Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein–DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.
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First-passage processes on a filamentous track in a dense traffic: optimizing diffusive search for a target in crowding conditions
Several important biological processes are initiated by the binding
of a protein to a specific site on the DNA. The strategy adopted by a protein,
called transcription factor (TF), for searching its specific binding site on the
DNA has been investigated over several decades. In recent times the effects
obstacles, like DNA-binding proteins, on the search by TF has begun to receive
attention. RNA polymerase (RNAP) motors collectively move along a segment
of the DNA during a genomic process called transcription. This RNAP trac
is bound to affect the diffusive scanning of the same segment of the DNA by
a TF searching for its binding site. Motivated by this phenomenon, here we
develop a kinetic model where a ‘particle’, that represents a TF, searches
for a specific site on a one-dimensional lattice. On the same lattice another
species of particles, each representing a RNAP, hop from left to right exactly
as in a totally asymmetric simple exclusion process (TASEP) which forbids
simultaneous occupation of any site by more than one particle, irrespective of
their identities. Although the TF is allowed to attach to or detach from any
lattice site, the RNAPs can attach only to the first site at the left edge and
detach from only the last site on the right edge of the lattice. We formulate the search as a first-passage process; the time taken to reach the target site
for the first time, starting from a well defined initial state, is the search time.
By approximate analytical calculations and Monte Carlo (MC) computer
simulations, we calculate the mean search time. We show that RNAP traffic
rectifies the diffusive motion of TF to that of a Brownian ratchet, and the
mean time of successful search can be even shorter than that required in the
absence of RNAP traffic. Moreover, we show that there is an optimal rate of
detachment that corresponds to the shortest mean search time.
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- Award ID(s):
- 1664218
- NSF-PAR ID:
- 10094147
- Date Published:
- Journal Name:
- Journal of statistical mechanics
- ISSN:
- 1742-5468
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/https://doi.org/10.1088/1742-5468/aaf31d
