24 research outputs found
Stochastic kinetics of a single headed motor protein: dwell time distribution of KIF1A
KIF1A, a processive single headed kinesin superfamily motor, hydrolyzes
Adenosine triphosphate (ATP) to move along a filamentous track called
microtubule. The stochastic movement of KIF1A on the track is characterized by
an alternating sequence of pause and translocation. The sum of the durations of
pause and the following translocation defines the dwell time. Using the NOSC
model (Nishinari et. al. PRL, {\bf 95}, 118101 (2005)) of individual KIF1A, we
systematically derive an analytical expression for the dwell time distribution.
More detailed information is contained in the probability densities of the
"conditional dwell times" in between two consecutive steps each
of which could be forward (+) or backward (-). We calculate the probability
densities of these four conditional dwell times. However, for
the convenience of comparison with experimental data, we also present the two
distributions of the times of dwell before a forward (+) and a
backward (-) step. In principle, our theoretical prediction can be tested by
carrying out single-molecule experiments with adequate spatio-temporal
resolution.Comment: Author-edited final version published in EP
Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA
We report a structural polymorphism of the S-DNA when a canonical B-DNA is
stretched under different pulling protocols and provide a fundamental molecular
understanding of the DNA stretching mechanism. Extensive all atom molecular
dynamics simulations reveal a clear formation of S-DNA when the B-DNA is
stretched along the 3' directions of the opposite strands (OS3) and is
characterized by the changes in the number of H-bonds, entropy and free energy.
Stretching along 5' directions of the opposite strands (OS5) leads to force
induced melting form of the DNA. Interestingly, stretching along the opposite
ends of the same strand (SS) leads to a coexistence of both the S- and melted
M-DNA structures. We also do the structural characterization of the S-DNA by
calculating various helical parameters. We find that S-DNA has a twist of ~10
degrees which corresponds to helical repeat length of ~ 36 base pairs in close
agreement with the previous experimental results. Moreover, we find that the
free energy barrier between the canonical and overstretched states of DNA is
higher for the same termini (SE) pulling protocol in comparison to all other
protocols considered in this work. Overall, our observations not only reconcile
with the available experimental results qualitatively but also enhance the
understanding of different overstretched DNA structures.Comment: To be published in the The Journal of Chemical Physics (AIP
Intra-cellular transport by single-headed kinesin KIF1A: effects of single-motor mechano-chemistry and steric interactions
In eukaryotic cells, many motor proteins can move simultaneously on a single
microtubule track. This leads to interesting collective phenomena like jamming.
Recently we reported ({\it Phys. Rev. Lett. {\bf 95}, 118101 (2005)}) a
lattice-gas model which describes traffic of unconventional (single-headed)
kinesins KIF1A. Here we generalize this model, introducing a novel interaction
parameter , to account for an interesting mechano-chemical process which has
not been considered in any earlier model. We have been able to extract all the
parameters of the model, except , from experimentally measured quantities.
In contrast to earlier models of intra-cellular molecular motor traffic, our
model assigns distinct ``chemical'' (or, conformational) states to each kinesin
to account for the hydrolysis of ATP, the chemical fuel of the motor. Our model
makes experimentally testable theoretical predictions. We determine the phase
diagram of the model in planes spanned by experimentally controllable
parameters, namely, the concentrations of kinesins and ATP. Furthermore, the
phase-separated regime is studied in some detail using analytical methods and
simulations to determine e.g. the position of shocks. Comparison of our
theoretical predictions with experimental results is expected to elucidate the
nature of the mechano-chemical process captured by the parameter .Comment: 17 pages including 14 embedded EPS figures; accepted for publication
in Physical Review
Traffic of single-headed motor proteins KIF1A: effects of lane changing
KIF1A kinesins are single-headed motor proteins which move on cylindrical
nano-tubes called microtubules (MT). A normal MT consists of 13 protofilaments
on which the equispaced motor binding sites form a periodic array. The
collective movement of the kinesins on a MT is, therefore, analogous to
vehicular traffic on multi-lane highways where each protofilament is the
analogue of a single lane. Does lane-changing increase or decrease the motor
flux per lane? We address this fundamental question here by appropriately
extending a recent model [{\it Phys. Rev. E {\bf 75}, 041905 (2007)}]. By
carrying out analytical calculations and computer simulations of this extended
model, we predict that the flux per lane can increase or decrease with the
increasing rate of lane changing, depending on the concentrations of motors and
