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Michael E. Paulaitis

Publications and source records attributed to Michael E. Paulaitis.

5 recordsLinked to original sources

Thermodynamics of Hydration from the Perspective of the Molecular Quasi-Chemical Theory of Solutions

The quasi-chemical organization of the potential distribution theorem -- molecular quasi-chemical theory (QCT) -- enables practical calculations and also provides a conceptual framework for molecular hydration phenomena. QCT can be viewed from multiple perspectives: (a) As a way to regularize an ill-conditioned statistical thermodynamic problem; (b) As an introduction of and emphasis on the neighborship characteristics of a solute of interest; (c) Or as a way to include accurate electronic structure descriptions of near-neighbor interactions in defensible statistical thermodynamics by clearly defining neighborship clusters. The theory has been applied to solutes of a wide range of chemical complexity, ranging from ions that interact with water with both long-ranged and chemically intricate short-ranged interactions, to solutes that interact with water solely through traditional van~der~Waals interations, and including water itself. The solutes range in variety from monoatomic ions to chemically heterogeneous macromolecules. A notable feature of QCT is that in applying the theory to this range of solutes, the theory itself provides guidance on the necessary approximations and simplifications that can facilitate the calculations. In this Perspective, we develop these ideas and document them with examples that reveal the insights that can be extracted using the QCT formulation.

physics.chem-ph↗

Long-Range Interactions Dominate the Inverse-Temperature Dependence of Polypeptide Hydration Free Energies

Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the solvent explain the inverse temperature signatures that have been interpreted traditionally in favor of hydrophobic mechanisms for stabilizing the structure and function of soluble proteins.

physics.chem-ph↗

Direct observation of a hydrophobic bond in loop-closure of a capped (-OCH2CH2-)n oligomer in water

The small r variation of the probability density P(r) for end-to-end separations of a -CH2CH3 capped (-OCH2CH2-)n oligomer in water is computed to be closely similar to the CH4 ... CH4 potential of mean force under the same circumstances. Since the aqueous solution CH4 ... CH4 potential of mean force is the natural physical definition of a primitive hydrophobic bond, the present result identifies an experimentally accessible circumstance for direct observation of a hydrophobic bond which has not been observed previously because of the low solubility of CH4 in water. The physical picture is that the soluble chain molecule carries the capping groups into aqueous solution, and permits them to find one another with reasonable frequency. Comparison with the corresponding results without the solvent shows that hydration of the solute oxygen atoms swells the chain molecule globule. This supports the view that the chain molecule globule might have a secondary effect on the hydrophobic interaction which is of first interest here. The volume of the chain molecule globule is important for comparing the probabilities with and without solvent because it characterizes the local concentration of capping groups. Study of other capping groups to enable X-ray and neutron diffraction measurements of P(r) is discussed.

physics.chem-ph↗

Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity

The KcsA potassium channel belongs to a class of K+ channels that is selective for K+ over Na+ at rates of K+ transport approaching the diffusion limit. This selectivity is explained thermodynamically in terms of favorable partitioning of K+ relative to Na+ in a narrow selectivity filter in the channel. One mechanism for selectivity based on the atomic structure of the KcsA channel invokes the size difference between K+ and Na+, and the molecular complementarity of the selectivity filter with the larger K+ ion. An alternative view holds that size-based selectivity is precluded because atomic structural fluctuations are greater than the size difference between these two ions. We examine these hypotheses by calculating the distribution of binding energies for Na+ and K+ in a simplified model of the selectivity filter of the KcsA channel. We find that Na+ binds strongly to the selectivity filter with a mean binding energy substantially lower than that for K+. The difference is comparable to the difference in hydration free energies of Na+ and K+ in bulk aqueous solution. Thus, the average filter binding energies do not discriminate Na+ from K+ when measured from the baseline of the difference in bulk hydration free energies. Instead, Na+/K+ discrimination can be attributed to scarcity of good binding configurations for Na+ compared to K+. That relative scarcity is quantified as enhanced binding energy fluctuations, and is consistent with predicted relative constriction of the filter by Na+.

physics.bio-ph↗

Origin of entropy convergence in hydrophobic hydration and protein folding

An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy convergence follows from the weak temperature dependence of occupancy fluctuations for molecular-scale volumes in water. The macroscopic expression of the contrasting entropic behavior between water and common organic solvents is the relative temperature insensitivity of the water isothermal compressibility. The information theory model provides a quantitative description of small molecule hydration and predicts a negative entropy at convergence. Interpretations of entropic contributions to protein folding should account for this result.

physics.chem-ph↗