The statistical-thermodynamic basis for computation of binding affinities: a critical review

Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly

Capillary Condensation and Interface Structure of a Model Colloid-Polymer Mixture in a Porous Medium

We consider the Asakura-Oosawa model of hard sphere colloids and ideal polymers in contact with a porous matrix modeled by immobilized configurations of hard spheres. For this ternary mixture a fundamental measure density functional theory is employed, where the matrix particles are quenched and the colloids and polymers are annealed, i.e. allowed to equilibrate. We study capillary condensation of the mixture in a tiny sample of matrix as well as demixing and the fluid-fluid interface inside a bulk matrix. Density profiles normal to the interface and surface tensions are calculated and compared to the case without matrix. Two kinds of matrices are considered: (i) colloid-sized matrix particles at low packing fractions and (ii) large matrix particles at high packing fractions. These two cases show fundamentally different behavior and should both be experimentally realizable. Furthermore, we argue that capillary condensation of a colloidal suspension could be experimentally accessible. We find that in case (ii), even at high packing fractions, the main effect of the matrix is to exclude volume and, to high accuracy, the results can be mapped onto those of the same system without matrix via a simple rescaling.Comment: 12 pages, 9 figures, submitted to PR

Abnormal Patterns of Insulin Secretion in Non-Insulin-Dependent Diabetes Mellitus

To determine whether non-insulin-dependent diabetes is associated with specific alterations in the pattern of insulin secretion, we studied 16 patients with untreated diabetes and 14 matched controls. The rates of insulin secretion were calculated from measurements of peripheral C-peptide in blood samples taken at 15- to 20-minute intervals during a 24-hour period in which the subjects ate three mixed meals. Incremental responses of insulin secretion to meals were significantly lower in the diabetic patients (P<0.005), and the increases and decreases in insulin secretion after meals were more sluggish. These disruptions in secretory response were more marked after dinner than after break-fast, and a clear secretory response to dinner often could not be identified. Both the control and diabetic subjects secreted insulin in a series of discrete pulses. In the controls, a total of seven to eight pulses were identified in the period from 9 a.m. to 11 p.m. including the three post-meal periods (an average frequency of one pulse per 105 to 120 minutes), and two to four pulses were identified in the remaining 10 hours. The number of pulses in the patients and controls did not differ significantly. However, in the patients, the pulses after meals had a smaller amplitude (P<0.03) and were less frequently concomitant with a glucose pulse (54.7±4.9 vs. 82.2±5.0, P<0.001). Pulses also appeared less regularly in the patients. During glucose clamping to produce hyperglycemia (glucose level, 16.7 mmol per liter [300 mg per deciliter]), the diabetic subjects secreted, on the average, 70 percent less insulin than matched controls (P<0.001). These data suggest that profound alterations in the amount and temporal organization of stimulated insulin secretion may be important in the pathophysiology of beta-cell dysfunction in diabetes. (N Engl J Med 1988; 318:1231–9.) © 1988, Massachusetts Medical Society. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Monte Carlo Method for Calculating the Electrostatic Energy of a Molecule

The problem of computing the electrostatic energy of a large molecule is considered. It is reduced to solving the Poisson equation inside and the linear Poisson-Boltzmann equation in the exterior, coupled by boundary conditions. A Monte Carlo estimate for the potential point values, their derivatives, and the energy is constructed. The estimate is based on the walk on spheres and Green&apos;s function first passage algorithms; the walk in subdomains technique; and finite-difference approximations of the boundary condition. Results of some illustrative calculations are presented