J. Wereszczynski

Modeling Allosteric Mechanisms of Eukaryotic Type II Topoisomerases

This study uses molecular dynamics simulations to investigate how nucleotide binding and hydrolysis regulate the allosteric mechanisms of yeast TopoII and how mutations affect these processes.

Conformational and Thermodynamic Differences Underlying Wild-type and Mutant ENL YEATS Domain Specificity for Epigenetic Marks

This study uses molecular dynamics simulations to analyze how mutations in the ENL YEATS domain affect its binding specificity for different acetylated histone peptides.

The Effects of RNA.DNA-DNA Triple Helices on Nucleosome Structures and Dynamics

This study uses molecular dynamics simulations to investigate how RNA.DNA-DNA triple helices affect nucleosome structure and dynamics, revealing RNA sequence effects and interactions with histone tails.

Directed inter-domain motions enable the IsdH Staphylococcus aureus receptor to rapidly extract heme from human hemoglobin

This study shows directed inter-domain motions in the IsdH receptor enable efficient heme extraction from human hemoglobin by distorting the heme pocket.

Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways

This study characterizes the dynamic structure of archaeal chromatin complexes using simulations and cryoEM, revealing their inherent flexibility and DNA wrapping patterns.

The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array

This paper uses molecular dynamics simulations to study how linker histone H1 binding affects chromatin fiber structure and dynamics, showing it stabilizes compact structures and enhances long-range epigenetic signaling.

WASP: A software package for correctly characterizing the topological development of ribbon structures

WASP characterizes the topology of ribbon structures using twist-writhe decomposition, showing it provides more accurate insights than traditional methods.

The Molecular Basis of Specific DNA Binding by the BRG1 AT-hook and Bromodomain

This study identifies the DNA specificity and structural basis of BRG1's composite domain using SELEX-seq, NMR, and modeling, showing how cancer mutations alter DNA binding.

BEES: Bayesian Ensemble Estimation from SAS

BEES is a Bayesian tool for fitting ensemble models to SAS data, allowing users to sample and compare models while incorporating additional data.

Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy

The paper compares alternative exon skip repairs for Duchenne muscular dystrophy, finding stability differences between edits and identifying structural perturbations as the cause.