The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.

A force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and Kirkwood-Buff integrals for N-methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N'-dimethylacetamide and acetamide with good success. Analysis of the simulations of low concentrations of NMA in water indicates a high degree of solvation with only 15% of the NMA molecules involved in solute-solute hydrogen bonding. There is only a weak angular dependence of the solute-solute hydrogen bonding interaction with a minimum at an angle of 65 degrees for the N-H and C=O dipole vectors. The models presented here provide a basis for an accurate force field for peptides and proteins.

While a great diversity of peptide-based supra-molecular filaments have been reported, the impact of an auxiliary segment on the chiral assembly of peptides remains poorly understood. Herein we report on the formation of chiral filaments by the self-assembly of a peptide-drug conjugate containing an aromatic drug camptothecin (CPT) in a computational study. We find that the chirality of the filament is mediated by the π‒π stacking between CPTs, not only by the well-expected intermolecular hydrogen bonding between peptide segments. Our simulations show that π‒π stacking of CPTs governs the early stages of the self-assembly process, while a hydrogen bonding network starts at a relatively later stage to contribute to the eventual morphology of the filament. Our results also show the possible presence of water within the core of the CPT filament. These results provide very useful guiding principles for the rational design of supramolecular assemblies of peptide conjugates with aromatic segments.

Recent results concerning the formulation and evaluation of preferential interactions in biological systems in terms of Kirkwood-Buff (KB) integrals are presented.In particular, experimental and simulated preferential interactions of a cosolvent with a biomolecule in the presence of water are described. It is argued that the preferential interaction parameter defined in a system open to both cosolvent and solvent corresponds to the situation most relevant to the analysis of computer simulation results of cosolvent interactions with proteins and small peptides. Hence, KB theory provides a path from quantities determined from simulation data to the corresponding thermodynamic data.

Most biological processes are initiated or mediated by the association of ligands and proteins. This work studies multistep, ligand-protein association processes by Brownian dynamics simulations with coarse-grained models for HIV-1 protease (HIVp) and its neutral ligands. We report the average association times when the ligand concentration is 100 μM. The influence of crowding on the simulated binding time was also studied. HIVp has flexible loops that serve as a gate during the ligand binding processes. It is believed that the flaps are partially closed most of the time in its free state. To accelerate our simulations, we fixed a part of the HIVp and reparameterized our coarse-grained model, using atomistic molecular dynamics simulations, to reproduce the "gating" motions of HIVp. HIVp-ligand interactions changed the gating behavior of HIVp and helped ligands diffuse on HIVp surface to accelerate binding. The structural adjustment of the ligand toward its final stable state was the limiting step in the binding processes, which is highly system dependent. The intermolecular attraction between the ligands and crowder proteins contributes the most to the crowding effects. The results highlight broader implications in recognition pathways under more complex environment that considers molecular dynamics and conformational changes. This work brings insights into ligand-protein associations and is helpful in the design of targeted ligands.

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Isosteric replacement of the phenolic hydroxyl group in potent vanilloid receptor (VR1) agonists with the alkylsulfonamido group provides a series of compounds which are effective antagonists to the action of the capsaicin on rat VR1 heterologously expressed in Chinese hamster ovary (CHO) cells. In particular, compound 61, N-[2-(3,4-dimethylbenzyl)-3-pivaloyloxypropyl]-N'-[3-fluoro-4-(methylsulfonylamino)benzyl]thiourea was a full antagonist against capsaicin, displayed a K(i) value of 7.8 nM (compared to 520 nM for capsazepine and 4 nM for 5-iodoRTX), and showed excellent analgesic activity in mice. Structure-activity analysis of the influence of modifications in the A- and C-regions of 4-methylsulfonamide ligands on VR1 agonism/antagonism indicated that 3-fluoro substitution in the A-region and a 4-tert-butylbenzyl moiety in the C-region favored antagonism, whereas a 3-methoxy group in the A-region and 3-acyloxy-2-benzylpropyl moieties in the C-region favored agonism.

This review describes recent progress in the area of molecular simulations of peptide assemblies, including peptide-amphiphiles, and drug-amphiphiles. The ability to predict the structure and stability of peptide self-assemblies from the molecular level up is vital to the field of nanobiotechnology. Computational methods such as molecular dynamics offer the opportunity to characterize intermolecular forces between peptide-amphiphiles that are critical to the self-assembly process. Furthermore, these computational methods provide the ability to computationally probe the structure of these supramolecular assemblies at the molecular level, which is a challenge experimentally. Herein, we briefly highlight progress in the areas of all-atomistic and coarse-grained simulation studies investigating the self-assembly process of short peptides and peptide amphiphiles. We also discuss recent all-atomistic and coarse-grained simulations of the self-assembly of a drug-amphiphile into elongated filaments. Next, we discuss how these computational methods can provide further insight on the pathway of cylindrical nanofiber formation and predict their biocompatibility by studying the interaction of these peptide-amphiphile nanostructures with model cell membranes.