The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies.

BACKGROUND: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. RESULTS: In this paper, we ask whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. CONCLUSIONS: At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels.

Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment.

The accuracy of computational models of water is key to atomistic simulations of biomolecules. We propose a computationally efficient way to improve the accuracy of the prediction of hydration-free energies (HFEs) of small molecules: the remaining errors of the physics-based models relative to the experiment are predicted and mitigated by machine learning (ML) as a postprocessing step. Specifically, the trained graph convolutional neural network attempts to identify the "blind spots" in the physics-based model predictions, where the complex physics of aqueous solvation is poorly accounted for, and partially corrects for them. The strategy is explored for five classical solvent models representing various accuracy/speed trade-offs, from the fast analytical generalized Born (GB) to the popular TIP3P explicit solvent model; experimental HFEs of small neutral molecules from the FreeSolv set are used for the training and testing. For all of the models, the ML correction reduces the resulting root-mean-square error relative to the experiment for HFEs of small molecules, without significant overfitting and with negligible computational overhead. For example, on the test set, the relative accuracy improvement is 47% for the fast analytical GB, making it, after the ML correction, almost as accurate as uncorrected TIP3P. For the TIP3P model, the accuracy improvement is about 39%, bringing the ML-corrected model's accuracy below the 1 kcal/mol threshold. In general, the relative benefit of the ML corrections is smaller for more accurate physics-based models, reaching the lower limit of about 20% relative accuracy gain compared with that of the physics-based treatment alone. The proposed strategy of using ML to learn the remaining error of physics-based models offers a distinct advantage over training ML alone directly on reference HFEs: it preserves the correct overall trend, even well outside of the training set.

AmberTools.

AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

Why Na+ has higher propensity than K+ to condense DNA in a crowded environment.

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.

Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.

BACKGROUND: Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics; however, relevant genome-wide experiments that may provide statistically significant conclusions remain difficult. RESULTS: We have developed a coarse-grained dynamical model of D. melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. The simulations include an ensemble of nuclei, corresponding to the experimentally observed set of several possible mutual arrangements of chromosomal arms. The model is validated against multiple structural features of chromatin from several different experiments not used in model development. Predicted positioning of all LADs at the NE is highly dynamic-the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome, which also has the same strong effect on the predicted positioning of individual TADs -- higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a small (0.5 kT) increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region. CONCLUSIONS: A dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. We conjecture that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions.

Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.

Stability of a protein-ligand complex may be sensitive to pH of its environment. Here we explore, computationally, stability of a set of protein-nucleic acid complexes using fundamental thermodynamic linkage relationship. The nucleosome, as well as an essentially random selection of 20 protein complexes with DNA or RNA, are included in the analysis. An increase in intra-cellular/intra-nuclear pH destabilizes most complexes, including the nucleosome. We propose to quantify the effect by ΔΔG0.3-the change in the binding free energy due to pH increase of 0.3 units, corresponding to doubling of the H + activity; variations of pH of this amplitude can occur in living cells, including in the course of the cell cycle, and in cancer cells relative to normal ones. We suggest, based on relevant experimental findings, a threshold of biological significance of 1 2 k B T ( ∼ 0.3 k c a l / m o l ) for changes of stability of chromatin-related protein-DNA complexes: a change in the binding affinity above the threshold may have biological consequences. We find that for 70% of the examined complexes, Δ Δ G 0.3 > 1 2 k B T (for 10%, ΔΔG0.3 is between 3 and 4 k B T). Thus, small but relevant variations of intra-nuclear pH of 0.3 may have biological consequences for many protein-nucleic acid complexes. The binding affinity between the histone octamer and its DNA, which directly affects the DNA accessibility in the nucleosome, is predicted to be highly sensitive to intra-nuclear pH. A variation of 0.3 units results in ΔΔG0.3 ∼ 10k B T ( ∼ 6 k c a l / m o l ) ; for spontaneous unwrapping of 20 bp long entry/exit fragments of the nucleosomal DNA, ΔΔG0.3 = 2.2k B T; partial disassembly of the nucleosome into the tetrasome is characterized by ΔΔG0.3 = 5.2k B T. The predicted pH -induced modulations of the nucleosome stability are significant enough to suggest that they may have consequences relevant to the biological function of the nucleosome. Accessibility of the nucleosomal DNA is predicted to positively correlate with pH variations during the cell cycle; an increase in intra-cellular pH seen in cancer cells is predicted to lead to a more accessible nucleosomal DNA; a drop in pH associated with apoptosis is predicted to make nucleosomal DNA less accessible. We speculate that processes that depend on accessibility to the DNA in the nucleosomes, such as transcription or DNA replication, might become upregulated due to relatively small, but nevertheless realistic increases of intra-nuclear pH.

Fast Polarizable Water Model for Atomistic Simulations.

Simulating water accurately has been a major challenge in atomistic simulations for decades. Inclusion of electronic polarizability effects holds considerable promise, yet existing approaches suffer from significant computational overheads compared to the widely used nonpolarizable water models. We have developed a globally optimal polarizable water model, OPC3-pol, that explicitly accounts for electronic polarizability with minimal impact on the computational efficiency. OPC3-pol reproduces five key bulk water properties at room temperature with an average relative error of 0.6%. In atomistic simulations, OPC3-pol's computational efficiency is in between that of 3- and 4-point nonpolarizable models; the model supports increased (4 fs) integration time step. OPC3-pol is tested in simulations of globular protein ubiquitin and a B-DNA dodecamer with several AMBER force fields, ff99SB, ff14SB, ff19SB, and OL15, demonstrating structure stability close to reference on multi-microsecond time scale. Simulation of an intrinsically disordered amyloid ß-peptide yields an ensemble with the radius of gyration of a random coil. The proposed water model can be trivially adopted by any package that supports standard nonpolarizable force fields and water models; its intended use is in long classical atomistic simulations where water polarization effects are expected to be important.

A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules.

Closed-form, analytical approximations for electrostatic properties of molecules are of unique value as these can provide computational speed, versatility, and physical insight. Here, we have derived a simple, closed-form formula for the apparent surface charge (ASC) as well as for the electric field generated by a molecular charge distribution in aqueous solution. The approximation, with no fitted parameters, was tested against numerical solutions of the Poisson equation, where it has produced a significant speed-up. For neutral small molecules, the hydration free energies estimated from the closed-form ASC formula are within 0.8 kcal/mol RMSD from the numerical Poisson reference; the electric field at the surface is in quantitative agreement with the reference. Performance of the approximation was also tested on larger structures, including a protein, a DNA fragment, and a viral receptor-target complex. For all structures tested, a near-quantitative agreement with the numerical Poisson reference was achieved, except in regions of high negative curvature, where the new approximation is still qualitatively correct. A unique efficiency feature of the proposed "source-based″ closed-form approximation is that the ASC and electric field can be estimated individually at any point or surface patch, without the need to obtain the full global solution. An open-source software implementation of the method is available: https://people.cs.vt.edu/~onufriev/CODES/aasc.zip.

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach.

We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.

How to Count Bugs: A Method to Estimate the Most Probable Absolute Population Density and Its Statistical Bounds from a Single Trap Catch.

Knowledge of insect population density is crucial for establishing management and conservation tactics and evaluating treatment efficacies. Here, we propose a simple and universal method for estimating the most probable absolute population density and its statistical bounds. The method is based on a novel relationship between experimentally measurable characteristics of insect trap systems and the probability to catch an insect located a given distance away from the trap. The generality of the proposed relationship is tested using 10 distinct trapping datasets collected for insects from 5 different orders and using major trapping methods, i.e., chemical-baited traps and light. For all datasets, the relationship faithfully (R¯=0.91) describes the experiment. The proposed approach will take insect detection and monitoring to a new, rigorously quantitative level. It will improve conservation and management, while driv-ing future basic and applied research in population and chemical ecology.

