Molecular Recognition by Pillar[5]arenes: Evidence for Simultaneous Electrostatic and Hydrophobic Interactions

The formation of inclusion complexes between alkylsulfonate guests and a cationic pillar[5]arene receptor in water was investigated by NMR and ITC techniques. The results show the formation of host-guest complexes stabilized by electrostatic interactions and hydrophobic effects with binding constants of up to 107 M−1 for the guest with higher hydrophobic character. Structurally, the alkyl chain of the guest is included in the hydrophobic aromatic cavity of the macrocycle while the sulfonate groups are held in the multicationic portal by ionic interactions.

Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices

During SecYEG-mediated cotranslational insertion of membrane proteins, transmembrane helices (TMHs) first make contact with the membrane when their N-terminal end is ~45 residues away from the peptidyl transferase center. However, we recently uncovered instances where the first contact is delayed by up to ~10 residues. Here, we recapitulate these effects using a model TMH fused to two short segments from the BtuC protein: a positively charged loop and a re-entrant loop. We show that the critical residues are two Arg residues in the positively charged loop and four hydrophobic residues in the re-entrant loop. Thus, both electrostatic and hydrophobic interactions involving sequence elements that are not part of a TMH can impact the way the latter behaves during membrane insertion.

The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation

Yeast Cadmium Factor-1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4Å and 4.0Å in distinct inward-facing open conformations capturing a previously unobserved ordered state of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the lasso domain. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide long-sought after insights into how R-domains control ABCC transporter activity.

Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities.

Over the years, structure-based design programs and specifically docking small molecules to proteins have become prominent in drug discovery. However, many of these computational tools have been developed to primarily dock enzyme inhibitors (and ligand to other protein classes) relying heavily on hydrogen bonds, electrostatic and hydrophobic interactions. In reality, many drug targets either feature metal ions, can be targeted covalently, or are simply not even proteins (e.g., nucleic acids). Herein, we describe several new features that we have implemented into FITTED to broaden its applicability to a wide range of covalent enzyme inhibitors, and to metalloenzymes, where metal coordination is essential for drug binding. We also report new datasets that were essential demonstrate areas of success and those where additional efforts are required. This resource could be used by other program developers to assess their own

Docking Ligands into Flexible and Solvated Macromolecules. 8. Forming New Bonds – Challenges and Opportunities.

Over the years, structure-based design programs and specifically docking small molecules to proteins have become prominent in drug discovery. However, many of these computational tools have been developed to primarily dock enzyme inhibitors (and ligand to other protein classes) relying heavily on hydrogen bonds, electrostatic and hydrophobic interactions. In reality, many drug targets either feature metal ions, can be targeted covalently, or are simply not even proteins (e.g., nucleic acids). Herein, we describe several new features that we have implemented into FITTED to broaden its applicability to a wide range of covalent enzyme inhibitors, and to metalloenzymes, where metal coordination is essential for drug binding. We also report new datasets that were essential demonstrate areas of success and those where additional efforts are required. This resource could be used by other program developers to assess their own

Assessing the Influence of Dyes Physico-Chemical Properties on Incorporation and Release Kinetics in Silk Fibroin Matrices

Silk fibroin (SF) is a promising and versatile biodegradable protein for biomedical applications. This study aimed to develop a prolonged release device by incorporating SF microparticles containing dyes into SF hydrogels. The influence of dyes on incorporation and release kinetics in SF based devices were evaluated regarding their hydrophilicity, molar mass, and cationic/anionic character. Hydrophobic and cationic dyes presented high encapsulation efficiency, probably related to electrostatic and hydrophobic interactions with SF. The addition of SF microparticles in SF hydrogels was an effective method to prolong the release, increasing the release time by 10-fold.

Interaction of sulphone based reactive dyes with cationic surfactant: a spectroscopic and conductometric study

Interaction of sulphone based reactive dyes, designated as dye-1 and dye-2, with cationic micellar system of cetyltrimethylammonium bromide (CTAB), has been investigated by spectroscopic and conductometeric measurements. Efficiency of the selected micellar systems is assessed by the values of binding constant (K b ), partition coefficient (K x ) and respective Gibbs energies. Critical micelle concentration (CMC) of surfactant, electrostatic and hydrophobic interactions as well as polarity of the medium plays significant role in this phenomenon. The negative values of Gibbs energies of binding (∆G b ) and partition (∆G p ) predicts the feasibility and spontaneity of respective processes. Similarly negative values of ∆G m and ∆H m and positive values of ∆S m , calculated from conductometeric data, further, revealed the exothermicity, spontaneity and, thus, stability of system. The results, herein, have disclosed the strong interaction between dye and surfactant molecules. The dye-2 has been observed to be solubilized to greater extent, as compared to dye 1, due to strong interaction ith hydrophiles of CTAB and accommodation of its molecules in palisade layer of micelle closer to the micelle/water interface.

Interactions between adsorbents and adsorbates in aqueous solutions

Adsorption is one of the most widely used processes in physicochemical operations. To design an adsorbent for a specific adsorbate, it is important to understand the interactions between adsorbents and adsorbates, which are very important for both adsorption capacity and selectivity. Electrostatic interactions, hydrogen bonding, hydrophobic interactions, complexation, and precipitation are comprehensively discussed. Adjusting solution pH and ionic strength is an effective method to improve the adsorption, especially when electrostatic and hydrophobic interactions are main interactions. With the increase in ionic strength, the hydrophobic interactions between adsorbents and adsorbates increase, while the electrostatic interactions decrease.