An official website of the United States government
Abstract Cooperativity plays a critical role in self‐assembly and molecular recognition. A rigid aromatic oligoamide macrocycle with a cyclodirectional backbone binds with DABCO‐based cationic guests in a 2 : 1 ratio in high affinities (Ktotal≈1013 M−2) in the highly polar DMF. The host–guest binding also exhibits exceptionally strong positive cooperativity quantified by interaction factors α that are among the largest for synthetic host–guest systems. The unusually strong positive cooperativity, revealed by isothermal titration calorimetry (ITC) and fully corroborated by mass spectrometry, NMR and computational studies, is driven by guest‐induced stacking of the macrocycles and stabilization from the alkyl end chains of the guests, interactions that appear upon binding the second macrocycle. With its tight binding driven by extraordinary positive cooperativity, this host–guest system provides a tunable platform for studying molecular interactions and for constructing stable supramolecular assemblies.
more »
« less
Intramolecularly enhanced molecular tweezers with unusually strong binding for aromatic guests in unfavorable solvents
Molecular tweezers using aromatic interactions for binding normally work best in polar instead of nonpolar solvents due to the strong solvophobic effect in the binding. Inspired by biological receptors that utilize “delocalized binding interactions” remote from the binding interface to strengthen guest-binding, we constructed molecular tweezers that have a reversed solvent effect. As the direct aromatic binding interactions were weakened by nonpolar solvent, guest-triggered intrahost interactions between two strategically placed carboxylic acids became stronger and contributed to the binding.
more »
« less
- Award ID(s):
- 1708526
- PAR ID:
- 10065276
- Date Published:
- Journal Name:
- Organic & Biomolecular Chemistry
- Volume:
- 16
- Issue:
- 21
- ISSN:
- 1477-0520
- Page Range / eLocation ID:
- 3885 to 3888
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Hydrophobic interactions drive the binding of nonpolar ligands to the oily pockets of proteins and supramolecular species in aqueous solution. As such, the wetting of host pockets is expected to play a critical role in determining the thermodynamics of guest binding. Here we use molecular simulations to examine the impact of pressure on the wetting and dewetting of the nonpolar pockets of a series of deep-cavity cavitands in water. The portals to the cavitand pockets are functionalized with both nonpolar (methyl) and polar (hydroxyl) groups oriented pointing either upward or inward toward the pocket. We find wetting of the pocket is favored by the hydroxyl groups and dewetting is favored by the methyl groups. The distribution of waters in the pocket is found to exhibit a two-state-like equilibrium between wet and dry states with a free energy barrier between the two states. Moreover, we demonstrate that the pocket hydration of the cavitands can be collapsed onto a unified adsorption isotherm by assuming the effective pressures within each cavitand pocket differ by a shift pressure that depends on the chemical identity and number of functional groups placed about the portal. These observations support the development of a twostate capillary evaporation model that accurately describes the equilibrium between states and naturally gives rise to the effective shift pressures observed from simulation. This work demonstrates that the hydration of host pockets can be tuned following simple design rules that in turn are expected to impact the thermodynamics of guest complexation.more » « less
-
Improper reaction coordinates can pose significant problems for path-based binding free energy calculations. Particularly, omission of long timescale motions can lead to over-estimation of the energetic barriers between the bound and unbound states. Many methods exist to construct the optimal reaction coordinate using a pre-defined basis set of features. Although simulations are typically conducted in explicit solvent, the solvent atoms are often excluded by these feature sets—resulting in little being known about their role in reaction coordinates, and ultimately, their role in determining (un)binding rates and free energies. In this work, analysis is done on an extensive set of host-guest unbinding trajectories, working to characterize differences between high and low probability unbinding trajectories with a focus on solvent-based features, including host-ion interactions, guest-ion interactions and location-dependent ion densities. We find that differences in ion densities as well as guest-ion interactions strongly correlate with differences in the probabilities of reactive paths that are used to determine free energies of (un)binding and play a significant role in the unbinding process.more » « less
-
Abstract Many proteins must interact with molecular chaperones to achieve their native state in the cell. Yet, how chaperone binding‐site characteristics affect the folding process is poorly understood. The ubiquitous Hsp70 chaperone system prevents client‐protein aggregation by holding unfolded conformations and by unfolding misfolded states. Hsp70 binding sites of client proteins comprise a nonpolar core surrounded by positively charged residues. However, a detailed analysis of Hsp70 binding sites on a proteome‐wide scale is still lacking. Further, it is not known whether proteins undergo some degree of folding while chaperone bound. Here, we begin to address the above questions by identifying Hsp70 binding sites in 2258Escherichia coli(E. coli) proteins. We find that most proteins bear at least one Hsp70 binding site and that the number of Hsp70 binding sites is directly proportional to protein size. Aggregation propensity upon release from the ribosome correlates with number of Hsp70 binding sites only in the case of large proteins. Interestingly, Hsp70 binding sites are more solvent‐exposed than other nonpolar sites, in protein native states. Our findings show that the majority ofE. coliproteins are systematically enabled to interact with Hsp70 even if this interaction only takes place during a fraction of the protein lifetime. In addition, our data suggest that some conformational sampling may take place within Hsp70‐bound states, due to the solvent exposure of some chaperone binding sites in native proteins. In all, we propose that Hsp70‐chaperone‐binding traits have evolved to favor Hsp70‐assisted protein folding devoid of aggregation.more » « less
-
Helical aromatic oligoamide foldamers (1a–c) with tunable lengths were computationally examined for their ability to bind selected sugars and sugar alcohols. These helices feature cylindrically shaped inner cavities lined with multiple inward-facing amide carbonyl oxygens acting as hydrogen-bond acceptors, enabling sugar binding via hydrogen bonding. Each of the helical foldamers has an overall dipole moment that increases with the length of the helix. The binding of a guest typically results in a reduction of the overall helix dipole moment within the complex, although there are several exceptions. The strength of host–guest interactions correlated positively with the number of hydrogen bonds formed. Longer helix 1c showed stronger interaction energies (up to −84.45 kcal mol−1), particularly with disaccharides, while shorter helix 1a bound sugars more weakly due to fewer established hydrogen bonds. The helical hosts exhibit structural adaptibility upon binding guests, with host distortion upon binding decreased with increasing helix length. Despite reduced binding energies, the complexes retained binding capability in aqueous environments, demonstrating their viability for aqueous-phase applications. This study underscores the critical roles of helical length and dipole alignment in optimizing sugar binding, providing a theoretical foundation for designing synthetic receptors for sugars and sugar alcohols based on aromatic oligoamide foldamers.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/C8OB00786A
