Electrostatic and hydrophobic interaction

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 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... 

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. 

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... 

An example of the above mentioned cascade complexation of carboxylates by macrocyclic receptors containing metal ionic centers is the inclusion of oxalate by the dien dicobalt complex 9 (Martell, Mitsokaitis) [12]. Similarly, the -cyclodextrin (jS-CD) 10, modified with a zinc cation bound by a triamine side chain, encapsulates anions like 1-adamantylcarboxylate in its cavity, fixing them by combined electrostatic and hydrophobic interactions [13], Zinc s group achieved the enantioselective transport of the potassium salts of N-protected amino acids and dipeptides by making use of the cation affinity of... 

Nanostructures are, literally, facts of life in biology. Proteins, viruses, and bacteria are nanosized, three-dimensional structures which have been self assembled from smaller subunits. Although individual atoms in the subunits (polypeptides, for example) are covalently linked, assembly of the subunits is maintained by non-covalent (van der Waals, hydrogen-bonding, electrostatic, and hydrophobic) interactions. 

As with other multisubunit enzymes (e.g., allosteric enzymes), the structural integrity of a membrane-bound enzyme primarily is maintained by noncovalent interactions such as hydrogen bonding, electrostatics, and hydrophobic interactions. Hydrophobic polypeptides (or hydrophobic portions of polypeptides) apparently are used to anchor the enzymes to the membrane through interactions with phospholipids. Therefore, I would characterize the interaction between the enzyme and membrane as chemical in nature rather than as geometric. ... 

Recently, considerable progress has been made on the calculation of electrostatic and hydrophobic interactions in biochemical systems 189 19 >. We can expect such calculations to become common for protein-solid surface interactions. Thus we can expect approximate values for the adsorption energy in selected systems to appear in the near future. The problem of time-dependent conformational adaptation of the protein to the surface (and vice versa) will be much more difficult. Initially, we will have to resort to crude measures of the structural stability of a protein, such as the temperature at which thermal denaturation occurs, the urea molar concentration for solution denaturation, etc. One or more of the models given in Fig. 13 should apply. 

Charged colloids and water-in-oil microemulsions provide organized environments that control photosensitized electron transfer reactions. Effective charge separation of the primary encounter cage complex, and subsequent stabilization of the photoproducts against back electron transfer reactions is achieved by means of electrostatic and hydrophobic interactions of the photoproducts and the organized media. 

The effect of micelles on organic reactions can be attributed to both electrostatic and hydrophobic interactions (Rosen, 1979). Electrostatic interaction is important because it may affect the transition state of a reaction orthe concentration of reactant in the vicinity ofthe reaction site. The hydrophobic interactions are important because they determine the extent and the locus of solubilization in the micelle. 

A poly(propylenamine) dendrimer (11, Fig. 6.37) functionalised with poly-(N-isopropylacrylamide) (PIPAAm) (see Section 4.1.2) was used as dendritic host for anionic cobalt(II)-phthalocyanine complexes (a, b) as guests, which are held together by supramolecular (electrostatic and hydrophobic) interactions [57]. These dendritic complexes were investigated as catalysts in the above-mentioned oxidation of thiols, where they show a remarkable temperature dependence the reaction rate suddenly increases above 34°C. One attempted explanation assumes that the dendritic arms undergo phase separation and contraction above the Lower Critical Solubility Temperature (LCST). At this temperature the phthalocyanine complex site is more readily accessible for substrates and the reaction rate is therefore higher. 

The precipitation mechanism is governed by the solubility of the foulant, while the adsorption is affected by electrostatic and hydrophobic interactions between the foulant and the membrane surface. The molecular size and... 

The balance of electrostatic and hydrophobic interactions can be such as to cause the locus of solubilisation to be anywhere in the micelle from close to the surface to the inner core. 

Benfenati F, Greengard P, Brunner J et al (1989b) Electrostatic and hydrophobic interactions of synapsin I and synapsin I fragments with phospholipid bilayers. J Cell Biol 108 1851-62 Benfenati F, Valtorta F, Chieregatti E et al (1992a) Interaction of free and synaptic vesicle-bound synapsin I with F-actin. Neuron 8 377-86... 

In a model borrowed from the study of bacterial chemotaxis, it was initially proposed that OBPs not only solubilize specific pheromones, but trigger the olfactory receptors when bound to odorant molecules (Pelosi, 1994). Later, it was further hypothesized that electrostatic and hydrophobic interactions from both the bound ligand and ligated protein are necessary and sufficient for receptor activation (Prestwich and Du, 1997). To the best of my knowledge the protein-ligand complex model has never been tested in bacteria. Certainly, it is not... 

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