Closed 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. 

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.

Fig. 2. Conformational free energy of closed, intermediate and open protein kinase conformations. cAPK indicates the unbound form of cAMP-dependent protein kinase, cAPKiATP the binary complex of cAPK with ATP, cAPKiPKP the binary complex of cAPK with the peptide inhibitor PKI(5-24), and cAPK PKI ATP the ternary complex of cAPK with ATP and PKI(5-24). Shown are averaged values for the three crystal structures lATP.pdb, ICDKA.pdb, and ICDKB.pdb. All values have been normalized with respect to the free energy of the closed conformations.

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. 

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

Here and below, T , 1, , and e, i, j = 1,. . . , 5, denote atomic position vectors, atom-atom distances, and the corresponding unit vectors, respectively. In order to construct a correctly closed conformation, variables qi,. . . , q4 are considered independent, and the last valence angle q is computed from Eq. (7) as follows. Variables qi,.. ., q4 determine the orientation of the plane of q specified by vector 634 and an in-plane unit vector 6345 orthogonal to it. In the basis of these two vectors, condition (7) results in... 

AE Garcia, JG Harman. Simulations of CRP (cAMP)2 in noncrystalhne environments show a subunit transition from the open to the closed conformation. Protein Sci 5 62-71, 1996. 

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. 

The two domains of the kinase in the inactive state are held in a closed conformation by assembly of the regulatory domains... 

In the absence of an electric field, the dome-closed conformation must be the most stable tip structure, even when spot-welds are considered, since only the perfectly dome-closed tip has no dangling bonds (i.e., it is a true hemifullerene). At the 3000°C temperature of the arc, the rate of tip annealing should be so fast that it is sure to find its most stable structure (i.e., to close as a dome). Clear evidence of this facile closure is the fact that virtually all nanotubes found in the arc deposit are dome-closed. (Even stronger evidence is the observation of only dome-closed nanotubes made at 1200°C by the oven laser vaporization method.) Such considerations constituted the original motivation for the electric field hypothesis. 

Figure 8. A schematic for the toxin binding sites on the voltage-gated Na channel. Toxin-free open and closed conformations are drawn at the left and center. Separate sites are depicted within the membrane for activators such as BTX, VTD (A), and brevetoxin (B) these are coupled to each other and to the a-peptide toxin site (a), which is kinetically linked to the -peptide toxin site (P see ref. 20). Near the outer opening of the pore is a site (G) for STX and TTX which is affected by binding at site A and which can modify inactivation gating.

Figure 2 Depiction of the active ( open ) and inactive ( closed ) conformations of Src kinase based on the analysis of x-ray structures of c-Src tyrosine kinase crystallized in its inactive state [7]. The stabilization of the inactive conformation is influenced by multiple events including intramolecular binding of the tyrosine-phosphorylated C-terminus tail to the SH2 domain as well as interactions between the SH3 domain and the SH2-kinase linker. CT, C-terminal NT, N-terminal. 

Figure 6.18 Structure of HIV-1 aspartyl protease in the flap open (left panel) and flap closed conformation with an active site-directed inhibitor bound right panel). See color insert.

Notice that the problem states that the distribution of open times is a single exponential. This tells you that a mechanism containing a single open state of the receptor can describe the data. Using the above hint, the channel closing rate (call this a) is therefore the reciprocal of the mean open time. Thus, at -60 mV, a = 1/5 msec, or 200 sec-1 at -120 mV, a = 1/10 msec, or 100 sec-1. This indicates that the channel closing conformational change is affected by the electric held across the membrane. 

In the closed conformation (Fig. 5-10A) the two NBD domains bind to each other and, as shown in Figure 5-11, nucleotide binding occurs in pockets formed between these two domains. The stoichiometry and nucleotide selectivity of these binding pockets have been determined for an ABC transporter that functions to export peptides from yeast mitochondria [34]. The results of this study has led to the proposed reaction cycle diagrammed and described in Figure 5-12. 

Chang, G. Structure of MsbA from Vibrio cholerae. a multidrug resistance ABC transporter homolog in a closed conformation. /. Mol. Biol. 330 419-430, 2003. 

Figure 9.4 Structures of potassium channels in open and closed conformations. The selectivity filter is orange, and the conserved glycine residue is in red. (From Yu et al., 2005. Reproduced with permission of Blackwell Publishing Ltd.)...

Lee, J.Y., Urbatsch, I.L., Senior, A.E. and Wilkens, S. (2002) Projection structure of P-glycoprotein by electron microscopy. Evidence for a closed conformation of the nucleotide binding domains. Journal of Biological Chemistry, 277, 40125-40131. 

The termination module of surfactin synthetase is a 144 kDa four-domain enzyme responsible for the incorporation of the final amino acid (L-Leu) into the surfactin peptide and subsequent cyclization of the resulting product. The structure of the TE domain of this construct was previously solved. In the recently determined 2.6 A X-ray structure of the C-A-PCP-TE construct, the entire protein chain is evident in the electron density maps. " " The structural folds of the individual domains in this module are similar to structures of monomeric domains (Figure 13). The deviations observed in this multidomain structure include a slight difference in the hinge region of C domain subdomains and an orientation of the subdomains of the A domain that is not consistent with the open or closed conformations previously described. The A domain contains... 

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