Noncovalent interactions, disruption

Thus, aside from the covalently polymerized a-chain itself, the majority of protein structure is determined by weaker, noncovalent interactions that potentially can be disturbed by environmental changes. It is for this reason that protein structure can be easily disrupted or denatured by fluctuations in pH, temperature, or by substances that can alter the structure of water, such as detergents or chaotropes. 

As for the covalent type, modification of CNTs by this approach has as its first goal to lead to debundling of the tubes, thus increasing their solubility and facilitating their manipulation. However, while the covalent method destroys the extended aromatic framework, noncovalent interactions preserve the original regular carbon network. This is important in those applications requiring use of the nanotubes without alteration of their electronic and optical properties, a process that normally occurs when the aromatic periodicity is disrupted. 

So what do CAMs tell us about GPGR activation We have seen how active states can be achieved by destabilizing the normal arrangement of TM domains by mutations at several different sites. As discussed above, TM domains are held in the basal state primarily by a network of noncovalent interactions between side chains. Thus, any compound that disrupts one of the many intramolecular interactions that stabilize the basal state could have, in principle, agonist activity. The process of disrupting a stabilizing... 

SDS disrupts noncovalent interactions between subunits of a protein, so if a protein has two subunits, two bands will appear. In the absence of SDS, only one band will appear. This reagent and mercaptoethanol reduce protein subunits that are disulfide bonded. This property of SDS may be responsible for protein denaturation. It should be noted that SDS also permeabilizes cells for antibody access to intracellular epitopes. 

Double-helical DNA in solution can undergo strand separation or dena-turation as a consequence of extremes of pH, heat, or exposure to chemicals such as urea or amides. Decrease in viscosity, increase in absorbance at 260 nm (hyperchromic effect), decrease in buoyant density, or negative optical rotation indicates denaturation of DNA. The denaturation process disrupts only noncovalent interactions between the two strands of DNA. Since G-C base pairs are held together by three hydrogen bonds in contrast to two for an A-T base pair, A-T rich DNA is easily denatured compared to G-C rich DNA (Figure 6.3). Electron microscopy can detect these A-T-rich regions in a DNA molecule since they form bubblelike structures. Hence the temperature of melting (Tm) of DNA increases in a linear fashion with... 

Temperature affects the rate of an enzyme-catalyzed reaction by increasing the thermal energy of the substrate molecules. This increases the proportion of molecules with sufficient energy to overcome the activation barrier and hence increases the rate of the reaction. In addition, the thermal energy of the component molecules of the enzyme is increased, which leads to an increased rate of denaturation of the enzyme protein due to the disruption of the noncovalent interactions holding the structure together. 

Each enzyme has an optimum pH at which the rate of the reaction that it catalyzes is at its maximum. Slight deviations in the pH from the optimum lead to a decrease in the reaction rate. Larger deviations in pH lead to denaturation of the enzyme due to changes in the ionization of amino acid residues and the disruption of noncovalent interactions. 

Proteins that possess a quaternary structure are composed of several separate polypeptide chains held together by noncovalent interactions. When such proteins are examined under dissociating conditions (e.g., 8 M urea to weaken hydrogen bonds and hydrophobic interaction, 1 m/lf mercaptoethanol to disrupt disulfide bonds), the molecular weight of the component polypeptide chains can be determined. By comparison with the native molecular weight, it is often possible to determine how many polypeptide chains are involved in the native structure. 

Beyond covalent connections within protein and lipid molecules, weak noncovalent interactions between large molecules govern properties of cellular structure and interfadal adhesion in biology. These bonds and structures have limited lifetimes and so will fail under any level of force if pulled on for the right length of time. As such, the strength of interaction is the level of force most likely to disrupt a bond on a particular time scale. 

Occurs when a protein loses quaternary, tertiary, or secondary structure (disruption of noncovalent interactions)... 

The three-dimensional structures of DNA, RNA, and proteins are determined by weak noncovalent interactions, principally hydrogen bonds and hydrophobic interactions. The free energies of these interactions are not much greater than the energy of thermal motion at room temperature, so that at elevated temperatures the structures of these molecules are disrupted. A macromolecule in a disrupted state is said to be denatured the ordered state, which is presumably that originally present in nature, is called the native state. A transition from the native to the denatured state is called denaturation. When double-stranded (native) DNA is heated, the bonding forces between the strands are disrupted and the two DNA strands separate thus, completely denatured DNA is single stranded. 

Noncovalent interactions are usually electrostatic that is, they occur between the positive nucleus of one atom and the negative electron clouds of another nearby atom. Unlike the stronger covalent bonds, individual noncovalent interactions are relatively weak and are therefore easily disrupted (Table 3.1). Nevertheless, they play a vital role in determining the physical and chemical properties of water and the structure and function of biomolecules because the cumulative... 

What guides proteins to their native folded state The answer to this question Initially came from In vitro studies on protein refolding. Thermal energy from heat, extremes of pH that alter the charges on amino acid side chains, and chemicals such as urea or guanidine hydrochloride at concentrations of 6-8 M can disrupt the weak noncovalent Interactions that stabilize the native conformation of a protein. The denaturation resulting from such treatment causes a protein to lose both Its native conformation and Its biological activity. 

The noncovalent interactions that maintain the three-dimensional structure of a protein are weak, and it is not surprising that they can be disrupted easily. 

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