Similarities and Differences between Na+ and K+ Distributions around DNA Obtained with Three Popular Water Models.

We have compared distributions of sodium and potassium ions around double-stranded DNA, simulated using fixed charge SPC/E, TIP3P, and OPC water models and the Joung/Cheatham (J/C) ion parameter set, as well as the Li/Merz HFE 6-12 (L/M HFE) ion parameters for OPC water. In all the simulations, the ion distributions are in qualitative agreement with Manning's condensation theory and the Debye-Hückel theory, where expected. In agreement with experiment, binding affinity of monovalent ions to DNA does not depend on ion type in every solvent model. However, behavior of deeply bound ions, including ions bound to specific sites, depends strongly on the solvent model. In particular, the number of potassium ions in the minor groove of AT-tracts differs at least 3-fold between the solvent models tested. The number of sodium ions associated with the DNA agrees quantitatively with the experiment for the OPC water model, followed closely by TIP3P+J/C; the largest deviation from the experiment, ∼10%, is seen for SPC/E+J/C. On the other hand, SPC/E+J/C model is most consistent (67%) with the experimental potassium binding sites, followed by OPC+J/C (60%), TIP3P+J/C (53%), and OPC+L/M HFE (27%). The use of NBFIX correction with TIP3P+J/C improves its consistency with the experiment. In summary, the choice of the solvent model matters little for simulating the diffuse atmosphere of sodium and potassium ions around DNA, but ion distributions become increasingly sensitive to the solvent model near the helical axis. We offer an explanation for these trends. There is no single gold standard solvent model, although OPC water with J/C ions or TIP3P with J/C + NBFIX may offer an imperfect compromise for practical simulations of ionic atmospheres around DNA.

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure.

The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as K→Q. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins. Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state (q=+8) is essentially a random coil, hyper-acetylated H4 (q=+3) is virtually as compact and stable as a globular protein of the same number of amino-acids. Conformational ensembles of acetylated H4 match the corresponding K→X substitutions only approximately: based on the ensemble similarity, we propose K→M as a possible alternative to the commonly used K→Q. Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.

Bounds on Absolute Gypsy Moth (Lymantria dispar dispar) (Lepidoptera: Erebidae) Population Density as Derived from Counts in Single Milk Carton Traps.

Estimates of absolute pest population density are critical to pest management programs but have been difficult to obtain from capture numbers in pheromone-baited monitoring traps. In this paper, we establish a novel predictive relationship for a probability (spTfer(r)) of catching a male located at a distance r from the trap with a plume reach D.

Melting Points of OPC and OPC3 Water Models.

A recently introduced family of globally optimal water models, OPC, has shown promise in a variety of biomolecular simulations, but properties of these water models outside of the liquid phase remain mostly unexplored. Here, we contribute to filling the gap by reporting melting temperatures of ice I h of OPC and OPC3 water models. Through the direct coexistence method, which we make available in the AMBER package, the melting points of OPC and OPC3 are estimated as 242 and 210 K, similar to TIP4P-Ew and SPC/E models, respectively, and appreciably below the experimental value of 273.15 K under 1 bar pressure. Water models of the OPC family were optimized to best reproduce water properties in the liquid phase where these models offer noteworthy accuracy advantages over many models of previous generations. It is not surprising that the accuracy of OPC models in describing the phase transition to the solid state does not appear to offer similar improvements. The new anisotropic barostat option implemented in AMBER may benefit system preparation and simulation outside of the direct coexistence applications, such as modeling of membranes or very long DNA strands.

MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor.

