Electrostatic and hydrophobic

The work by Hammett and Taft in the 1950s had been dedicated to the separation and quantification of steric and electronic influences on chemical reactivity. Building on this, from 1964 onwards Hansch started to quantify the steric, electrostatic, and hydrophobic effects and their influences on a variety of properties, not least on the biological activity of drugs. In 1964, the Free-Wilson analysis was introduced to relate biological activity to the presence or absence of certain substructures in a molecule. 

Further, for studying the role of pH and salt concentrations on bulk-electrostatic and non-bulk electrostatic contributions the same approach was made to experiments on the influence of the alcohols mentioned above on the oxygen affinity at various KC1 concentrations and pH-values 144,146). The results obtained indicate that at a low alcohol concentration the bulk-electrostatic contributions are dominant and that with increasing size of the alkyl group, alcohol and KC1 concentration, the nonbulk electrostatic, hydrophobic contributions increase. Recent results of kinetic measurements of 02 release show that cosolvents such as alcohols and formamide influence mainly the allosteric parameter L, i.e. -the equilibrium between T and R conformation and that the separation of the alcohol effects into bulk-electrostatic and hydrophobic (non-bulk electrostatic) contributions is justified. 

Collectively, these thermal denaturation studies demonstrated that aPNAs bind to complementary ssDNA targets with high affinity and in a sequence-specific manner consistent with our proposed base-pairing model. Additional electrostatic and hydrophobic binding interactions can be incorporated into the aPNA design without affecting the primary Watson-Crick binding mode. 

An alternative possibility is a vertical stacking structure where the p-strands are arranged on top of each other, again satisfying electrostatic and hydrophobic packing considerations (Fig. 20). Whichever is more likely, this is still far from a complete picture because the exact arrangement of the two disulphide-linked peptide chains is not yet known. 

Wimley, W. C. and White, S. H., Quantitation of electrostatic and hydrophobic membrane interactions by equilibrium dialysis and reverse-phase HPLC, Anal. Biochem., 213, 213, 1993. 

Another interesting application area of PHMD simulations is to investigate electrostatic interactions in the unfolded states of proteins. A traditional view that unfolded proteins adopt random conformational states that are devoid of electrostatic and hydrophobic interactions, are recently challenged by experimental data [20, 69], REX-CPHMD folding simulations of the 35 residue C-terminal subdomain of the villin headpiece domain revealed a significant deviation from the standard pKa values for several titratable residues. Additional simulations, in which a charged group is neutralized confirmed the existence of specific electrostatic interactions in the unfolded states (JK and CLB, manuscript in preparation). 

The [Co(phen)3]3+ complex is photoactive and a powerful oxidant in its excited state. The ion has no H-bonding groups and hence is considerably more hydrophobic1279 than hexaamine relatives. These properties have proven particularly useful. Aryl and alkyl substituted [Co(phen)3]3+ complexes have received a great deal of attention due to their ability to intercalate within the helical structure of DNA through a combination of electrostatic and hydrophobic forces. The chirality of the tris-chelate complex is crucial in determining the degree of association between the complex and... 

The main contributions to AadsG for a globular protein are from electrostatic, dispersion, and hydrophobic forces and from changes in the structure of the protein molecule. Although in this section these contributions are discussed individually, strict separation of the influence of these forces on the overall adsorption process of a protein is not possible. For instance, adsorption-induced alteration of the protein structure affects the electrostatic and hydrophobic interaction between the protein and the surface. When the sorbent surface is not smooth but is covered with (polymeric)... 

Additionally the membrane itself can contribute to further modifications of the protein-protein interactions. It can provide additional electrostatic and hydrophobic interactions distinct from the lipid anchorage and thereby affect conformation and/or activity of membrane associated proteins. 

Xu QH, Gaylord BS, Wang S, Bazan GC, Moses D, Heeger AJ (2004) Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers the role of electrostatic and hydrophobic interactions. Proc Natl Acad Sci USA 101 11634-11639... 

The fluorescence spectrum of the tris-acridine cryptand A-13 shows the characteristic monomer and excimer bands. Upon complexation with various organic anions (carboxylates, sulfonates, phosphates), the monomer band increases at the expense of the excimer band. The stability of the complexes depends on the contribution of the electrostatic and hydrophobic forces and on the structural complementarity. Stability constants of the complexes ranging from 103 to 107 have been measured. In particular, A-13 binds tightly to mono- and oligonucleotides, and it can discriminate by its optical response between a pyridimic and a purinic sequence. 

Peptides larger than 10 to 20 residues adopt conformations in solution through the interplay of hydrogen bonding, electrostatic and hydrophobic interactions, positioning of polar residues on the solvated surface of the polypeptide, and sequestering of hydrophobic residues in the nonpolar interior. Protein shape is dynamic, changing continuously in response to the solvent environment. The retention process in RPLC is initiated as the protein approaches the stationary-phase surface. Structured water associated at the phase surface and adjacent to hydrophobic contact surfaces on the polypeptide is released into the bulk mobile... 

Scoring systems are set up to quantitatively calculate how well the ligand docks with the active site in terms of alignment, hydrogen bonding, van der Waals forces, and electrostatic and hydrophobic interactions. In addition, flexibilities of both the ligands and protein in the binding process as they accommodate each other have to be considered. 

The molecular interaction of cytochrome c and cardiolipin has been extensively studied. A mode of the interaction has been confirmed to be both electrostatic and hydrophobic, by using infrared spectroscopy (Choi and Swanson, 1995), fluorescence resonance energy transfer method (Rytdmaa and Kinnunen, 1994), protease digestion (de Jongh et al., 1995), cyclic voltammetry (Salamon and ToUin, 1997), deuterium and phosphorus NMR measurements (Spooner et al., 1993), and surface plasmon resonance spectroscopy (Salamon and Tollin, 1996). 

Catalysis can occur when micelUzed surfactants are themselves chemically inert, and this effect relies on electrostatic and hydrophobic interactions that alter the susceptibility of reactants to nucleophilic attack or electron... 

Polymeric polyamines are also strongly adsorbed in the compact region of the electric double layer as a combination of multisite electrostatic and hydrophobic interactions. The adsorption results in masking the silanol groups and the other adsorption active sites on the capillary wall and in altering the EOF, which is lowered and in most cases reversed from cathodic to anodic. One of the most widely employed polyamine coating agents is polybrene (or hexadimetrine bromide), a linear hydrophobic polyquaternary amine polymer of the ionene type [129]. 

Hemes encapsulated in aqueous detergent micelles find themselves in a large macromolecular cavity whose interaction is mainly hydrophobic. It has been suggested that such systems appear to simulate the electrostatic and hydrophobic interactions of the heme cavity in metalloproteins. The present article surveys reported studies on natural and synthetic hemes, both ferric and ferrous, incorporated inside micelles of different sizes and surface charges. The emphasis is laid on multinuclear NMR and optical spectroscopic studies. The effect of micellar interactions on the electronic properties of hemes is discussed and compared with that of the heme cavity in proteins. 

It has been suggested that aqueous micellar systems simulate the electrostatic and hydrophobic interactions of the heme cavity [15-23]. Pioneering studies by Simplicio et al. [15-17] have shown that the heme is monodispersed when encapsulated in aqueous micelles. They have studied binding of cyanide and other axial ligands to ferric hemes in micellar environments. These studies [15-23] indicated that a heme encapsulated in an aqueous detergent micelle finds itself inside a large macromolecular cavity whose interactions is primarily... 

The electrostatic and hydrophobic microenvironment of micells and polymers facilitates charge separation from the excited state. 

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