Particle and Energy Pair and Triplet Correlations in Liquids and Liquid Mixtures from Experiment and Simulation

Simulated pressure changes in LacI suggest a link between hydration and functional conformational changes

The functions of many proteins are associated with interconversions among conformational substates. However, these substates can be difficult to measure experimentally, and determining contributions from hydration changes can be especially difficult. Here, we assessed the use of pressure perturbations to sample the substates accessible to the Escherichia coli lactose repressor protein (LacI) in various liganded forms. In the presence of DNA, the regulatory domain of LacI adopts an Open conformation that, in the absence of DNA, changes to a Closed conformation. Increasing the simulation pressure prevented the transition from an Open to a Closed conformation, in a similar manner to the binding of DNA and anti-inducer, ONPF. The results suggest the hydration of specific residues play a significant role in determining the population of different LacI substates and that simulating pressure perturbation could be useful for assessing the role of hydration changes that accompany functionally-relevant amino acid substitutions.

Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20

A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.

Real Space Triplets in Quantum Condensed Matter: Numerical Experiments Using Path Integrals, Closures, and Hard Spheres

Path integral Monte Carlo and closure computations are utilized to study real space triplet correlations in the quantum hard-sphere system. The conditions cover from the normal fluid phase to the solid phases face-centered cubic (FCC) and cI16 (de Broglie wavelengths , densities ). The focus is on the equilateral and isosceles features of the path-integral centroid and instantaneous structures. Complementary calculations of the associated pair structures are also carried out to strengthen structural identifications and facilitate closure evaluations. The three closures employed are Kirkwood superposition, Jackson-Feenberg convolution, and their average (AV3). A large quantity of new data are reported, and conclusions are drawn regarding (i) the remarkable performance of AV3 for the centroid and instantaneous correlations, (ii) the correspondences between the fluid and FCC salient features on the coexistence line, and (iii) the most conspicuous differences between FCC and cI16 at the pair and the triplet levels at moderately high densities (. This research is expected to provide low-temperature insights useful for the future related studies of properties of real systems (e.g., helium, alkali metals, and general colloidal systems).

Computation of static quantum triplet structure factors of liquid para-hydrogen

The instantaneous and centroid triplet structure factors, S ( 3 ) ( k 1 , k 2 ) , of liquid (one-center) para-hydrogen are computed on the crystallization line for temperatures T/K ≤ 33. The focus is on salient equilateral and isosceles features, and the methods utilized are path integral Monte Carlo (PIMC) simulations and Ornstein-Zernike (OZ) integral equations, which involve Jackson-Feenberg convolution (JF3) and other distinct closures. Long path integral simulation runs are carried out in the canonical ensemble, so as to obtain sufficiently accurate direct PI triplet results. Conclusions are drawn regarding general triplet structure features and the role and usefulness of the OZ closures. The equilateral features are studied in more detail, and one finds that (a) PIMC results point to the existence of regularity in the centroid main peak amplitudes; (b) some of the studied closures give qualitative descriptions for wave numbers below k ≈ 1 Å^-1, but they all fail to describe the main peak amplitude regions (1.75 < k/Å^-1 < 2.5); and (c) JF3 plays the role of a limit closure that is valid for increasing wave numbers (k ≥ 2.6 Å^-1). In addition, representative isosceles PI features turn out to be reasonably bounded (within Δk = 0.1 Å^-1) by those of some closures.

Experimental Investigation of Triplet Correlation Approximations for Fluid Water

Triplet correlations play a central role in our understanding of fluids and their properties. Of particular interest is the relationship between the pair and triplet correlations. Here we use a combination of Fluctuation Solution Theory and experimental pair radial distribution functions to investigate the accuracy of the Kirkwood Superposition Approximation (KSA), as given by integrals over the relevant pair and triplet correlation functions, at a series of state points for pure water using only experimental quantities. The KSA performs poorly, in agreement with a variety of other studies. Several additional approximate relationships between the pair and triplet correlations in fluids are also investigated and generally provide good agreement for the fluid thermodynamics for regions of the phase diagram where the compressibility is small. A simple power law relationship between the pair and triplet fluctuations is particularly successful for state points displaying low to moderately high compressibilities.

On static triplet structures in fluids with quantum behavior

The problem of the equilibrium triplet structures in fluids with quantum behavior is discussed. Theoretical questions of interest to the real space structures are addressed by studying the three types of structures that can be determined via path integrals (instantaneous, centroid, and total thermalized-continuous linear response). The cases of liquid para-H₂ and liquid neon on their crystallization lines are examined with path-integral Monte Carlo simulations, the focus being on the instantaneous and the centroid triplet functions (equilateral and isosceles configurations). To analyze the results further, two standard closures, Kirkwood superposition and Jackson-Feenberg convolution, are utilized. In addition, some pilot calculations with path integrals and closures of the instantaneous triplet structure factor of liquid para-H₂ are also carried out for the equilateral components. Triplet structural regularities connected to the pair radial structures are identified, a remarkable usefulness of the closures employed is observed (e.g., triplet spatial functions for medium-long distances, triplet structure factors for medium k wave numbers), and physical insight into the role of pair correlations near quantum crystallization is gained.

Origin of non-linearity in phase solubility: solubilisation by cyclodextrin beyond stoichiometric complexation

The low solubility of drugs, which poses a serious problem in drug development, can in part be overcome by the use of cyclodextrins (CDs) and their derivatives. Here, the key to solubilisation is identified as the formation of inclusion complexes with the drug molecule. If inclusion complexation were the only contribution to drug solubility, it would increase linearly with CD concentration (as per the Higuchi-Connors model); this is because inclusion complexation is a 1 : 1 stoichiometric process. However, solubility curves often deviate from this linearity, whose mechanism is yet to be understood. Here we aim to clarify the origin of such non-linearity, based on the Kirkwood-Buff and the McMillan-Mayer theories of solutions. The rigorous statistical thermodynamic theory shows that non-linearity of solubilisation can be rationalised by two contributions: CD-drug interaction and the drug-induced change of CD-CD interaction.

How Osmolytes Counteract Pressure Denaturation on a Molecular Scale

Life in the deep sea exposes enzymes to high hydrostatic pressure, which decreases their stability. For survival, deep sea organisms tend to accumulate various osmolytes, most notably trimethylamine N-oxide used by fish, to counteract pressure denaturation. However, exactly how these osmolytes work remains unclear. Here, a rigorous statistical thermodynamics approach is used to clarify the mechanism of osmoprotection. It is shown that the weak, nonspecific, and dynamic interactions of water and osmolytes with proteins can be characterized only statistically, and that the competition between protein-osmolyte and protein-water interactions is crucial in determining conformational stability. Osmoprotection is driven by a stronger exclusion of osmolytes from the denatured protein than from the native conformation, and water distribution has no significant effect on these changes at low osmolyte concentrations.

Simulated pressure denaturation thermodynamics of ubiquitin

Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues.