Standard state and thermodynamic self-consistency

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.

Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

A structurally sensitive probe of the monomer/dimer equilibrium of insulin was developed using 2DIR spectroscopy and interpreted using calculated spectra.

Entropic cost of protein-ligand binding and its dependence on the entropy in solution

Two theoretical formulations are proposed and compared for the loss of translational and rotational entropy upon protein-ligand binding in water. The two theories share the same approach to evaluate the translational and rotational entropy of the ligand when bound. The potential of the bound ligand is modeled by six harmonic oscillators that are parametrized from the force and torque magnitudes measured in a molecular dynamics simulation, yielding vibrational and librational entropies. In the aqueous phase, the theories differ because there is no unique way to assign the total entropy to molecules in solution. In one approach, the ligand is allowed unrestricted access to the full solution volume at the standard concentration and is assigned the same translational and rotational entropy as if it were an ideal gas. We term this a "molecule-frame" (MF) theory because it considers configurational space in the reference frame of the molecule of interest. The entropy of the solvent is penalized because it is excluded from the molecule's volume. In the second theory, all molecules including the solvent are confined by their neighbors in mean-field configurational volumes. This we term a "system-frame" (SF) theory because the configurational space available to all molecules is considered in the reference frame of the whole system. Molecules have vibrational and librational entropy in the same way as they do when bound. In addition, the discrete size of the solvent molecules quantizes the configurational space into an effective number of minima according to the solute molecule's standard concentration and the mean volume of a solvent molecule. This leads to the cratic entropy expressed in terms of the solute molecule's mole fraction. The equivalent number of minima in rotational space depends on both the solute molecule's volume and the solvent molecule's volume. This leads to an equation for the orientational entropy based on the proposed concept of "angle fraction". The MF and SF theories are applied to calculate the translational and rotational entropy losses involved in the formation of six different protein-ligand complexes, in two of which the ligand is water. The MF entropy losses range from -80 to -142 J K(-1) mol(-1) for ligands at the 1 M standard-state concentration and from -52 to -63 J K(-1) mol(-1) for water at the 55.6 M standard-state concentration. They depend logarithmically on both the number and strength of interactions between the ligand and protein through the forces and torques. This is observed to lead to moderate dependencies on the ligands' moments of inertia and masses. The SF entropy losses are smaller and range from -50 to -75 J K(-1) mol(-1) for ligands at the 1 M standard-state concentration and from 0 to -12 J K(-1) mol(-1) for water. They depend logarithmically on the ligand solvent's molecular volume and weakly on the relative strengths of the ligand's interactions with the protein and water. The cratic entropy loss in water at the standard concentration is constant and is also demonstrated to be implicit in MF theories. Entropy losses from the two approaches are also compared with those from other computational approaches and with experiment. The use of the force and torque magnitudes leads to smaller bound volumes than are obtained from ligand-displacement approaches. The general agreement of the SF entropy losses with those from experiment suggests that the SF theory is more consistent with the assumptions made in experimental measurements than the MF solvation theories, which would require a compensating entropy gain in the solvent in order to agree.

Coiled-coils: stability, specificity, and drug delivery potential

The coiled-coil is a ubiquitous protein folding and assembly motif made of alpha-helices wrapping around each other forming a supercoil. The sequences of coiled-coils are made of seven-residue repeats, called heptads, and thus are polymer-like. Due to its simplicity and regularity, the coiled-coil is the most extensively studied protein motif. In this review, results on coiled-coil stability and specificity from structural and biophysical studies are summarized. It is pointed out that the primary sequences of coiled-coils over specify the secondary structure but under specify the tertiary/quaternary structure. This leads to two unique features of coiled-coil structure: linkage between stability and specificity and decoupling of secondary and tertiary/quaternary structural specificity. This is followed by a discussion of the potential of coiled-coils as drug delivery vehicles, particularly the prospect in two-staged pretargeted delivery. Such potentials are intimately related to the unique structural features of coiled-coils. The aim of this review is to illustrate how knowledge on protein stability and specificity can be used in the de novo design of peptide-based drug delivery vehicles with well-defined structure and interaction features.

Contribution of translational and rotational motions to molecular association in aqueous solution

Much uncertainty and controversy exist regarding the estimation of the enthalpy, entropy, and free energy of overall translational and rotational motions of solute molecules in aqueous solutions, quantities that are crucial to the understanding of molecular association/recognition processes and structure-based drug design. A critique of the literature on this topic is given that leads to a classification of the various views. The major stumbling block to experimentally determining the translational/rotational enthalpy and entropy is the elimination of vibrational perturbations from the measured effects. A solution to this problem, based on a combination of energy equi-partition and enthalpy-entropy compensation, is proposed and subjected to verification. This method is then applied to analyze experimental data on the dissociation/unfolding of dimeric proteins. For one translational/rotational unit at 1 M standard state in aqueous solution, the results for enthalpy (H degrees (tr)), entropy (S degrees (tr)), and free energy (G degrees (tr)) are H (degrees) (tr) = 4.5 +/- 1.5RT, S (degrees) (tr) = 5 +/- 4R, and G (degrees) (tr) = 0 +/- 5RT. Therefore, the overall translational and rotational motions make negligible contribution to binding affinity (free energy) in aqueous solutions at 1 M standard state.