Open conformation

The catalytic subunit of cAPK contains two domains connected by a peptide linker. ATP binds in a deep cleft between the two domains. Presently, crystal structures showed cAPK in three different conformations, (1) in a closed conformation in the ternary complex with ATP or other tight-binding ligands and a peptide inhibitor PKI(5-24), (2) in an intermediate conformation in the binary complex with adenosine, and (3) in an open conformation in the binary complex of mammalian cAPK with PKI(5-24). Fig.l shows a superposition of the three protein kinase configurations to visualize the type of conformational movement. 

As a template for an intermediate conformation of protein kinase, the crystal structure of the binary complex of cAPK with adenosine (Ibkx.pdb in the Protein Data Bank) was used. As templates for open conformations... 

Fig. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

The ranking of conformational free energies indicated that the closed state of cAPK is favored even in the absence of ligands, which is in contrast to experimental data that showed a preferred population of the open conformation. One reason for this discrepancy could be that the modelled intermediate ... 

The catalytic subunit then catalyzes the direct transfer of the 7-phosphate of ATP (visible as small beads at the end of ATP) to its peptide substrate. Catalysis takes place in the cleft between the two domains. Mutual orientation and position of these two lobes can be classified as either closed or open, for a review of the structures and function see e.g. [36]. The presented structure shows a closed conformation. Both the apoenzyme and the binary complex of the porcine C-subunit with di-iodinated inhibitor peptide represent the crystal structure in an open conformation [37] resulting from an overall rotation of the small lobe relative to the large lobe. 

Karlsson, R., Zheng, J., Zheng, N.-H., Taylor, S. S., Sowadski, J. M. Structure of the mamalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation. Acta Cryst. D 49 (1993) 381-388. 

Fig. 1. The penicillin thiazolidine ring (a) open conformation (b) closed conformation.

Long loop regions are often flexible and can frequently adopt several different conformations, making them "invisible" in x-ray structure determinations and undetermined in NMR studies. Such loops are frequently involved in the function of the protein and can switch from an "open" conformation, which allows access to the active site, to a "closed" conformation, which shields reactive groups in the active site from water. 

Demonstration of tlie ctitical roles of tlie open conformations of polymetallic dusters bigliliglits tlieotetical analysis in cuprate diemistty. Polymetallic dusters in various s7iitlietic reactions ate ctitietiidy attracting tlie attention of syn-tlietic and medianistic diemists alike [40, 180-183]. 

ISF). However, in the P6s crystal form ( intermediate state ), the cluster binding subdomain appears to be detached from the base fold fi sheets 1 and 2) in an open conformation 42). If the functional domains of the two crystal forms are superposed using the base fold residues, the rms deviation of the Ca positions of the cluster binding... 

The first approach applied for [cinchonidine (CD) - a-keto ester] complex was also unsuccessful. In the open conformation CD cannot provide the required steric shielding. In open form either the quinuclidine or the quinoline moiety of CD will interact with the substrate. It has already been demonstrated that the quinuclidine moiety has a crucial role both in the rate acceleration and the induction of ED [13]. 

Figure 7 Stereoview of the structure of EPSP synthase in its open conformation.

Another important factor in the hydrogenation of a,p-unsaturated acids was the solvent by increasing the polarity of the solvent used (n-hexane < toluene < methyl acetate < THF < methanol) a progressive decrease in ee was observed. This was probably due to the fact that H2 and the a,p-unsaturated acids were more soluble in the apolar solvents and also that CD was present in the open conformation, the enantioselective conformation (8). In fact, the highest conversion and ee were obtained with n-hexane (Figure 2). 

Figure 5-10 compares NBD structures from nearly identical transporters from Vibrio cholerae and Escherichia coli that crystallized with their TMDs in two closed and open conformations respectively. Hypothetically, substrate would be acquired and transported as a result of energizing a conformational cycle by coupling it to ATP hydrolysis. 

All isoforms of PKC are predominantly localized to the cytosol and, upon activation, undergo translocation to either plasma or nuclear membranes. However, newly synthesized PKCs are localized to the plasmalemma and are in an open conformation in which the auto inhibitory pseudosubstrate sequence is removed from the substrate binding domain. The maturation of PKC isoforms is effected by phosphoinositide-dependentkinase-I (PDK-I), which phosphorylates a conserved threonine residue in the activation loop of the catalytic (C4) domain [24]. This in turn permits the autophosphorylation of C-terminus threonine and serine residues in PKC, a step which is a prerequisite for catalytic activity (see also Chs 22 and 23). The phosphorylated enzyme is then released into the cytosol, where it is maintained in an inactive conformation by the bound pseudosubstrate. It was originally thought that 3-phosphoinositides such as PI(3,4)P2 and PI(3,4,5)P3 could directly activate PKCs. However, it now seems more likely that these lipids serve to activate PDK-1 (a frequent contaminant of PKC preparations). 

The cyclic H-bonded form (5.48) may be compared with the open conformer... 

An even stronger case of intramolecular RAHB coupling is provided by the maleate ion (HOOCCH=CHCOO-), whose H-bonded and open conformers are shown in Fig. 5.22. Skeletal bond lengths and bond orders of these conformers are compared in Table 5.18. As shown in Fig. 5.22, the H-bonded conformer is favored in this case by more than 26 kcalmol-1, which is indicative of a powerful intramolecular no aoH interaction (estimated second-order stabilization 104 kcalmol-1) that is sufficient to overcome the severe steric repulsion of the extremely short H- -O nonbonded distance ( 1.3 A).56... 

In contrast, resonance delocalization and bond alternation in the C—C=C—C backbone are only slightly affected by H-bond formation (namely, the C4—C5 bond order varies by only 0.008 between H-bonded and open conformers), because such resonance shifts do not intrinsically alter the charge distribution in the H-bonded O- H—O triad. This example illustrates the principle that H-bonding is not generally coupled to resonance per se, but only to such resonance as leads to effective CAHB enhancement (Section 5.2.2). 

Figure 1.4 Schematic drawing of the closed and open conformations of a chloride channel. (From Dutzler et al., 2003. Copyright (2003) American Association for the Advancement of Science.)...

A structural model for the open conformation of the mdrl P-glycoprotein based on the MsbA crystal structure. Journal of Biological Chemistry, 278, 30115-30124. 

It was shown74 that the folded conformation of bicyclic substrates is a prerequisite for isomerizations such as 177 - 178. Thus, vyw-9-vinyl triene 183, being in the open conformation, undergoes an unusual Cope rearrangement to give the intermediate 184 which starts a cascade of thermal isomerizations at 60-65 °C (equation 57) whereas the awft -9-vinyl epimer 185 rearranges into the indene derivative 186 at 110°C in benzene solution (equation 58)74. 

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