Circular permutation

Nagai, T., Yamada, S., Tominaga, T., Ichikawa, M. and Miyawaki, A. (2004). Expanded dynamic range of fluorescent indicators for Ca2+ by circularly permuted yellow fluorescent proteins. Proc. Natl. Acad. Sci. USA 101, 10554-9. 

Zapata-Hommer, O. and Griesbeck, O. (2003). Efficiently folding and circularly permuted variants of the Sapphire mutant of GFP. BMC Biotechnol. 3, 5. 

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. 

The principle of in vivo cyclization is based on the circular permutation of precursor proteins containing an intein (Fig. 1.6 C) [74, 75, 80, 81]. A naturally occurring split intein, DnaE from Synechocystis sp. PCC6803, was first successfully used for cyclization. However, similarly to the IPL/EPL approach, a mixture of linear and circular forms is obtained, presumably because of hydrolysis of an intermediate [73, 75]. On the other hand, artificially split inteins such as Pl-Pful, DnaB, and the RecA intein have been successfully applied for in vivo cyclization, and only circular forms were observed [80-82], suggesting that the circular permutation approach is more suitable for cyclization. Compared to the IPL/EPL or the TWIN system, in vivo cyclization does not require any external thiol group for cyclization, similarly to protein ligation with split inteins. Moreover, there are no undesired products, such as linear forms or polymers, originating from intermolecular reactions. 

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)... 

Circularly permuted proteins 586, 587 Cloning genes 410-415 Clostripain 482... 

One example, although not yet for optimization, is the shift of the catalytic lysine from one /3 strand to a neighboring strand catalytic competency is maintained despite spatial reorganization of the active site with respect to substrate this case could cover a) or b) (Wymer, 2001). Duplication and divergence (Section 16.4.2) and circular permutation (Section 16.3.4) are covered below. 

In proteins with a symmetric structure, circular permutation can account for the shift of active-site residues over the course of evolution. A very good model of symmetric proteins are the (/Ja)8-barrel enzymes with their typical eightfold symmetry. Circular permutation is characterized by fusion of the N and C termini in a protein ancestor followed by cleavage of the backbone at an equivalent locus around the circular structure. Both fructose-bisphosphate aldolase class I and transaldolase belong to the aldolase superfamily of (a/J)8-symmetric barrel proteins both feature a catalytic lysine residue required to form the Schiff base intermediate with the substrate in the first step of the reaction (Chapter 9, Section 9.6.2). In most family members, the catalytic lysine residue is located on strand 6 of the barrel, but in transaldolase it is not only located on strand 4 but optimal sequence and structure alignment with aldolase class I necessitates rotation of the structure and thus circular permutation of the jS-barrel strands (Jia, 1996). 

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. 

Other methods of assembly (1. a—e and 2.a) are easier to implement, but they restrict the choice of labeling sites to the ends of the molecule (l.a—c and 2. a), and/or require assumptions that modifications of the sequence— that is, binding of oligos at the ends and at internal sites (l.b—d), circular permutations (l.e) or nicks in the continuous backbone (2.a)—do not affect the dynamics of interest. Testing such assumptions can be nontrivial. 

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. 

Lease, R. A., Adilakshmi, T., Heilman-Mifler, S., and Woodson, S. A. (2007). Communication between RNA folding domains revealed by folding of circularly permuted ribozymes.J. Mol. Biol. 373, 197—210. 

Pan, T. (2000). Probing RNA structure and function by circular permutations. Methods Enzymol. 317, 313—330. 

Pan, T., Fang, X., and Sosnick, T. (1999). Pathway modulation, circular permutation and rapid RNA folding trader kinetic control. J. Mol. Biol. 286, 721—731. 

FIGURE 5.3 The VB structures for singlet and triplet states of C3H3 +, along with the graphical representation of their interaction matrix elements. The spread of the states is easily predicted from the circle mnemonic used in simple Hiickel theory. The expressions for the VB structures (dropping normalization) are deduced from each other by circular permutations 1 , = ab — ab, 1 <1>2 = bc — bc, 3 = ca — cI = ab, 34>2 = bc, 33 = ca. ... 

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... 

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