Joshua Lequieu

Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects

A recently published coarse-grained DNA model [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization mechanism of DNA oligomers. Forward flux sampling is used to construct ensembles of reactive trajectories from which the effects of sequence, length, and ionic strength are revealed. Heterogeneous sequences are observed to hybridize via the canonical zippering mechanism. In contrast, homogeneous sequences hybridize through a slithering mechanism, while more complex base pair displacement processes are observed for repetitive sequences. In all cases, the formation of non-native base pairs leads to an increase in the observed hybridization rate constants beyond those observed in sequences where only native base pairs are permitted. The scaling of rate constants with length is captured by extending existing hybridization theories to account for the formation of non-native base pairs. Furthermore, that scaling is found to be similar for oligomeric and polymeric systems, suggesting that similar physics is involved.

Coarse-grained modeling of DNA curvature

The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)], into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles.

Tension-Dependent Free Energies of Nucleosome Unwrapping

Nucleosomes form the basic unit of compaction within eukaryotic genomes, and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails contribute asymmetrically to the stability of the outer and inner turn of nucleosomal DNA and that depending on which histone tails are modified, the tension-dependent response is modulated differently.

SSAGES: Software Suite for Advanced General Ensemble Simulations

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

In silico evidence for sequence-dependent nucleosome sliding

Significance The dynamic compaction of DNA into chromatin is essential for gene expression. Errors during compaction are associated with numerous diseases. Several molecular factors are known to affect chromatin dynamics, but their relative importance and the interplay between them are poorly understood. A detailed molecular model is used here to examine chromatin dynamics at the level of its most fundamental building block, namely the nucleosome. Nucleosome dynamics are demonstrated to be encoded in the DNA sequence itself, and key fundamental factors are uncovered that can significantly alter these dynamics at the molecular level. The results serve to complete a hitherto unavailable description of nucleosome dynamics by introducing previously unappreciated molecular processes, with the potential to influence macroscopic chromatin structure and genetics. Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nucleosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nucleosome repositioning. The mechanism of nucleosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

Towards a Hybrid Human-Computer Scientific Information Extraction Pipeline

The emerging field of materials informatics has the potential to greatly reduce time-to-market and development costs for new materials. The success of such efforts hinges on access to large, high-quality databases of material properties. However, many such data are only to be found encoded in text within esoteric scientific articles, a situation that makes automated extraction difficult and manual extraction time-consuming and error-prone. To address this challenge, we present a hybrid Information Extraction (IE) pipeline to improve the machine-human partnership with respect to extraction quality and person-hours, through a combination of rule-based, machine learning, and crowdsourcing approaches. Our goal is to leverage computer and human strengths to alleviate the burden on human curators by automating initial extraction tasks before prioritizing and assigning specialized curation tasks to humans with different levels of training: using non-experts for straightforward tasks such as validation of higher accuracy results (e.g., completing partial facts) and domain experts for low-certainty results (e.g., reviewing specialized compound labels). To validate our approaches, we focus on the task of extracting the glass transition temperature of polymers from published articles. Applying our approaches to 6 090 articles, we have so far extracted 259 refined data values. We project that this number will grow considerably as we tune our methods and process more articles, to exceed that found in standard, expert-curated polymer data handbooks while also being easier to keep up-to-date. The freely available data can be found on our Polymer Properties Predictor and Database website at http://pppdb.uchicago.edu.

A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions

Genome packing in viruses and prokaryotes relies on positively charged ions to reduce electrostatic repulsions, and induce attractions that can facilitate DNA condensation. Here we present molecular dynamics simulations spanning several microseconds of dsDNA packing inside nanometer-sized viral capsids. We use a detailed molecular model of DNA that accounts for molecular structure, basepairing, and explicit counterions. The size and shape of the capsids studied here are based on the 30-nanometer-diameter gene transfer agents of bacterium Rhodobacter capsulatus that transfer random 4.5-kbp (1.5 μm) DNA segments between bacterial cells. Multivalent cations such as spermidine and magnesium induce attraction between packaged DNA sites that can lead to DNA condensation. At high concentrations of spermidine, this condensation significantly increases the shear stresses on the packaged DNA while also reducing the pressure inside the capsid. These effects result in an increase in the packing velocity and the total amount of DNA that can be packaged inside the nanometer-sized capsids. In the simulation results presented here, high concentrations of spermidine3+ did not produce the premature stalling observed in experiments. However, a small increase in the heterogeneity of packing velocities was observed in the systems with magnesium and spermidine ions compared to the system with only salt. The results presented here indicate that the effect of multivalent cations and of spermidine, in particular, on the dynamics of DNA packing, increases with decreasing packing velocities.

Mechanical Response of DNA–Nanoparticle Crystals to Controlled Deformation

The self-assembly of DNA-conjugated nanoparticles represents a promising avenue toward the design of engineered hierarchical materials. By using DNA to encode nanoscale interactions, macroscale crystals can be formed with mechanical properties that can, at least in principle, be tuned. Here we present in silico evidence that the mechanical response of these assemblies can indeed be controlled, and that subtle modifications of the linking DNA sequences can change the Young’s modulus from 97 kPa to 2.1 MPa. We rely on a detailed molecular model to quantify the energetics of DNA–nanoparticle assembly and demonstrate that the mechanical response is governed by entropic, rather than enthalpic, contributions and that the response of the entire network can be estimated from the elastic properties of an individual nanoparticle. The results here provide a first step toward the mechanical characterization of DNA–nanoparticle assemblies, and suggest the possibility of mechanical metamaterials constructed using DNA.