Dataset Information

Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force.

ABSTRACT: The organization of chromatin in 30 nm fibers remains a topic of debate. Here, we quantify the mechanical properties of the linker DNA and evaluate the impact of these properties on chromatin fiber folding. We extended a rigid basepair DNA model to include (un)wrapping of nucleosomal DNA and (un)stacking of nucleosomes in one-start and two-start chromatin fibers. Monte Carlo simulations that mimic single-molecule force spectroscopy experiments of folded nucleosomal arrays reveal different stages of unfolding as a function of force and are largely consistent with a two-start folding for 167 and one-start folding for 197 nucleosome repeat length fibers. The major insight is that nucleosome unstacking and subsequent unwrapping is not necessary to obtain quantitative agreement with experimental force extension curves up to the overstretching plateau of folded chromatin fibers at 3-5 pN. Nucleosome stacking appears better accommodated in one-start than in two-start conformations, and we suggest that this difference can compensate the increased energy for bending the linker DNA. Overall, these simulations capture the dynamic structure of chromatin fibers while maintaining realistic physical properties of the linker DNA.

SUBMITTER: de Jong BE

PROVIDER: S-EPMC6303278 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Publications

Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force.

de Jong Babette E BE Brouwer Thomas B TB Kaczmarczyk Artur A Visscher Bert B van Noort John J

Biophysical journal 20181011 10

The organization of chromatin in 30 nm fibers remains a topic of debate. Here, we quantify the mechanical properties of the linker DNA and evaluate the impact of these properties on chromatin fiber folding. We extended a rigid basepair DNA model to include (un)wrapping of nucleosomal DNA and (un)stacking of nucleosomes in one-start and two-start chromatin fibers. Monte Carlo simulations that mimic single-molecule force spectroscopy experiments of folded nucleosomal arrays reveal different stages ...[more]

PMID: 30366627

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Project description:Design of proteins with desired thermal properties is important for scientific and biotechnological applications. Here we developed a theoretical approach to predict the effect of mutations on protein stability from non-equilibrium unfolding simulations. We establish a relative measure based on apparent simulated melting temperatures that is independent of simulation length and, under certain assumptions, proportional to equilibrium stability, and we justify this theoretical development with extensive simulations and experimental data. Using our new method based on all-atom Monte-Carlo unfolding simulations, we carried out a saturating mutagenesis of Dihydrofolate Reductase (DHFR), a key target of antibiotics and chemotherapeutic drugs. The method predicted more than 500 stabilizing mutations, several of which were selected for detailed computational and experimental analysis. We find a highly significant correlation of r=0.65-0.68 between predicted and experimentally determined melting temperatures and unfolding denaturant concentrations for WT DHFR and 42 mutants. The correlation between energy of the native state and experimental denaturation temperature was much weaker, indicating the important role of entropy in protein stability. The most stabilizing point mutation was D27F, which is located in the active site of the protein, rendering it inactive. However for the rest of mutations outside of the active site we observed a weak yet statistically significant positive correlation between thermal stability and catalytic activity indicating the lack of a stability-activity tradeoff for DHFR. By combining stabilizing mutations predicted by our method, we created a highly stable catalytically active E. coli DHFR mutant with measured denaturation temperature 7.2°C higher than WT. Prediction results for DHFR and several other proteins indicate that computational approaches based on unfolding simulations are useful as a general technique to discover stabilizing mutations.

Dataset Information

Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force.

Publications

Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force.

Similar Datasets

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