Lijiang Yang

Probing Allostery through DNA

Allostery Across DNA Proteins, such as transcription factors and RNA polymerase, bind close to each other on DNA and their function is coordinated. Kim et al. (p. 816; see the Perspective by Crothers) report single-molecule experiments that show that the DNA binding affinity of a protein is significantly altered by a second protein bound nearby. The effect oscillates between stabilizing and destabilizing the binding with a periodicity equal to the helical pitch of DNA. Allosteric coupling between a transcriptional repressor and RNA polymerase modulated gene expression in living bacteria. Proteins bound to the same, but not overlapping, stretch of DNA modulate each others DNA binding affinity. [Also see Perspective by Crothers] Allostery is well documented for proteins but less recognized for DNA-protein interactions. Here, we report that specific binding of a protein on DNA is substantially stabilized or destabilized by another protein bound nearby. The ternary complexs free energy oscillates as a function of the separation between the two proteins with a periodicity of ~10 base pairs, the helical pitch of B-form DNA, and a decay length of ~15 base pairs. The binding affinity of a protein near a DNA hairpin is similarly dependent on their separation, which—together with molecular dynamics simulations—suggests that deformation of the double-helical structure is the origin of DNA allostery. The physiological relevance of this phenomenon is illustrated by its effect on gene expression in live bacteria and on a transcription factors affinity near nucleosomes.

On the Structure of Water at the Aqueous/Air Interface

Vibrational sum frequency spectroscopy (VSFS) and molecular dynamics (MD) simulations were used in concert to investigate the molecular structure and hydrogen bonding of the air/water interface. MD simulations were performed with a variety of water models. The results indicated that only the upper most two layers of water molecules are ordered in this system. There is a strong preference to have the top layer arranged such that the OH moiety points upward into the air. This orientational preference arises from two factors that involve the maximization of the number of hydrogen bonds formed and the minimization of partial charge that is exposed. Specifically, the lone pairs from oxygen are less likely to face into the air compared with the OH moiety because this would expose more partial charge and, therefore, be unfavorable on enthalpic grounds. The two-layer interfacial water structure model implies that there should be four distinct types of OH stretches for this system. Namely, one directs upward and another points downward in each layer. Interestingly, VSFS experiments revealed the presence of four OH stretch region peaks at 3117, 3222, 3448, and 3696 cm(-1). The phases of the 3117 and 3696 cm(-1) resonances carried a positive sign, which indicates that these features arise from OH groups with protons facing upward toward the air. The other two resonances emanate from OH groups with protons facing downward toward the bulk aqueous solution. On the basis of this, we assign the 3117 cm(-1) peak to the OH moiety from a water molecule in the second layer, which is hydrogen bonded upward toward the top layer. On the other hand, the peak at 3222 cm(-1) should arise from water molecules in the top layer with the OH moiety facing downward to hydrogen bond to the second layer. The 3448 cm(-1) peak arises from hydrogen bonding between water molecules in the second layer and the more disordered water molecules of the bulk liquid. Finally, the peak at 3696 cm(-1) is assigned to the free OH moiety pointing upward in the top layer.

Differences of cations and anions: their hydration, surface adsorption, and impact on water dynamics.

The higher tendency for anions to accumulate at the salt aqueous solution/air interface than that of cations has been observed experimentally and theoretically, suggesting that the size and polarizability of the ions play essential roles in this effect. Here, we investigate the influence of the nonsymmetrical positive-vs-negative charge distribution in water molecules to the hydration and surface/bulk partition of the solvated positively and negatively charged particles by using molecular dynamics simulations with hypothetical ions to validate our theoretical models. The results indicate that positive and negative charges (called cations and anions, respectively, although they may not really exist in experiments) with all other properties identical are hydrated differently and that the anions are more likely to populate at the surface. The simulation on a combination series of cations and anions in aqueous solution shows significant variations on water dynamics, likely due to the specific cooperativity between oppositely charged ions.