The ability to estimate protein-protein binding free energy in a computationally efficient via a physics-based approach is beneficial to research focused on the mechanism of viruses binding to their target proteins. Implicit solvation methodology may be particularly useful in the early stages of such research, as it can offer valuable insights into the binding process, quickly. Here we evaluate the potential of the related molecular mechanics generalized Born surface area (MMGB/SA) approach to estimate the binding free energy ΔGbind between the SARS-CoV-2 spike receptor-binding domain and the human ACE2 receptor. The calculations are based on a recent flavor of the generalized Born model, GBNSR6. Two estimates of ΔGbind are performed: one based on standard bondi radii, and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein-ligand binding. We take the average of the resulting two ΔGbind values as the consensus estimate. For the well-studied Ras-Raf protein-protein complex, which has similar binding free energy to that of the SARS-CoV-2/ACE2 complex, the consensus ΔGbind = -11.8 ± 1 kcal/mol, vs. experimental -9.7 ± 0.2 kcal/mol. The consensus estimates for the SARS-CoV-2/ACE2 complex is ΔGbind = -9.4 ± 1.5 kcal/mol, which is in near quantitative agreement with experiment (-10.6 kcal/mol). The availability of a conceptually simple MMGB/SA-based protocol for analysis of the SARS-CoV-2 /ACE2 binding may be beneficial in light of the need to move forward fast.

Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.

Accuracy of protein-ligand binding free energy calculations utilizing implicit solvent models is critically affected by parameters of the underlying dielectric boundary, specifically, the atomic and water probe radii. Here, a global multidimensional optimization pipeline is developed to find optimal atomic radii specifically for protein-ligand binding calculations in implicit solvent. The computational pipeline has these three key components: (1) a massively parallel implementation of a deterministic global optimization algorithm (VTDIRECT95), (2) an accurate yet reasonably fast generalized Born implicit solvent model (GBNSR6), and (3) a novel robustness metric that helps distinguish between nearly degenerate local minima via a postprocessing step of the optimization. A graph-based "kT-connectivity" approach to explore and visualize the multidimensional energy landscape is proposed: local minima that can be reached from the global minimum without exceeding a given energy threshold (kT) are considered to be connected. As an illustration of the capabilities of the optimization pipeline, we apply it to find a global optimum in the space of just five radii: four atomic (O, H, N, and C) radii and water probe radius. The optimized radii, ρW = 1.37 Å, ρC = 1.40 Å, ρH = 1.55 Å, ρN = 2.35 Å, and ρO = 1.28 Å, lead to a closer agreement of electrostatic binding free energies with the explicit solvent reference than two commonly used sets of radii previously optimized for small molecules. At the same time, the ability of the optimizer to find the global optimum reveals fundamental limits of the common two-dielectric implicit solvation model: the computed electrostatic binding free energies are still almost 4 kcal/mol away from the explicit solvent reference. The proposed computational approach opens the possibility to further improve the accuracy of practical computational protocols for binding free energy calculations.

Three-dimensional Organization of Polytene Chromosomes in Somatic and Germline Tissues of Malaria Mosquitoes.

Spatial organization of chromosome territories and interactions between interphase chromosomes themselves, as well as with the nuclear periphery, play important roles in epigenetic regulation of the genome function. However, the interplay between inter-chromosomal contacts and chromosome-nuclear envelope attachments in an organism's development is not well-understood. To address this question, we conducted microscopic analyses of the three-dimensional chromosome organization in malaria mosquitoes. We employed multi-colored oligonucleotide painting probes, spaced 1 Mb apart along the euchromatin, to quantitatively study chromosome territories in larval salivary gland cells and adult ovarian nurse cells of Anopheles gambiae, An. coluzzii, and An. merus. We found that the X chromosome territory has a significantly smaller volume and is more compact than the autosomal arm territories. The number of inter-chromosomal, and the percentage of the chromosome-nuclear envelope, contacts were conserved among the species within the same cell type. However, the percentage of chromosome regions located at the nuclear periphery was typically higher, while the number of inter-chromosomal contacts was lower, in salivary gland cells than in ovarian nurse cells. The inverse correlation was considerably stronger for the autosomes. Consistent with previous theoretical arguments, our data indicate that, at the genome-wide level, there is an inverse relationship between chromosome-nuclear envelope attachments and chromosome-chromosome interactions, which is a key feature of the cell type-specific nuclear architecture.