the rate of hydrolysis of ATP, the ``fuel'' molecules. Our predictions can be
tested, in principle, by carrying out {\it in-vitro} experiments with
fluorescently labelled KIF1A molecules.Comment: 4 pages REVTEX with 4 EPS figures; new schematic figure of the mode
Ionic liquids make DNA rigid
Persistence length of dsDNA is known to decrease with increase in ionic
concentration of the solution. In contrast to this, here we show that
persistence length of dsDNA increases dramatically as a function of ionic
liquid (IL) concentration. Using all atomic explicit solvent molecular dynamics
simulations and theoretical models we present, for the first time, a systematic
study to determine the mechanical properties of dsDNA in various hydrated ionic
liquids at different concentrations. We find that dsDNA in 50 wt% ILs have
lower persistence length and stretch modulus in comparison to 80 wt% ILs. We
further observe that both persistence length and stretch modulus of dsDNA
increase as we increase the ILs concentration. Present trend of stretch modulus
and persistence length of dsDNA with ILs concentration supports the predictions
of the macroscopic elastic theory, in contrast to the behavior exhibited by
dsDNA in monovalent salt. Our study further suggests the preferable ILs that
can be used for maintaining DNA stability during long-term storage.Comment: 16 pages, 3 figures, Supplementary Information (Accepted for
publication in the Journal of Chemical Physics, AIP (USA)
A two-state model for helicase translocation and unwinding of nucleic acids
Helicases are molecular motors that unwind double-stranded nucleic acids
(dsNA), such as DNA and RNA). Typically a helicase translocates along one of
the NA single strands while unwinding and uses adenosine triphosphate (ATP)
hydrolysis as an energy source. Here we model of a helicase motor that can
switch between two states, which could represent two different points in the
ATP hydrolysis cycle. Our model is an extension of the earlier
Betterton-J\"ulicher model of helicases to incorporate switching between two
states. The main predictions of the model are the speed of unwinding of the
dsNA and fluctuations around the average unwinding velocity. Motivated by a
recent claim that the NS3 helicase of Hepatitis C virus follows a flashing
ratchet mechanism, we have compared the experimental results for the NS3
helicase with a special limit of our model which corresponds to the flashing
ratchet scenario. Our model accounts for one key feature of the experimental
data on NS3 helicase. However, contradictory observations in experiments
carried out under different conditions limit the ability to compare the model
to experiments.Comment: minor modification
Footprint traversal by ATP-dependent chromatin remodeler motor
ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in
eukaryotic cells. These are driven by a chemical fuel, namely, adenosine
triphosphate (ATP). CREs actively participate in many cellular processes that
require accessibility of specific segments of DNA which are packaged as
chromatin. The basic unit of chromatin is a nucleosome where 146 bp 50
nm of a double stranded DNA (dsDNA) is wrapped around a spool formed by histone
proteins. The helical path of histone-DNA contact on a nucleosome is also
called "footprint". We investigate the mechanism of footprint traversal by a
CRE that translocates along the dsDNA. Our two-state model of a CRE captures
effectively two distinct chemical (or conformational) states in the
mechano-chemical cycle of each ATP-dependent CRE. We calculate the mean time of
traversal. Our predictions on the ATP-dependence of the mean traversal time can
be tested by carrying out {\it in-vitro} experiments on mono-nucleosomes.Comment: 11 pages, 12 figures; minor revision of tex
Stochastic kinetics of ribosomes: single motor properties and collective behavior
Synthesis of protein molecules in a cell are carried out by ribosomes. A
ribosome can be regarded as a molecular motor which utilizes the input chemical
energy to move on a messenger RNA (mRNA) track that also serves as a template
for the polymerization of the corresponding protein. The forward movement,
however, is characterized by an alternating sequence of translocation and
pause. Using a quantitative model, which captures the mechanochemical cycle of
an individual ribosome, we derive an {\it exact} analytical expression for the
distribution of its dwell times at the successive positions on the mRNA track.
Inverse of the average dwell time satisfies a ``Michaelis-Menten-like''
equation and is consistent with the general formula for the average velocity of
a molecular motor with an unbranched mechano-chemical cycle. Extending this
formula appropriately, we also derive the exact force-velocity relation for a
ribosome. Often many ribosomes simultaneously move on the same mRNA track,
while each synthesizes a copy of the same protein. We extend the model of a
single ribosome by incorporating steric exclusion of different individuals on
the same track. We draw the phase diagram of this model of ribosome traffic in
3-dimensional spaces spanned by experimentally controllable parameters. We
suggest new experimental tests of our theoretical predictions.Comment: Final published versio