Chromatin Remodeler: Nucleosome Sliding Simulator

Remodeler Mode

Motor Controls

ATP turnover rate 55%

Active remodelers 2

Live Readouts

Promoter accessibility 0%

Mean linker DNA— bp

ATP hydrolyzed0

How it works

A nucleosome wraps ~147 bp of DNA in ~1.65 left-handed turns around a histone octamer. ATP-dependent chromatin remodelers (SWI/SNF, ISWI, CHD families) grip the nucleosomal DNA and pump it around the octamer using a DNA-translocase motor domain, sliding the histone core along the fiber without breaking DNA:

Footprint:  F = 147 bp (fixed octamer contact)
Linker(i):  D_i = x_(i+1) − x_i − F   (free bp between neighbors)
Motor step: Δx = ± s per ATP cycle, s ≈ 2–10 bp (coarse-grained here)

Spacing mode mimics ISWI/CHD1: each remodeler measures the linker DNA on both sides of a nucleosome and steps it toward the longer side, Δ = −sign(D_left − D_right)·s, converging the array to evenly spaced nucleosomes (minimizing linker-length variance) — the mechanism that regularly phases nucleosomes genome-wide after replication.

Clear promoter mode mimics SWI/SNF/RSC at active promoters: the remodeler nearest the marked transcription-start-site window is stepped away from it each ATP cycle, opening a nucleosome-depleted region (NDR) that exposes DNA for transcription-factor and Pol II binding. Accessibility A = 1 − (bp of the promoter window covered by a footprint) / (window width).

A step is only accepted if it does not push the histone core into a neighboring nucleosome's footprint — remodelers cannot pass through each other, so repositioning propagates one collision at a time, just as it does on real chromatin fibers.

▮ promoter window (TSS)

Histone octamer Wrapped DNA Remodeler (ATP motor)

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