Exploring optimization strategies for improving explicit water models: Rigid n-point model and polarizable model based on Drude oscillator.

Rigid n-point water models are widely used in atomistic simulations, but have known accuracy drawbacks. Increasing the number of point charges, as well as adding electronic polarizability, are two common strategies for accuracy improvements. Both strategies come at considerable computational cost, which weighs heavily against modest possible accuracy improvements in practical simulations. In an effort to provide guidance for model development, here we have explored the limiting accuracy of "electrostatically globally optimal" n-point water models in terms of their ability to reproduce properties of water dimer-a mimic of the condensed state of water. For a given n, each model is built upon a set of reference multipole moments (e.g. ab initio) and then optimized to reproduce water dimer total dipole moment. The models are then evaluated with respect to the accuracy of reproducing the geometry of the water dimer. We find that global optimization of the charge distribution alone can deliver high accuracy of the water model: for n = 4 or n = 5, the geometry of the resulting water dimer can be almost within 50 of the ab initio reference, which is half that of the experimental error margin. Thus, global optimization of the charge distribution of classical n-point water models can lead to high accuracy models. We also find that while the accuracy improvement in going from n = 3 to n = 4 is substantial, the additional accuracy increase in going from n = 4 to n = 5 is marginal. Next, we have explored accuracy limitations of the standard practice of adding electronic polarizability (via a Drude particle) to a "rigid base"-pre-optimization rigid n-point water model. The resulting model (n = 3) shows a relatively small improvement in accuracy, suggesting that the strategy of merely adding the polarizability to an inferior accuracy water model used as the base cannot fix the defects of the latter. An alternative strategy in which the parameters of the rigid base model are globally optimized along with the polarizability parameter is much more promising: the resulting 3-point polarizable model out-performs even the 5-point optimal rigid model by a large margin. We suggest that future development efforts consider 3- and 4-point polarizable models where global optimization of the "rigid base" is coupled to optimization of the polarizability to deliver globally optimal solutions.

General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins.

Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP) remain a challenge: widely used, "general purpose" water models tend to favor overly compact structures relative to experiment. Here we have performed a total of 93 µs of unrestrained MD simulations to explore, in the context of IDPs, a recently developed "general-purpose" 4-point rigid water model OPC, which describes liquid state of water close to experiment. We demonstrate that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks: 55-residue apo N-terminal zinc-binding domain of HIV-1 integrase ("protein IN"), amyloid ß-peptide (Aß42) (residues 1-42), and 26-reside H4 histone tail. As a negative control, computed folding profile of a regular globular miniprotein (CLN025) in OPC water is in appreciably better agreement with experiment than that obtained in TIP3P, which tends to overstabilize the compact native state relative to the extended conformations. We employed Aß42 peptide to investigate the possible influence of the solvent box size on simulation outcomes. We advocate a cautious approach for simulations of IDPs: we suggest that the solvent box size should be at least four times the radius of gyration of the random coil corresponding to the IDP. The computed free energy landscape of protein IN in OPC resembles a shallow "tub" - conformations with substantially different degrees of compactness that are within 2 kB T of each other. Conformations with very different secondary structure content coexist within 1 kB T of the global free energy minimum. States with higher free energy tend to have less secondary structure. Computed low helical content of the protein has virtually no correlation with its degree of compactness, which calls into question the possibility of using the helicity as a metric for assessing performance of water models for IDPs, when the helicity is low. Predicted radius of gyration ( R g) of H4 histone tail in OPC water falls in-between that of a typical globular protein and a fully denatured protein of the same size; the predicted R g is consistent with two independent predictions. In contrast, H4 tail in TIP3P water is as compact as the corresponding globular protein. The computed free energy landscape of H4 tail in OPC is relatively flat over a significant range of compactness, which, we argue, is consistent with its biological function as facilitator of internucleosome interactions.