A circular permutation

E. A. MacGregor, H. M. Jespersen, and B. Svensson, A circularly permuted alpha-amylase-type alpha/beta-barrel structure in glucan-synthesizing glucosyl-transferases, FEBS Lett., 378 (1996) 263-266. 

Potato type II (Potll) inhibitors are disulfide-rich peptides of approximately 50 amino acids in size. They were first discovered in leaves, seeds, and other organs of Solanaceae and are a source of much interest as plant defense proteins. Recently, Barta et analyzed expressed sequence tag (EST) and genomic data and discovered 11 genes that code for Potll inhibitors in various monocotyledonous and dicotyledonous plants. Potll inhibitors are expressed as large precursor proteins that contain up to eight sequence repeats of the inhibitor precursor. In one particularly fascinating case from the ornamental tobacco (N. data), the precursor adopts a circular permuted structure.Barta et al. observed that genes outside the Solanaceae family seem... 

Tougard, P. Bizebard, T. Ritco-Vonsovici, M. Minard, P. Desmadril, M. Structure of a circularly permuted phosphoglycerate kinase. Acta Crystal-logr. Sect. D, 58, 2018-2023 (2002)... 

G. Schneider, Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the a/ P-barrel within the class I aldolase family, Structure 1996, 4, 715-724. 

In principle, the ends of an RNA molecule can be moved by making circular permutations (Pan, 2000). As it is known that circular permutations can strongly affect folding mechanisms of RNA (Lease et al., 2007 Pan et al., 1999), this approach may be mosdy useful for studying structure and local dynamics of RNA. Also, after a circular permutation the ends of the molecule are expected to be right next to each other, so that the second dye has to be placed at some internal position. 

Then, inserting twice the closeness relation (32) and after a circular permutation within the trace, the ACF (30) becomes... 

Next, in view of Eq. (31) and again using the invariance of the trace with respect to a circular permutation, the ACF transforms into... 

After using a circular permutation of the bra and kets that do not belong to the spaces where the exponential operators work and then, after simplification using the orthogonality property ( 0) = 8 it reads... 

Again, after a circular permutation inside the trace and simplifications using orthonormal properties of the kets fc ), one obtains... 

Of course, using the fact that the operators involved in the ACF do not work on the space of the fast mode, because of the orthonormality, the above ACF reduces after a circular permutation within the trace and making the trace explicit, to... 

Then, by using the above equations, it is possible to get for the (p) ACF (0.4) an expression that, after a circular permutation within the trace, gives... 

Kreitman, R. J., Puri, R. K., and Pastan, I. (1994). A circularly permuted recombinant interleukin 4 toxin with increased activity. Proc. Natl. Acad. Sci. USA, 91, 6889-6893. 

I, y, k denotes a circular permutation / Ij, are the molecular moments of inertia and F is an external potential depending on molecular orientation and /(I) white stochastic forces defined by... 

The specific activity and thermodynamic stability of the (C2A, ClOA) mutant confirm that the Cys-2 to Cys-10 disulfide bond imparts thermodynamic stability but has litde effect on catalytic activity. Hence this mutant was selected as the starting point for constructing a circularly permuted form of RNase-Tl so that as short a linker as possible could be used to bridge the original N- and C-termini. The activity and stability of the circularly permuted variant indicate that it adopts an overall tertiary fold very similar to that of the native protein. Therefore, transposing the first 34 residues to the C-terminus has little effect on the overall folding to the final tertiary structure. The real effect, however, may be more evident in the kinetics of the specific folding pathway. 

Figure 2. Improvement of yellow cameleon by using a circularly permuted YFP variant. (A) The three-dimensional structure of GFP with the positions of the original (Metl) and new N-termini (Aspl73). (B) Domain structures of YCS.12 and YC3.60. CaM, Xenopus calmodulin Ml3, a CaM binding peptide derived from myosin light chain kinase (C, D) Emission spectra of YCS. 12 (C) and YC3.60 (D) (excitation at 435 nm) at zero (doted line) and saturated Ca (solid line). (E) A series of confocal pseudo-B/W images showing propagation of [Ca c- These images were taken at...

Nagai T, Sawano A, Park ES, Miyawaki A. Circularly permuted green fluorescent proteins engineered to sense Ca ". Proc Natl Acad Sci USA 2001 98 3197-202. 

In an important discovery, Foriers and coworkers [71], and others [72,73], observed an intriguing relationship between concanavalin A, a homotetramer, and the pea, lentil, Vicia faba (all composed of two light a-chains and two heavy P-chains), as well as other leguminous plant lectins. Termed a circular permutation of amino acid sequences. 

The subunits of fimbriae are constructed essentially as Ig-like P-sandwiches, but with a circular permutation that positions the sequence corresponding to the seventh, C-terminal, Ig P-strand (strand G of a canonical Ig domain) at the N-terminus of the polypeptide sequence [32-35] (Figs. 3a and 4a). In a typical Ig fold, the top edge of the sandwich, defined by the A and F strands, is capped by the C-terminal G strand, which is hydrogen bonded to the F strand and provides hydrophobic residues to the core of the fold. Free pilin subunits are only marginally stable, and no structure for a monomeric pilin in the absence of chaperone has been obtained. Sometimes, in the absence of the chaperone, soluble, domain-swapped pilin dimers [36] or trimers [37, 38] are formed and have been reported in their crystal structures. However, the oligomerization of pilins in this manner is a dead-end process, and the pilins in these oligomers are not able to assemble into fibrillar structures. 

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