Structure, three-dimensional electrostatic interactions

The biological activity of molecules such as proteins, cells, and viruses can easily be destroyed by processing conditions that do not conform to their natural environment. Therefore, traditional separation processes such as distillation or solvent extraction are seldom used to isolate them. Affinity adsorption is one of the most effective methods for the direct isolation and purification of biomolecules from complex mixtures (Camperi et al., 2003). It is based on recognition between a pair of molecules determined by the steric structure (three-dimensional arrangement of its atoms) of the molecules. When molecules have complementary steric structures, they can interact to maximize the hydrogen bonds and electrostatic interactions. Affinity adsorption allows a separation with high specificity and purity. 

When spherical objects are stacked to produce a three-dimensional array (crystal lattice), the relative sizes of the spheres determine what types of arrangements are possible. It is the interaction of the cations and anions by electrostatic forces that leads to stability of any ionic structure. Therefore, it is essential that each cation be surrounded by several anions and each anion be surrounded by several cations. This local arrangement is largely determined by the relative sizes of the ions. The number of ions of opposite charge surrounding a given ion in a crystal is called the coordination number. This is actually not a very good term because the bonds are not coordinate bonds (see Chapter 16). For a specific cation, there will be a limit to the number of anions that can surround the cation because... 

The active site of an enzyme is generally a pocket or cleft that is specialized to recognize specific substrates and catalyze chemical transformations. It is formed in the three-dimensional structure by a collection of different amino acids (active-site residues) that may or may not be adjacent in the primary sequence. The interactions between the active site and the substrate occur via the same forces that stabilize protein structure hydrophobic interactions, electrostatic interactions (charge-charge), hydrogen bonding, and van der Waals interactions. Enzyme active sites do not simply bind substrates they also provide catalytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reaction. 

Noncovalent interactions in metal complexes of biomolecules may play an important role in the creation of supramolecular structures around the metal center. For instance, extensive three-dimensional hydrogen-bonded stmcmres grow around metal complexes of barbiturates, recognized as the most widely used drugs for the treatment of epilepsy.Electrostatic interactions between a cation and the Trring of an aromatic molecule (cation-tt interactions) are common motifs in protein structures. Little is known about alkali and alkali-earth cation-tt inter-... 

N-Myristoylation is achieved by the covalent attachment of the 14-carbon saturated myristic acid (C14 0) to the N-terminal glycine residue of various proteins with formation of an irreversible amide bond (Table l). 10 This process is cotranslational and is catalyzed by a monomeric enzyme called jV-myri s toy 11ransferase. 24 Several proteins of diverse families, including tyrosine kinases of the Src family, the alanine-rich C kinase substrate (MARKS), the HIV Nef phosphoprotein, and the a-subunit of heterotrimeric G protein, carry a myr-istoylated N-terminal glycine residue which in some cases is in close proximity to a site that can be S-acylated with a fatty acid. Functional studies of these proteins have shown an important structural role for the myristoyl chain not only in terms of enhanced membrane affinity of the proteins, but also of stabilization of their three-dimensional structure in the cytosolic form. Once exposed, the myristoyl chain promotes membrane association of the protein. 5 The myristoyl moiety however, is not sufficiently hydrophobic to anchor the protein to the membrane permanently, 25,26 and in vivo this interaction is further modulated by a variety of switches that operate through covalent or noncovalent modifications of the protein. 4,5,27 In MARKS, for example, multiple phosphorylation of a positively charged domain moves the protein back to the cytosolic compartment due to the mutated electrostatic properties of the protein, a so-called myristoyl-electrostatic switch. 28 ... 

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. 

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