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 complex's 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 factor's affinity near nucleosomes.

Although molecular dynamics simulations have become a useful tool in essentially all fields of chemistry, condensed matter physics, materials science, and biology, there is still a large gap between the time scale which can be reached in molecular dynamics simulations and that observed in experiments. To address the problem, many enhanced sampling methods were introduced, which effectively extend the time scale being approached in simulations. In this perspective, we review a variety of enhanced sampling methods. We first discuss collective-variables-based methods including metadynamics and variationally enhanced sampling. Then, collective variable free methods such as parallel tempering and integrated tempering methods are presented. At last, we conclude with a brief introduction of some newly developed combinatory methods. We summarize in this perspective not only the theoretical background and numerical implementation of these methods but also the new challenges and prospects in the field of the enhanced sampling.

We have quantitatively studied the performance of a finite-difference Poisson-Boltzmann implicit solvent with respect to the TIP3P explicit solvent in a range of systems of biochemical interest. An overall agreement was found between the tested implicit and explicit solvents for hydrogen-bonding/salt-bridging dimers and peptide monomers and dimers of different conformations and different lengths. These comparative analyses also indicate a good transferability of empirically optimized parameters for the implicit solvent from small training molecules to large testing peptides. However, deviations between the two tested solvents are also apparent. Specifically, a consistent deviation was observed when hydrogen-bonding or salt-bridging dimers are within 4-6 A. The deviation reaches a maximum at about 5.5 A, the so-called water-bridging distance. The tested implicit solvent, even with optimized parameters, cannot capture the subtle fluctuation in the distance-dependent reaction field energy profiles, although smoothed profiles can still be obtained and are in overall agreement with those in the explicit solvent. Interestingly, the same mechanism underlining the above discrepancy is also responsible for the larger deviations of certain peptide conformations, such as parallel beta-strand dimers. It is likely that the observed discrepancy may cause improper conformational distributions in simulations with the implicit solvent when hydrogen-bonding or salt-bridging interactions are crucial, such as secondary structure populations in proteins. Validation of the implicit solvent with optimized parameters in dynamics simulations will be the next step to study the influences of the observed discrepancy at biological conditions.

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.

We have developed a new-generation Amber united-atom force field for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. In the new united-atom force field, all hydrogens on aliphatic carbons in all amino acids are united with carbons except those on Calpha. Our choice of explicit representation of all protein backbone atoms aims at minimizing perturbation to protein backbone conformational distributions and to simplify development of backbone torsion terms. Tests with dipeptides and solvated proteins show that our goal is achieved quite successfully. The new united-atom force field uses the same new RESP charging scheme based on B3LYP/cc-pVTZ//HF/6-31g** quantum mechanical calculations in the PCM continuum solvent as that in the Duan et al. force field. van der Waals parameters are empirically refitted starting from published values with respect to experimental solvation free energies of amino acid side-chain analogues. The suitability of mixing new point charges and van der Waals parameters with existing Amber covalent terms is tested on alanine dipeptide and is found to be reasonable. Parameters for all new torsion terms are refitted based on the new point charges and the van der Waals parameters. Molecular dynamics simulations of three small globular proteins in the explicit TIP3P solvent are performed to test the overall stability and accuracy of the new united-atom force field. Good agreements between the united-atom force field and the Duan et al. all-atom force field for both backbone and side-chain conformations are observed. In addition, the per-step efficiency of the new united-atom force field is demonstrated for simulations in the implicit generalized Born solvent. A speedup around two is observed over the Duan et al. all-atom force field for the three tested small proteins. Finally, the efficiency gain of the new united-atom force field in conformational sampling is further demonstrated with a well-known toy protein folding system, an 18 residue polyalanine in distance-dependent dielectric. The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide.

No abstract

DNA base flipping is a fundamental theme in DNA biophysics. The dynamics for a B-DNA base to spontaneously flip out of the double helix has significant implications in various DNA-protein interactions but are still poorly understood. The spontaneous base-flipping rate obtained previously via the imino proton exchange assay is most likely the rate of base wobbling instead of flipping. Using the diffusion-decelerated fluorescence correlation spectroscopy together with molecular dynamics simulations, we show that a base of a single mismatched base pair (T-G, T-T, or T-C) in a doublestranded DNA can spontaneously flip out of the DNA duplex. The extrahelical lifetimes are on the order of 10 ms, whereas the intrahelical lifetimes range from 0.3 to 20 s depending on the stability of the base pairs. These findings provide detailed understanding on the dynamics of DNA base flipping and lay down foundation to fully understand how exactly the repair proteins search and locate the target mismatched base among a vast excess of matched DNA bases.fluctuation spectroscopy | integrated tempering sampling | rate constants | free-energy landscape A base in normal B-DNA spontaneously swinging out of the double helix to an extrahelical position is known as spontaneous base flipping. The dynamics of such base flipping is a fundamental issue in DNA biophysics. It is also related to how DNA repair or modification proteins search and fix the lesion bases to maintain the genome integrity or modify the DNA. Although extensive structural studies have found that many DNA base repair/modification proteins completely flip their target base out extrahelically (so-called enzymatic base flipping) (1-5), it is still under debate (6-11) whether the base flipping occurs spontaneously (9, 10, 12) or not (6-8). Accurate information on the dynamics of spontaneous base flipping is therefore of high interest and importance.However, the study of spontaneous base flipping is deemed to be difficult. The probability is extremely low for a single base to flip out of the DNA double helix in the absence of proteins. Hence only sensitive relaxation methods are able to detect such kind of fluctuation under equilibrium. As a well-known relaxation method, NMR has been applied to tackle this problem through the imino proton exchange assay (9,(13)(14)(15)(16)(17). In this assay, it is assumed that the exchange of the imino proton (in either G or T base) with the catalysts in the solution occurs only when the base flips out (13), and the extrapolated imino proton exchange rate at an infinite catalyst concentration is taken to be the base-flipping rate (14,15,17). According to these NMR studies the lifetime of the extrahelical state is on the order of microseconds, and that of the intrahelical state ranges from milliseconds to hundreds of milliseconds, depending on the stability of individual base pairs. MacKerell and coworkers as well as others have done extensive theoretical investigations and found that the target imino proton on the base already becomes accessible...

The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism, especially the sequence dependence for the formation of varied chromatin structures in different cells remains to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI (CpG island) forest and prairie genomic domains based on CGI densities of a species, dividing the genome into two sequentially, epigenetically, and transcriptionally distinct regions. These two megabase-sized domains also spatially segregate to different extents in different cell types. Forests and prairies show enhanced segregation from each other in development, differentiation, and senescence, meanwhile the multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, helping to define cell identity. We propose that the phase separation of the 1D mosaic sequence in space serves as a potential driving force, and together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types. The mosaicity in genome of different species in terms of forests and prairies could relate to observations in their biological processes like development and aging. In this way, we provide a bottoms-up theory to explain the chromatin structural and epigenetic changes in different processes.