From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions

It is well known that alcohols can have strong effects on protein structures. For example, monohydric methanol and ethanol normally denature, whereas polyhydric glycol and glycerol protect, protein structures. In a recent combined theoretical and NMR experimental study, we showed that molecular dynamics simulations can be effectively used to understand the molecular mechanism of methanol denaturing protein. In this study, we used molecular dynamics simulations to investigate how alcohols with varied hydrophobicity and different numbers of hydrophilic groups (hydroxyl groups) exert effects on the structure of the model polypeptide, BBA5. First, we showed that methanol and trifluoroethanol (TFE) but not glycol or glycerol disrupt hydrophobic interactions. The latter two alcohols instead protect the assembly of the α- and β-domains of the polypeptide. Second, all four alcohols were shown to generally increase the stability of secondary structures, as revealed by the increased number of backbone hydrogen bonds formed in alcohol/water solutions compared to that in pure water, although individual hydrogen bonds can be weakened by certain alcohols, such as TFE. The two monohydric alcohols, methanol and TFE, display apparently different sequence-dependence in affecting the backbone hydrogen bond stability: methanol tends to enhance the stability of backbone hydrogen bonds of which the carbonyl groups are from polar residues, whereas TFE tends to stabilize those involving non-polar residues. These results demonstrated that subtle differences in the solution environment could have distinct consequences on protein structures.

Effects of Cosolvents on the Hydration of Carbon Nanotubes

Molecular dynamics simulations of a nonpolar single-walled carbon nanotube (SWNT) solvated in aqueous solutions of urea, methanol, and trimethylamine N-oxide (TMAO) show clearly the effects of cosolvents on the hydration of the interior of the SWNT. The size of the SWNT was chosen to be small enough that water but not the cosolvent molecules can penetrate into its interior. Urea as a protein denaturant improves hydration of the interior of the SWNT, while the protein protectant TMAO dehydrates the SWNT. The interior of the SWNT is also dehydrated when methanol is added to the solution. The analysis of interaction energies of the water confined inside the SWNT pore shows that the stability of the confined water in the methanol and TMAO solutions mainly depends on electrostatic interactions. In contrast, both van der Waals and electrostatic interactions were shown to be important in stabilizing the confined water when the SWNT is immersed in the urea solution.

Application of the accelerated molecular dynamics simulations to the folding of a small protein

In this paper, we further explore the applicability of the accelerated molecular dynamics simulation method using a bias potential. The method is applied to both simple model systems and real multidimensional systems. The method is also compared to replica exchange simulations in folding a small protein, Trp cage, using an all atom potential for the protein and an implicit model for the solvent. We show that the bias potential method allows quick searches of folding pathways. We also show that the choice of the bias potential has significant influence on the efficiency of the bias potential method.

Comparison between integrated and parallel tempering methods in enhanced sampling simulations

Recently, we introduced an integrated tempering approach to enhance sampling in the energy and configuration space for large systems. In this paper, we show that this new method has a higher efficiency than bias potential and generalized ensemble methods, such as accelerated molecular dynamics and replica-exchange molecular dynamics (parallel tempering) methods, in yielding thermodynamic averages. Particularly, the sampling efficiencies in both energy and configuration spaces are compared in details between integrated and parallel tempering methods. Related issues regarding the efficiency involved in the usage of the parallel tempering method are also discussed.

A selective integrated tempering method

In this paper, based on the integrated tempering sampling we introduce a selective integrated tempering sampling (SITS) method for the efficient conformation sampling and thermodynamics calculations for a subsystem in a large one, such as biomolecules solvated in aqueous solutions. By introducing a potential surface scaled with temperature, the sampling over the configuration space of interest (e.g., the solvated biomolecule) is selectively enhanced but the rest of the system (e.g., the solvent) stays largely unperturbed. The applications of this method to biomolecular systems allow highly efficient sampling over both energy and configuration spaces of interest. Comparing to the popular and powerful replica exchange molecular dynamics (REMD), the method presented in this paper is significantly more efficient in yielding relevant thermodynamics quantities (such as the potential of mean force for biomolecular conformational changes in aqueous solutions). It is more important that SITS but not REMD yielded results that are consistent with the traditional umbrella sampling free energy calculations when explicit solvent model is used since SITS avoids the sampling of the irrelevant phase space (such as the boiling water at high temperatures).

On the enhanced sampling over energy barriers in molecular dynamics simulations.

We present here calculations of free energies of multidimensional systems using an efficient sampling method. The method uses a transformed potential energy surface, which allows an efficient sampling of both low and high energy spaces and accelerates transitions over barriers. It allows efficient sampling of the configuration space over and only over the desired energy range(s). It does not require predetermined or selected reaction coordinate(s). We apply this method to study the dynamics of slow barrier crossing processes in a disaccharide and a dipeptide system.

Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems

We discuss in this review paper the recent development of enhanced sampling methods for searching in energy and configuration space, as well as that for the reactive transition paths. These methods allow accelerated calculations of thermodynamics and kinetics. We summarize in this review the theoretical background and numerical implementation of a variety of methods. Examples of applications are given for each method.