Binding reactions intracellular

Fig. 4 Stages in synaptic vesicle exocytosis. Putative intermediate steps on the molecular pathway to synaptic vesicle fusion. Vesicle delivery and tethering to the presynaptic membrane most likely involves Rab-proteins and their effectors. So far, the nature of a speculative docking complex (dc) is unclear, but docking appears to be independent from SNARE proteins. In the primed state, SNAREs have assembled into a complex probably stabilized by complexin (Cpx). The fusion reaction is arrested until the intracellular calcium concentration increases. The putative calcium sensor for fast neurotransmitter release, synaptotagmin 1 (Syt), binds to intracellular calcium and in turn triggers fusion by associating with the presynaptic membrane and interacting with the SNARE complex, thereby displacing complexin (Tang et al. 2006).

Nucleic acids that can perform a wide variety of binding reactions have been selected from random sequence pools by affinity immobilization. Oliphant et al. [2] selected DNA molecules that could bind to the yeast transcriptional activator GCN4 from a random-sequence DNA pool that spanned nine positions. Since then, aptamers (nucleic acid ligands) have been selected against a variety of protein targets that naturally bind to nucleic acids, such as EF-Tu, ribosomal proteins, QP replicase, and reverse transcriptase (reviewed in Ref. 3). In addition, aptamers have been selected against intracellular and... 

When the binding reactions are rapid, the amount of intracellular or bound drug can be assumed to be directly proportional, with an equilibrium coefficient A bind> W the amount of drug available for internalization or binding ... 

We start by defining the membrane binding reaction between the extracellular ligand (L) and the receptors (R) on the cell membrane. As this reaction includes molecules in both the membrane and extracellular compartments, it takes place in the membrane compartment. Right click on the cell membrane compartment, and choose the Reactions... option. This will open a new window (Fig. 2a) where all membrane reactions can be defined. This window is divided into three sections, representing the EC (extracellular compartment), CM (cell membrane), and IC (intracellular compartment). All available molecules are displayed in the appropriate compartments. 

Smooth muscle contractions are subject to the actions of hormones and related agents. As shown in Figure 17.32, binding of the hormone epinephrine to smooth muscle receptors activates an intracellular adenylyl cyclase reaction that produces cyclic AMP (cAMP). The cAMP serves to activate a protein kinase that phosphorylates the myosin light chain kinase. The phosphorylated MLCK has a lower affinity for the Ca -calmodulin complex and thus is physiologically inactive. Reversal of this inactivation occurs via myosin light chain kinase phosphatase. 

The catalytic cycle of the Na+/K+-ATPase can be described by juxtaposition of distinct reaction sequences that are associated with two different conformational states termed Ei and E2 [1]. In the first step, the Ei conformation is that the enzyme binds Na+ and ATP with very high affinity (KD values of 0.19-0.26 mM and 0.1-0.2 pM, respectively) (Fig. 1A, Step 1). After autophosphorylation by ATP at the aspartic acid within the sequence DKTGS/T the enzyme occludes the 3 Na+ ions (Ei-P(3Na+) Fig. la, Step 2) and releases them into the extracellular space after attaining the E2-P 3Na+ conformation characterized by low affinity for Na+ (Kq5 = 14 mM) (Fig. la, Step 3). The following E2-P conformation binds 2 K+ ions with high affinity (KD approx. 0.1 mM Fig. la, Step 4). The binding of K+ to the enzyme induces a spontaneous dephosphorylation of the E2-P conformation and leads to the occlusion of 2 K+ ions (E2(2K+) Fig. la, Step 5). Intracellular ATP increases the extent of the release of K+ from the E2(2K+) conformation (Fig. la, Step 6) and thereby also the return of the E2(2K+) conformation to the EiATPNa conformation. The affinity ofthe E2(2K+) conformation for ATP, with a K0.5 value of 0.45 mM, is very low. 

Obelin is a Ca2+-activated bioluminescent photoprotein that has been isolated from the marine polyp Obelia longissima. Binding of calcium ions determines a luminescent emission. The protein consists of 195 amino acid residues [264] and is composed of apoobelin, coelenterazine, and oxygen. As aequorin, it contains three EF-hand Ca2+-binding sites and the luminescent reaction may be the result of coelenterazine oxidation by way of an intramolecular reaction that produces coelenteramide, C02, and blue light. As for aequorin, the luminescent reaction of obelin is sensitive to calcium and the protein was used in the past as an intracellular Ca2+ indicator. More recently, the cloning of cDNA for apoobelin led to the use of recombinant obelin as a label in different analytical systems. 

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