Binding event

There have been notable successes in the replacement of individual peptide residues by peptoid monomers with retention of in vitro activity and enhancement of specificity. Unfortunately, attempts to completely transform those bioactive peptides that function via specific peptide-protein binding events into entirely pep-toid-based ohgomers have so far proven successful only at short chain lengths (e.g. [23]). It remains to be seen whether any general strategy can be developed in... 

The examples just presented give initial impressions of how DNA can be utilized as a template in the synthesis of nanometric and mesoscopic aggregates. However, the studies emphasize the importance of fundamental research on the interaction between DNA and the various binders, such as metal and organic cations. Of particular importance are the consequences of binding events on the structure and topology of the nucleic acid components involved. 

As a complement to any (and perhaps all) of the above methods, calorimetry can be utilized in developing an understanding of the overall energetic behavior of the binding event [20]. The overall thermodynamics of any molecular interaction is the sum of both the enthalpic and entropic energy components of the species involved [21]. While these measurements have historically been somewhat limited due to a requirement for a significant amount of protein, new techniques have alleviated the situation substantially [22]. 

Clustering of a certain number of CD4 and coreceptor molecules is presumed to be necessary for the efficient HIV-1 Env-mediated fusion pore formation. It has been proposed that four to six CCR5 molecules (91) and three CD4 binding events are needed to induce fusion between the viral and host cell membranes (92). Both CD4 (93) and chemokine receptors can form functional dimers (94) in the plasma membrane. It was proposed that formation of CD4 dimers, mediated by a disulfide bond between the cysteine residues of the D2 domain, might enhance HIV-1 entry and infection (95,96). In contrast, others have provided... 

Mosesson MW. Fibrinogen and fibrin polymerization appraisal of the binding events that accompany fibrin generation and fibrin clot assembly. Blood Coagul Fibrinol 1997 8 257-267. 

In most cases the initial interactions between the enzyme and the substrate molecule (i.e., the initial binding event) are noncovalent, making use of hydrogen bonding, electrostatic, hydrophobic interactions, and van der Waals forces to effect binding. 

A second ternary complex reaction mechanism is one in which there is a compulsory order to the substrate binding sequence. Reactions that conform to this mechanism are referred to as bi-bi compulsory ordered ternary complex reactions (Figure 2.13). In this type of mechanism, productive catalysis only occurs when the second substrate binds subsequent to the first substrate. In many cases, the second substrate has very low affinity for the free enzyme, and significantly greater affinity for the binary complex between the enzyme and the first substrate. Thus, for all practical purposes, the second substrate cannot bind to the enzyme unless the first substrate is already bound. In other cases, the second substrate can bind to the free enzyme, but this binding event leads to a nonproductive binary complex that does not participate in catalysis. The formation of such a nonproductive binary complex would deplete the population of free enzyme available to participate in catalysis, and would thus be inhibitory (one example of a phenomenon known as substrate inhibition see Copeland, 2000, for further details). When substrate-inhibition is not significant, the overall steady state velocity equation for a mechanism of this type, in which AX binds prior to B, is given by Equation (2.16) ... 

C. Intrinsically Unstructured Proteins Coupled Folding and Binding Events... 

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