrams that
take into account the dynamical transition, as well as the static ones.Comment: 41 pages, LaTeX, 9 EPS figure
A Neutral Polyampholyte in an ionic solution
The behavior of a neutral polyampholyte () chain with monomers, in an
ionic solution, is analyzed in the framework of the full Debye-Hckel-Bjerrum-Flory theory. A chain, that in addition to the
neutral monomers, also contains an equal number of positively and negatively
charged monomers, is dissolved in an ionic solution. For \underline{high}
concentrations of salt and at high temperatures, the exists in an extended
state. As the temperature is decreased, the electrostatic energy becomes more
relevant and at a the system collapses into a dilute globular
state, or microelectrolyte. This state contains a concentration of salt higher
than the surrounding medium. As the temperature is decreased even further,
association between the monomers of the polymer and the ions of the salt
becomes relevant and there is a crossover from this globular state to a low
temperature extended state. For \underline{low} densities of salt, the system
is collapsed for almost all temperatures and exhibits a first-order phase
transition to an extended state at an unphysical low temperature.Comment: 10 pages, Revtex with epsf, 9 Postscript figures. Submitted to PR
Constraint methods for determining pathways and free energy of activated processes
Activated processes from chemical reactions up to conformational transitions
of large biomolecules are hampered by barriers which are overcome only by the
input of some free energy of activation. Hence, the characteristic and
rate-determining barrier regions are not sufficiently sampled by usual
simulation techniques. Constraints on a reaction coordinate r have turned out
to be a suitable means to explore difficult pathways without changing potential
function, energy or temperature. For a dense sequence of values of r, the
corresponding sequence of simulations provides a pathway for the process. As
only one coordinate among thousands is fixed during each simulation, the
pathway essentially reflects the system's internal dynamics. From mean forces
the free energy profile can be calculated to obtain reaction rates and insight
in the reaction mechanism. In the last decade, theoretical tools and computing
capacity have been developed to a degree where simulations give impressive
qualitative insight in the processes at quantitative agreement with
experiments. Here, we give an introduction to reaction pathways and
coordinates, and develop the theory of free energy as the potential of mean
force. We clarify the connection between mean force and constraint force which
is the central quantity evaluated, and discuss the mass metric tensor
correction. Well-behaved coordinates without tensor correction are considered.
We discuss the theoretical background and practical implementation on the
example of the reaction coordinate of targeted molecular dynamics simulation.
Finally, we compare applications of constraint methods and other techniques
developed for the same purpose, and discuss the limits of the approach
A Subset of Replication Proteins Enhances Origin Recognition and Lytic Replication by the Epstein-Barr Virus ZEBRA Protein
ZEBRA is a site-specific DNA binding protein that functions as a transcriptional activator and as an origin binding protein. Both activities require that ZEBRA recognizes DNA motifs that are scattered along the viral genome. The mechanism by which ZEBRA discriminates between the origin of lytic replication and promoters of EBV early genes is not well understood. We explored the hypothesis that activation of replication requires stronger association between ZEBRA and DNA than does transcription. A ZEBRA mutant, Z(S173A), at a phosphorylation site and three point mutants in the DNA recognition domain of ZEBRA, namely Z(Y180E), Z(R187K) and Z(K188A), were similarly deficient at activating lytic DNA replication and expression of late gene expression but were competent to activate transcription of viral early lytic genes. These mutants all exhibited reduced capacity to interact with DNA as assessed by EMSA, ChIP and an in vivo biotinylated DNA pull-down assay. Over-expression of three virally encoded replication proteins, namely the primase (BSLF1), the single-stranded DNA-binding protein (BALF2) and the DNA polymerase processivity factor (BMRF1), partially rescued the replication defect in these mutants and enhanced ZEBRA's interaction with oriLyt. The findings demonstrate a functional role of replication proteins in stabilizing the association of ZEBRA with viral DNA. Enhanced binding of ZEBRA to oriLyt is crucial for lytic viral DNA replication
Lattice Boltzmann simulations of soft matter systems
This article concerns numerical simulations of the dynamics of particles
immersed in a continuum solvent. As prototypical systems, we consider colloidal
dispersions of spherical particles and solutions of uncharged polymers. After a
brief explanation of the concept of hydrodynamic interactions, we give a
general overview over the various simulation methods that have been developed
to cope with the resulting computational problems. We then focus on the
approach we have developed, which couples a system of particles to a lattice
Boltzmann model representing the solvent degrees of freedom. The standard D3Q19
lattice Boltzmann model is derived and explained in depth, followed by a
detailed discussion of complementary methods for the coupling of solvent and
solute. Colloidal dispersions are best described in terms of extended particles
with appropriate boundary conditions at the surfaces, while particles with
internal degrees of freedom are easier to simulate as an arrangement of mass
points with frictional coupling to the solvent. In both cases, particular care
has been taken to simulate thermal fluctuations in a consistent way. The
usefulness of this methodology is illustrated by studies from our own research,
where the dynamics of colloidal and polymeric systems has been investigated in
both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures,
76 page
Diffusion in crowded biological environments: applications of Brownian dynamics
Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions
Cytomegalovirus Replicon-Based Regulation of Gene Expression In Vitro and In Vivo
There is increasing evidence for a connection between DNA replication and the expression of adjacent genes. Therefore, this study addressed the question of whether a herpesvirus origin of replication can be used to activate or increase the expression of adjacent genes. Cell lines carrying an episomal vector, in which reporter genes are linked to the murine cytomegalovirus (MCMV) origin of lytic replication (oriLyt), were constructed. Reporter gene expression was silenced by a histone-deacetylase-dependent mechanism, but was resolved upon lytic infection with MCMV. Replication of the episome was observed subsequent to infection, leading to the induction of gene expression by more than 1000-fold. oriLyt-based regulation thus provided a unique opportunity for virus-induced conditional gene expression without the need for an additional induction mechanism. This principle was exploited to show effective late trans-complementation of the toxic viral protein M50 and the glycoprotein gO of MCMV. Moreover, the application of this principle for intracellular immunization against herpesvirus infection was demonstrated. The results of the present study show that viral infection specifically activated the expression of a dominant-negative transgene, which inhibited viral growth. This conditional system was operative in explant cultures of transgenic mice, but not in vivo. Several applications are discussed
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