Functioning to store the genetic material and to control gene expression, the nucleoprotein complex chromatin is constructed as a polymer of nucleosomes where the DNA is are wrapped around histone octamers. Numerous chromatin aspects have been studied for many years, but the exact structure of the chromatin fiber at different levels of compactness (over the cell cycle) remains unknown. Recent discoveries on epigenetic inheritance and nucleosome modifications have made chromatin research a hot field, investigated by both experimental and theoretical scientists. We are interested in the global structural aspects of the chromatin fiber, because modern molecular modeling technologies can investigate chromatin at this level, and available to our lab are macroscopic models developed for such large systems. Changes of chromatin structures alter gene expression, and these changes can be caused by both cellular environment (such as the salt concentration) and nucleosome modifications (such as histone variations, post-translational modifications, and ATP-dependent remodeling). Therefore, building a computationally feasible and reliable model of nucleosomes is essential for obtaining insights into the structure and dynamics of the chromatin fiber. Our group has available newly developed Brownian dynamics code for simulations of systems at this size, DNA bead model for long DNA, and DiSCO algorithm for rigid macromolecules. Still, the flexibility of the nucleosome's histone tails, required for both intra/inter-nucleosome interactions and nucleosome modifications, has inspired us to develop a new protein bead model for the histone tails. We propose and build such a protein bead model based on the subunit model used in the University of Houston Brownian Dynamics program. The protein bead model is then integrated into our Brownian dynamics code and shown to reproduce well an experimental result (the maximal extension of nucleosomes) on the histone tail conformation study (Mangenot et al. 2002 Biophys. J. 82, 345-356). We also employ protein homology technologies (multiple sequence alignments and structure superimpositions) to add missing histone tails to tail-less nucleosomes. This new model opens the way to many important investigations in chromatin structure and function.
Used with Gaussian 98 and AMBER 6. Download the protocol, Perl programs, and a sample.
In citing the protocol, please refer to:
Zhang, Q. & Schlick, T., Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. Biophysical Journal, 90: 1865-1877, 2006.
The TATA-Box Binding Protein (TBP) is required by eukaryotic RNA polymerases for correct transcription initiation. TBP binds to the the minor groove of an 8-basepair (bp) DNA promoter element known as the TATA box and severely bends the TATA box. The promoter DNA substrate can be damaged by components present in the cell or the environment to produce covalent carcinogen-DNA adducts. These may lead to transcription blockage or unfaithful transcription. Benzo[a]pyrene (BP) is a widespread environmental chemical carcinogen which can be metabolically converted to DNA-reactive enantiomeric (+) and (-)-anti-BPDEs. Recent experimental studies of a pair of stereoisomeric adenine adducts, derived from (+) and (-)-anti-BPDEs, have revealed how these lesions influence the complexation of TBP with the TATA box. Depending on the adduct's location in the TATA box and its stereochemistry, the stability of monomeric TATA/TBP complexes was found to increase or decrease relative to the unmodified DNA. We report here analyses of molecular dynamics simulations to interpret these findings. Structural analyses of twelve DNA/protein systems representing different combinations of adduct stereoisomer type and placement within the promoter reveal that the location of the adduct within the TATA octamer determines whether stability of TATA/TBP complexes is increased or decreased. The effect on binding stability can be interpreted in terms of conformational freedom and major-groove space available to BP due to the hydrogen bonds and inserted phenylalanines of the TATA/TBP complex. That is, depending on the position of the adenine to which BP is covalently bound, BP can be accommodated in an intercalated or major-groove orientation with ease or with great difficulty (due to interference with TATA/TBP interactions). The unraveled structures and interactions thus reveal the effect of different adduct locations on TATA/TBP complex formation and suggest how transcription initiation may be affected by the presence of a bulky BP.
Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Since macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a 5.5% residual. Since regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level.
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Last updated on: 02.01.2005
