Computational models for large-scale simulations of facilitated diffusion

The binding of site-specific transcription factors to their genomic target sites is a key step in gene regulation. While the genome is huge, transcription factors belong to the least abundant protein classes in the cell. It is therefore fascinating how short the time frame is that they require to home in on their target sites. The underlying search mechanism is called facilitated diffusion and assumes a combination of three-dimensional diffusion in the space around the DNA combined with one-dimensional random walk on it. In this review, we present the current understanding of the facilitated diffusion mechanism and identify questions that lack a clear or detailed answer. One way to investigate these questions is through stochastic simulation and, in this manuscript, we support the idea that such simulations are able to address them. Finally, we review which biological parameters need to be included in such computational models in order to obtain a detailed representation of the actual process. © 2012 The Royal Society of Chemistry

Physicochemical Properties of Ion Pairs of Biological Macromolecules

Ion pairs (also known as salt bridges) of electrostatically interacting cationic and anionic moieties are important for proteins and nucleic acids to perform their function. Although numerous three-dimensional structures show ion pairs at functionally important sites of biological macromolecules and their complexes, the physicochemical properties of the ion pairs are not well understood. Crystal structures typically show a single state for each ion pair. However, recent studies have revealed the dynamic nature of the ion pairs of the biological macromolecules. Biomolecular ion pairs undergo dynamic transitions between distinct states in which the charged moieties are either in direct contact or separated by water. This dynamic behavior is reasonable in light of the fundamental concepts that were established for small ions over the last century. In this review, we introduce the physicochemical concepts relevant to the ion pairs and provide an overview of the recent advancement in biophysical research on the ion pairs of biological macromolecules

Temperature Dependence of Internal Motions of Protein Side-Chain NH₃⁺ Groups: Insight into Energy Barriers for Transient Breakage of Hydrogen Bonds

Although charged side chains play important roles in protein function, their dynamic properties are not well understood. Nuclear magnetic resonance methods for investigating the dynamics of lysine side-chain NH₃⁺ groups were established recently. Using this methodology, we have studied the temperature dependence of the internal motions of the lysine side-chain NH₃⁺ groups that form ion pairs with DNA phosphate groups in the HoxD9 homeodomain–DNA complex. For these NH₃⁺ groups, we determined order parameters and correlation times for bond rotations and reorientations at 15, 22, 28, and 35 °C. The order parameters were found to be virtually constant in this temperature range. In contrast, the bond-rotation correlation times of the NH₃⁺ groups were found to depend strongly on temperature. On the basis of transition state theory, the energy barriers for NH₃⁺ rotations were analyzed and compared to those for CH₃ rotations. Enthalpies of activation for NH₃⁺ rotations were found to be significantly higher than those for CH₃ rotations, which can be attributed to the requirement of hydrogen bond breakage. However, entropies of activation substantially reduce the overall free energies of activation for NH₃⁺ rotations to a level comparable to those for CH₃ rotations. This entropic reduction in energy barriers may accelerate molecular processes requiring hydrogen bond breakage and play a kinetically important role in protein function